Abstract: Efficient charge transport has been observed in iodine-doped, iodide-based room-temperature ionic liquids, yielding high ionic conductivity. To elucidate preferred mechanistic pathways for the iodide (I−)-to-triiodide (I3−) exchange reactions, we have performed 10 ns reactive molecular-dynamics calculations in the liquid state for 1-butyl-3-methylimidazolium iodide ([BMIM][I]) at 450 to 750 K. Energy-barrier distributions for the iodine-swapping process were determined as a function of temperature, employing a charge-reassignment scheme drawn in part from electronic-structure calculations. Bond-exchange events were observed with rate-determining energy barriers ranging from ~0.19 to 0.23 ± 0.06 eV at 750 and 450 K, respectively, with an approximately Arrhenius temperature dependence for iodine self-diffusivity and reaction kinetics, although diffusion dominates/limits the bond-exchange events. This charge transfer is not dissimilar in energetics to those in solid-state superionic conductors. read less

Abstract: In this paper, the thermal properties of graphene oxide (GO) with vacancy defects were studied using a non-equilibrium molecular dynamics method. The results showed that the thermal conductivity of GO increases with the model length. A linear relationship of the inverse length and inverse thermal conductivity was observed. The thermal conductivity of GO decreased monotonically with an increase in the degree of oxidation. When the degree of oxidation was 10%, the thermal conductivity of GO decreased by ~90% and this was almost independent of chiral direction. The effect of vacancy defect on the thermal conductivity of GO was also considered. The size effect of thermal conductivity gradually decreases with increasing defect concentration. When the vacancy defect ratio was beyond 2%, the thermal conductivity did not show significant change with the degree of oxidation. The effect of vacancy defect on thermal conductivity is greater than that of oxide group concentration. Our results can provide effective guidance for the designed GO microstructures in thermal management and thermoelectric applications. read less

Abstract: Carbonaceous materials, such as graphite, carbon nanotubes (CNTs), and graphene, are in high demand for a broad range of applications, including batteries, capacitors, and composite materials. Studies on the transformation between different types of carbon, especially from abundant and low-cost carbon to high-end carbon allotropes, have received surging interest. Here, we report that, without a catalyst or an external carbon source, biomass-derived amorphous carbon and defective reduced graphene oxide (RGO) can be quickly transformed into CNTs in highly confined spaces by high temperature Joule heating. Combined with experimental measurements and molecular dynamics simulations, we propose that Joule heating induces a high local temperature at defect sites due to the corresponding high local resistance. The resultant temperature gradient in amorphous carbon or RGO drives the migration of carbon atoms and promotes the growth of CNTs without using a catalyst or external carbon source. Our findings on the growth of CNTs in confined spaces by fast high temperature Joule heating shed light on the controlled transition between different carbon allotropes, which can be extended to the growth of other high aspect ratio nanomaterials. read less

Abstract: In the present study, the thermal decomposition characteristics of polyethylene (PE) in oxygen-free and low oxygen content circumstances were examined by molecular dynamic (MD) simulations at atomic scale using reactive force field (ReaxFF). Temporal evolutions of species were captured reasonably during the processes of thermal decomposition. The effects of oxygen content, temperature and heating rate were also analysed. In addition, the kinetic properties were predicted with reliable parameters. The results show good agreements with the available ones, which illustrate that the species with two carbon atoms are the vast majority of final products. Higher oxygen content and temperature promote the generation of small molecules with carbon atom number less than or equal to 10. In the presence of oxygen, greater activation energy span and reaction order are calculated with lower adjust R2, which indicates complex reactions according to kinetic analysis. The initial decomposition temperature of PE is proportional to the heating rate owing to heat transfer lag. read less

Abstract: We report a novel atomistic model of carbide-derived carbons (CDCs), which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors. read less

Abstract: The study focused on the structural sensitivity of lignin during the phosphoric acid–acetone pretreatment process and the resulting hydrolysis and phosphorylation reaction mechanisms using density functional theory calculations. The chemical stabilities of the seven most common linkages (β-O-4, β-β, 4-O-5, β-1, 5-5, α-O-4, and β-5) of lignin in H3PO4, CH3COCH3, and H2O solutions were detected, which shows that α-O-4 linkage and β-O-4 linkage tend to break during the phosphoric acid–acetone pretreatment process. Then α-O-4 phosphorylation and β-O-4 phosphorylation follow a two-step reaction mechanism in the acid treatment step, respectively. However, since phosphorylation of α-O-4 is more energetically accessible than phosphorylation of β-O-4 in phosphoric acid, the phosphorylation of α-O-4 could be controllably realized under certain operational conditions, which could tune the electron and hole transfer on the right side of β-O-4 in the H2PO4− functionalized lignin. The results provide a fundamental understanding for process-controlled modification of lignin and the potential novel applications in lignin-based imprinted polymers, sensors, and molecular devices. read less

Abstract: High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface hydrophilicity and angle resolved x-ray photoelectron spectroscopy was carried out to identify the functional groups responsible for wettability changes and to study their subsurface depth profiles, up to 9 nm in depth. The reactions leading to the formation of C–O, C = O and O–C = O groups were simulated by molecular dynamics. These simulations demonstrate that impinging oxygen atoms do not react immediately upon impact but rather remain at or close to the surface before eventually reacting. The simulations also explain the release of gaseous species in the ambient environment as well as the ejection of low molecular weight oxidized materials from the surface. read less

Abstract: Carbon nanotube sheets or films, also known as ‘buckypaper’, have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young’s modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2–3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures. read less

Abstract: To explore the thermal behavior of Zhundong coal from the perspective of maceral, it is essential to conduct molecular simulations based on constructing a realistic aggregate model of coal. Here, two Zhundong coal samples ZD-V (vitrinite-rich) and ZD-I (inertinite-rich) were collected, and coal models were constructed using elemental analysis, solid-state 13C-nuclear magnetic resonance (13C-NMR), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectrometry (FTIR). The chemical formulas of 2D vitrinite-rich coal and inertinite-rich coal constructed are C152H167NO36 and C155H119NO28, respectively. The chemical structure information matches well with that determined by those analysis results, including elemental analysis, structural composition, and 13C-NMR spectra. The final aggregate models show that the dimension of the unit cell is 2.785 × 2.785 × 2.785 nm for ZD-V and 2.743 × 2.743 × 2.743 nm for ZD-I, including six macromolecules respectively. The final aggregate structure models were verified by comparing experiments and simulation results. In addition to the verification with He density, the spatial arrangement of the aggregate model was verified by simulated XRD spectrum. And moreover, the thermal behavior was verified by ReaxFF MD, and the simulated trend of thermal weight loss and cumulative total molecules released were consistent with TG-MS. The final models show the visual difference between ZD-V and ZD-I, whether the 2D molecular structure or aggregation state. ZD-V is dominated by chain hydrocarbons, while ZD-I is dominated by cyclic hydrocarbons with linked aromatic rings. The aromatic substitution of oxygen atoms is different, ZD-V is mainly composed of ortho-disubstituted arenes, and ZD-I is mainly composed of meta-disubstituted arenes. In addition, ZD-V has a lower ultra-micropore size distribution and porosity than ZD-I. This study presents a comprehensive approach to construct and verify aggregate models from the spatial arrangement and thermal behavior perspective, and the constructed Zhundong coal models can provide a foundation for further exploration of the thermal reactivity (e.g. combustion, liquefaction, etc.) of coal from maceral aspects. read less

Abstract: Graphyne and its family members (GFMs) are allotropes of carbon (a class of 2D materials) having unique properties in form of structures, pores and atom hybridizations. Owing to their unique properties, GFMs have been widely utilized in various practical and theoretical applications. In the past decade, GFMs have received considerable attention in the area of water purification and desalination, especially in theoretical and computational aspects. More recently, GFMs have shown greater prospects in achieving optimal separation performance than the experimentally derived commercial polyamide membranes. In this review, recent theoretical and computational advances made in the GFMs research as it relates to water purification and desalination are summarized. Brief details on the properties of GFMs and the commonly used computational methods were described. More specifically, we systematically reviewed the various computational approaches employed with emphasis on the predicted permeability and selectivity of the GFM membranes. Finally, the current challenges limiting their large-scale practical applications coupled with the possible research directions for overcoming the challenges are proposed. read less

Abstract: The advent of graphene has renewed the interest in other 2D carbon-based materials. In particular, new structures have been proposed by combining hexagonal and other carbon rings in different ways. Recently, Bhattacharya and Jana have proposed a new carbon allotrope, composed of different polygonal carbon rings containing 4, 5, 6, and 10 atoms, named tetra-penta-deca-hexagonal-graphene (TPDH-graphene). This unusual topology results in interesting mechanical, electronic, and optical properties with several potential applications, including UV protection. Like other 2D carbon structures, chemical functionalizations can be used to tune TPDH-graphene's physical/chemical properties. In this work, we investigate the hydrogenation dynamics of TPDH-graphene and its effects on its electronic structure, combining DFT and fully atomistic reactive molecular dynamics simulations. Our results show that H atoms are mainly incorporated on tetragonal ring sites (up to 80% at 300 K), leading to the appearance of well-delimited pentagonal carbon stripes. The electronic structure of the hydrogenated structures shows the formation of narrow bandgaps with the presence of Dirac cone-like structures, indicative of anisotropic transport properties. read less

Abstract: The experimental synthesis of biphenylene, a two-dimensional carbon allotrope, theoretically predicted in 1997, took place in 2021. Biphenylene is also called net C. Two close relatives of this structure, known as net W and net Y, have not yet been experimentally synthesized. In this article, the wettability properties of these three carbon allotropes are investigated, using molecular dynamics simulation. The electronic and mechanical properties of these allotropes have been extensively studied, but their wettability properties are unknown. The chemical structure of the three allotropes is similar and contain four, six, and eight carbon membered rings. The results of molecular dynamics calculations with reactive potential show that net C, net W and net Y are hydrophobic substrates with contact angles of 122.3° ± 1.3°, 126.2° ± 1.3° and 127.8° ± 1.2°, respectively. The droplets on the above-mentioned substrates have a completely layered structure. That is, the water molecules inside the droplet are completely placed in certain layers. Calculating the order parameter for water molecules shows that the degree of water molecules' tetrahedrality on all three substrates is exactly the same. In terms of hydrogen bonding at the interface, the three substrates act identically and show almost the same effect. The droplet displacement is the highest on net W and the lowest on net Y. Furthermore, the van der Waals potential on all three substrates has been scanned. It is demonstrated that the amount of droplet displacement on the surface is inversely related to the surface density of the potential peaks. read less

Abstract: We propose a route for the rational design of engineered graphene-based nanostructures, which feature enormously enhanced electric fields in their proximity. Geometrical arrangements are inspired by nanopatterns allowing single molecule detection on noble metal substrates, and are conceived to take into account experimental feasibility and ease in fabrication processes. The attention is especially focused on enhancement effects occurring close to edge defects and grain boundaries, which are usually present in graphene samples. There, very localized hot-spots are created, with enhancement factors comparable to noble metal substrates, thus potentially paving the way for single molecule detection from graphene-based substrates. read less

Abstract: The activity and stability of a platinum nanoparticle (NP) is not only affected by its size but additionally depends on its shape. To this end, simulations can identify structure-property relationships to make a priori decisions on the most promising structures. While activity is routinely probed by electronic structure calculations on simplified surface models, modeling the stability of NP model systems in electrochemical reactions is challenging due to the long timescale of relevant processes such as oxidation beyond the point of reversibility. In this work, a routine for simulating electrocatalyst stability is presented. The procedure is referred to as GREG after its main ingredients - a grand-canonical simulation approach using reactive force fields to model electrochemical reactions as a function of the galvanic cell potential. The GREG routine is applied to study the oxidation of 3 nm octahedral, cubic, dodecahedral, cuboctahedral, spherical, and tetrahexahedral platinum NPs. The oxidation process is analyzed using adsorption isobars as well as interaction energy heat maps that provide the basis for constructing electrochemical phase diagrams. Onset potentials for surface oxidation increase in the sequence cube ≈ dodecahedron ≤ octahedron ≤ tetrahexahdron < sphere < cuboctahedron, establishing a relationship between oxidation behavior and surface facet structure. The electrochemical results are rationalized using structural and electronic analysis. read less

Abstract: Graphene oxide (GO) represents a complex family of materials related to graphene: easy to produce in large quantities, easy to process, and convenient to use as a basis for further functionalization, with the potential for wide-ranging applications such as in nanocomposites, electronic inks, biosensors and more. Despite their importance, the key structural traits of GO, and the impact of these traits on properties, are still poorly understood due to the inherently berthollide character of GO which complicates the establishment of clear structure/property relationships. Widely accepted structural models of GO frequently neglect the presence of extended topological defects, structural changes to the graphene basal plane that are not removed by reduction methods. Here, a combination of experimental approaches and molecular simulations demonstrate that extended topological defects are a common feature across GO and that the presence of these defects strongly influences the properties of GO. We show that these extended topological defects are produced following even controlled 'gentle' functionalization by atomic oxygen and are comparable to those obtained by a conventional modified Hummers' method. The presence of the extended topological defects is shown to play an important role in the retention of oxygen functional groups after reduction. As an exemplar of their effect on the physical properties, we show that the GO sheets display a dramatic decrease in strength and stiffness relative to graphene and, due to the presence of extended structural defects, no improvement is seen in the mechanical properties after reduction. These findings indicate the importance of extended topological defects to the structure and properties of functionalized graphene, which merits their inclusion as a key trait in simple structural models of GO. read less

Abstract: ABSTRACT Nano-Fe2O3/C composites are widely used in the electrochemical energy storage field. Preparing nano-Fe2O3/C composites via graphitising the amorphous carbon inserting nano-Fe2O3 particles is potential if the influence mechanism of nano-Fe2O3 on the graphitisation of amorphous carbon is explored in-depth. Here, an amorphous carbon model (a-C model) and a nano-Fe2O3-inserting model (C\Fe2O3 model) were built via the liquid-quench method, and the reaction of Fe2O3 and C during graphitisation was explored via the reactive force field (ReaxFF) simulation. The results showed that nano-Fe2O3 could inhibit the graphitisation of amorphous carbon, and the mechanism was revealed. The Fe2O3 molecules collided with the aromatic carbon layer because of the thermal motion, which caused the breaking of the carbon layer and the generation of CO2 and Fe. Certain Fe reduced from Fe2O3 destroyed the aromatic carbon layers by the strong affinity between Fe and C atoms and generated intercalation compounds (FeCx). Furthermore, the regularisation and stacking of large carbon layers were impeded. Thus, the graphitisation of amorphous carbon was inhibited. read less

Abstract: Disclinations in a 2D sheet create regions of Gaussian curvature whose inversion produces a reconfigurable surface with many distinct metastable shapes, as shown by molecular dynamics of a disclinated graphene monolayer. This material has a near-Gaussian "density of shapes" and an effectively antiferromagnetic interaction between adjacent cones. A∼10  nm patch has hundreds of distinct metastable shapes with tunable stability and topography on the size scale of biomolecules. As every conical disclination provides an Ising-like degree of freedom, we call this technique "Isigami." read less

Abstract: We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths connecting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the Onsager-Machlup action leads to a NEB algorithm with adaptive spring lengths that automatically increase the resolution of the minimum energy path around the saddle point of the potential energy surface. The method has the same computational cost per optimization step of the standard NEB algorithm and does not introduce additional parameters. We present applications to the isomerization of alanine dipeptide, the elimination of hydrogen from ethane, and the healing of a 5-77-5 defect in graphene. read less

Abstract: The impact of micro and nanoplastic debris on our aquatic ecosystem is among the most prominent environmental challenges we face today. In addition, nanoplastics create significant concern for environmentalists because of their toxicity and difficulty in separation and removal. Here we report the development of a 3D printed moving bed water filter (M-3DPWF), which can perform as an efficient nanoplastic scavenger. The enhanced separation of the nanoplastics happens due to the creation of a charged filter material that traps the more surface charged nanoparticles selectively. Synthetic contaminated water from polycarbonate waste has been tested with the filter, and enhanced nanoplastic removal has been achieved. The proposed filtration mechanism of surface-charge based water cleaning is further validated using density function theory (semi-empirical) based simulation. The filter has also shown good structural and mechanical stability in both static and dynamic water conditions. The field suitability of the novel treatment system has also been confirmed using water from various sources, such as sea, river, and pond. Our results suggest that the newly developed water filter can be used for the removal of floating nanoparticles in water as a robust advanced treatment system. read less

Abstract: Nanoporous graphene is considered the next-generation material for reverse osmosis water desalination providing both high water permeability and almost complete salt rejection. The main problem with graphene is the difficulty of synthesizing membranes with a consistent subnanometer pore size distribution. A recently proposed solution involves processing as-grown graphene oxide (GO) monolayers via a mild temperature annealing pre-treatment causing GO functional groups to cluster into small oxidized islands. A following harsh thermal reduction process creates pores only in the small oxidized regions. However, a suitable relationship between the area of the GO islands and the pore dimension is still missing. Here, we study in detail the effects of such a thermal reduction process on the graphene oxide sheet by means of molecular dynamics simulations, particularly highlighting and analysing the process parameters affecting the final pore area. Besides proving that epoxides represent the most suitable functional group to induce carbon removal and, thus, pore generation in reduced GO, we find a twofold way to achieve control over the pore size: tuning the dimension and shape of the initial clustered GO areas or changing the harsh reduction process temperature. An accurate balance of these parameters consistently gives rise to targeted pore dimensions in graphene membranes. read less

Abstract: Gasification with supercritical water is an efficient process that can be used for the valorization of biomass. Lignin is the second most abundant biopolymer in biomass and its conversion is fundamental for future energy and value-added chemicals. In this paper, the supercritical water gasification process of lignin by employing reactive force field molecular dynamics simulations (ReaxFF MD) was investigated. Guaiacyl glycerol-β-guaiacyl ether (GGE) was considered as a lignin model to evaluate the reaction mechanism and identify the components at different temperatures from 1000 K to 5000 K. The obtained results revealed that the reactions and breaking of the lignin model started at 2000 K. At the primary stage of the reaction at 2000 K the β-O-4 bond tends to break into several compounds, forming mainly guaiacol and 1,3-benzodioxole. In particular, 1,3-benzodioxole undergoes dissociation and forms cyclopentene-based ketones. Afterward, dealkylation reaction occurred through hydroxyl radicals of water to form methanol, formaldehyde and methane. Above 2500 K, H2, CO and CO2 are predominantly formed in which water molecules contributed hydrogen and oxygen for their formation. Understanding the detailed reactive mechanism of lignin’s gasification is important for efficient energy conversion of biomass. read less

Abstract: In this work, a combined ReaxFF-MD simulation and density functional theory (DFT) study was performed to study the pyrolysis behavior of polycarbonates under nonisothermal and isothermal conditions... read less

Abstract: The employment of two-dimensional materials, as growth substrates or buffer layers, enables the epitaxial growth of layered materials with different crystalline symmetries with a preferential crystalline orientation and the synthesis of heterostructures with a large lattice constant mismatch. In this work, we employ single crystalline graphene to modify the sulfurization dynamics of copper foil for the deterministic synthesis of large-area Cu9S5 crystals. Molecular dynamics simulations using the Reax force-field are used to mimic the sulfurization process of a series of different atomistic systems specifically built to understand the role of graphene during the sulphur atom attack over the Cu(111) surface. Cu9S5 flakes show a flat morphology with an average lateral size of hundreds of micrometers. Cu9S5 presents a direct band-gap of 2.5 eV evaluated with light absorption and light emission spectroscopies. Electrical characterization shows that the Cu9S5 crystals present high p-type doping with a hole mobility of 2 cm2 V−1 s−1. read less

Abstract: Cementitious materials are commonly used in nuclear repository sites to immobilize intermediate-level radioactive wastes. This is due to the large surface area of the calcium silicate hydrate (C-S-H) gel, the main hydration product of ordinary Portland cement, which provides many sorption sites in which the contaminants can be adsorbed. The retention capacity of these materials is strongly dependent on the composition, the water content, the pH or the presence of additives. Likewise, it is also known that the durability and performance of cement and concrete are adversely affected in chloride and/or sulfate environments. In this work, atomistic simulations have been employed to analyze the effect of the presence of chlorides and sulfates in the retention and transport of Cs, one of the most hazardous radioisotopes, in calcium silicate hydrate. The simulations suggest that the presence of a moderate amount of chlorides does not alter significantly the Cs uptake in C-S-H gel, while a moderate content of sulfates enhances substantially the retention of Cs ions and reduces their migration throughout the pore. This behavior is attributed to the ability of the sulfates to pull Ca out the high-affinity sites from the C-S-H surface, allowing Cs ions to occupy them. read less

Abstract: Enhanced gas recovery (EGR) is believed to be a promising technology to improve the production of shale gas reservoirs and simultaneously reduce the emissions of greenhouse gas via the injection (s... read less

Abstract: Graphene-based materials (GBMs) are a large family of materials that have attracted great interest due to potential applications. In this work, we applied first-principles calculations based on density functional theory (DFT) and fully atomistic reactive molecular dynamics (MD) simulations to study the structural and electronic effects of hydrogenation in Me-graphene, a non-zero bandgap GBM composed of both sp2 and sp3-hybridized carbon. Our DFT results show the hydrogenation can tune the electronic properties of Me-graphene significantly. The bandgap varies from 0.64 eV to 2.81 eV in the GGA-PBE approach, passing through metallic ground-states and a narrower bandgap state depending on the hydrogen coverage. The analyses of structural properties and binding energies have shown that all carbon atoms are in sp3 hybridization in hydrogenated Me-graphene with strong and stable C-H bonds, resulting in a boat-like favorable conformation for fully-hydrogenated Me-graphene. Our MD simulations have indicated that the hydrogenation is temperature-dependent for Me-graphene, and the covalent adsorption tends to grow by islands. Those simulations also show that the most favorable site, predicted by our DFT calculations, acts as trigger adsorption for the extensive hydrogenation. read less

Abstract: The molecular mechanism of structural change caused by the beta-decay of substituted tritium on DNA or polymeric materials is still being unsolved and it is hard to study the decay effect of tritium solely by experiment. In order to study the structural changes of damaged polyethylene caused by the decay effect of tritium, we randomly removed hydrogen atoms from the polyethylene chain and performed molecular dynamics (MD) simulations using the reactive force field (ReaxFF). We adopted two parameter sets of ReaxFF and evaluated their reliability by comparing the atomic forces with density functional theory calculations. The results of MD simulations at a low temperature of 100 K show that the structure of polyethylene will be less ordered when losing more hydrogen atoms. It is observed that a double bond or a cyclic structure will be formed when two carbon atoms, which are the nearest or next-nearest neighbors, lose hydrogen atoms. read less

Abstract: The effects and action mechanism of tea polyphenols (TP) on the quality of rapeseed oil during frying process were investigated. Results showed that compared with control, TP (0.04%, w/w) exhibited the remarkable ability to inhibit the deterioration of acid value, peroxide value, anisidine value, viscosity, and color of frying oil. By using gas chromatography-mass spectrometry, frying oil with TP showed the higher content of unsaturated fatty acids (72.79%) and lower content of trans fatty acids (3.36%) than those of control. Meanwhile, frying oil with TP had a higher total phenolic content than control at the same frying time. In addition, the thermo gravimetric-differential scanning calorimetry results showed that TP could increase the oxidation stability of rapeseed oil. Furthermore, according to the Fourier transform infrared and molecular dynamic simulation results, TP could reduce the breaking degree of = C-H bond, C-O-C bond, and C = C bond in oil molecules, and inhibit the oxidation of oil components by inhibiting the generation of free radicals and eliminating free radicals. All present results suggested that TP showed the potential value to be used for protecting the quality of oil during the frying process in food and chemical industries. PRACTICAL APPLICATIONS: The inhibitory effect of tea polyphenols on the deterioration of quality of rapeseed oil during frying was found and the mechanism had also preliminarily interpretation. This work provided a method for monitoring the quality of fry oil and provided the theoretical basis for the use of tea polyphenols in frying. read less

Abstract: The controllable adjustment of an ideal graphene structure on the surface/interface is important to achieve many of the potential characteristics and applications of graphene. Here, a phenomenon is observed in which friction can induce the structural conversion of graphene oxide (GO) to graphene perfectly on a macroscale sliding interface. The controlling factors and molecular interaction mechanism are further revealed by experiments and theoretical simulation. The results show that shear force drives the tribochemical reactions between the –OH group of GO and active bond of the counterpart, as well as the –OH groups of adjacent GO sheets, leading to the breakage of the COH bond. This leads to the transformation of the sp3 C to sp2 C, thereby forming a perfect six‐membered ring. The as‐broken hydroxyl groups combine with the dangling bond of the frictional pair or capture hydrogen from the hydroxyl group of the adjacent GO sheet and generate water molecules. This study provides more information on a novel method of manipulating the interfacial structure of graphene at a macroscale by a simple sliding action. The method also provides a new way of force sensing through the detection of the released H2O molecules. read less

Abstract: The pulsed laser fragmentation in liquid (PLFL) process is a promising technique for the synthesis of carbon-based functional materials. In particular, there has been considerable attention on graphene quantum dots (GQDs) derived from multiwalled carbon nanotubes (MWCNTs) by the PLFL process, owing to the low cost and rapid processing time involved. However, a fundamental deep understanding of the formation of GQDs from MWCNTs by PLFL has still not been achieved despite the high demand. In this work, a mechanism for the formation of GQDs from MWCNTs by the PLFL process is reported, through the combination of experimental and theoretical studies. Both the experimental and computational results demonstrate that the formation of GQDs strongly depends on the pulse laser energy. Both methods demonstrate that the critical energy point, where a plasma plume is generated on the surface of the MWCNTs, should be precisely maintained to produce GQDs; otherwise, an amorphous carbon structure is favorably formed from the scattered carbons. read less

Abstract: Devices for electrical energy storage need to provide high energy yields and output power, guaranteeing at the same time safety, low costs, and long operation times. The porphyrin CuDEPP [5,15‐bis(ethynyl)‐10,20‐diphenylporphinato] copper(II) is a promising electrode material for various battery systems both as anode and cathode. While its functionality has been demonstrated experimentally, there is no atomistic information as to why CuDEPP expresses these interesting properties or how the incorporation of ions affects its structure so far. To answer these questions, CuDEPP is investigated using density functional theory (DFT). Starting with the smallest possible unit (i.e., a single molecule), the spatial dimensionality of the structure is successively increased by studying: 1) di‐ and trimers, 2) molecular stacking in a 1D chain, 3) extending these chains to planar CuDEPP sheets, and finally 4) a three‐dimensionally extended polymer structure. Having thoroughly investigated the isolated properties of the CuDEPP material itself, afterward the insertion (or intercalation) of different ions (including Li, Mg, and Na) is studied, to understand the energetics, diffusion barriers, and structural changes (e.g., volume expansion) within the CuDEPP host material. read less

Abstract: Cellulose acetate butyrate (CAB)/B2 (50 wt% bis(2,2‐dinitropropyl)‐acetal and 50 wt% bis(2,2‐dinitropropyl)‐formal) polymer composite material is a commonly used binder system to prepare polymer bonded explosives (PBXs). However, few literature report the influence of plasticizer B2 mass fraction on the performance of CAB/B2 polymer composite binder systems. In this study, experiment measurements and computer simulations are utilized to explore the influences of B2 mass fraction on the glass transition temperature, mechanical property, and thermal decomposition of CAB/B2 polymer composite materials. The results show that, with an increase in B2 content, the glass transition temperature and fragility of CAB/B2 are decreased, and the plasticity and ductility of CAB/B2 are enhanced. Moreover, the thermal decomposition mechanism, decomposition products, and decomposition path of CAB/B2 are unchanged with the increase in B2 content. Besides, the researchers also demonstrate that the addition of B2 is positive to the formability of CAB/B2 systems and is negative to the thermal stability of CAB/B2 systems, whereas the content of B2 has little influences on the thermal stability of CAB/B2 systems. The results obtained from this work can provide some guidance for the designs of high‐energy density PBXs. read less

Abstract: We present a low temperature and solution-based fabrication process for reduced graphene oxide (rGO) electrodes for electric double layer capacitors (EDLCs). Through the heat treatment at 180 °C between the spin coatings of graphene oxide (GO) solution, an electrode with loosely stacked GO sheets could be obtained, and the GO base coating was partially reduced. The thickness of the electrodes could be freely controlled as these electrodes were prepared without an additive as a spacer. The GO coating layers were then fully reduced to rGO at a relatively low temperature of 300 °C under ambient atmospheric conditions, not in any chemically reducing environment. Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) results showed that the changes in oxygen functional groups of GO occurred through the heat treatments at 180 and 300 °C, which clearly confirmed the reduction from GO to rGO in the proposed fabrication process at the low thermal reduction temperatures. The structural changes before and after the thermal reduction of GO to rGO analyzed using Molecular Dynamic (MD) simulation showed the same trends as those characterized using Raman spectroscopy and XPS. An EDLC composed of the low temperature reduced rGO-based electrodes and poly(vinyl alcohol)/phosphoric acid (PVA/H3PO4) electrolyte gel was shown to have high specific capacitance of about 240 F g−1 together with excellent energy and power densities of about 33.3 W h kg−1 and 833.3 W kg−1, respectively. Furthermore, a series of multiple rGO-based EDLCs was shown to have fast charging and slow discharging properties that allowed them to light up a white light emitting diode (LED) for 30 min. read less

Abstract: The 13C NMR chemical shifts corresponding to different sites in atomistic models of disordered carbons were computed at different H contents by employing DFT calculations. Structural models were ge... read less

Abstract: The influence of twinned crystals on the performance of TKX-50 is investigated using normal TKX-50 and twinned TKX-50 supercells. ReaxFF-lg reactive molecular dynamics simulations are performed to study thermal decomposition and oxidation. read less

Abstract: We investigate the interaction of polyfluorene and fluorene/carbazole copolymers bearing various functional groups and side chains with small to large diameter-from 1.7 nm to 9 nm-carbon nanotubes (CNTs) in vacuo. We use variable-charge molecular dynamics simulations based on the reactive force field ReaxFF. We show that non-covalent functionalization of nanotubes, driven by π - π interactions, is effective for all the polymers studied, thanks to their conjugated backbone and regardless of the presence of specific functional groups. The geometry at equilibrium of these polymer/CNT hybrids is analyzed in detail at the scale of each fluorene or carbazole unit. The role of both the functional groups and the alkyl chain length is analyzed in detail. Adsorption of the polymers on the nanotube sidewalls is shown to be either complete-with the whole chain physisorbed-or partial-due to intrachain coiling or interchain repulsion-depending on the initial geometry, number of polymers, and nanotube diameter. Energetic arguments supplement the described geometric features. Both energetic and geometric adsorption features are derived here for the first time for large diameter carbon nanotubes (up to 9 nm) and fluorene/carbazole copolymers having up to 30 monomers and bearing different functional groups. The force field ReaxFF and its available parameterization used for the simulations are validated, thanks to a benchmark and review on higher-level quantum calculations-for simple π - π interacting compounds made up of polycyclic aromatic molecules adsorbed on a graphene sheet or bilayer graphene. Although it is shown that the influence of the nanotube chirality on the adsorption pattern and binding strength cannot be discussed with our method, we highlight that an available force field such as ReaxFF and its parameterization can be transferable to simulate new systems without specific re-parameterization, provided that this model is validated against reference methods or data. This methodology proves to be a valuable tool for optimal polymer design for nanotube functionalization at no re-parameterization cost and could be adapted to simulate and assist the design of other types of molecular systems. read less

Abstract: One strategy to mitigate global warming is carbon capture and sequestration. Membrane separation is one promising approach to separation of CO2 from feed streams. Here we report the investigation of four zeolites that have been predicted to be effective at separating CO2 from methane, but which have not to date been synthesized experimentally as membranes. Using an in silico de novo design procedure, we identify organic structure-directing agents (OSDAs) that are predicted to aid the synthesis of these zeolites. Using a genetic algorithm approach, we designed OSDAs for zeolites for which no purely siliceous form is known, and we also designed OSDAs for predicted zeolites. Stabilization energies of the best OSDAs designed for the zeolites GIS, ABW, and predicted zeolite 8198030 lie within -8 to -12 kJ/(mol Si), in the range of values for other known OSDAs. Stabilization energies of the OSDAs designed for predicted zeolite 8186909 are -16 kJ/(mol Si), comparable to the best known OSDAs for any zeolite. The OSDAs reported here may lead to zeolites that could enable a practical separation of CO2 from methane. read less

Abstract: Cellulosic insulation paper is usually used in oil-immersed transformer insulation systems. In this study, the molecular dynamics method based on reaction force field (ReaxFF) was used to simulate the pyrolysis process of a cellobiose molecular model. Through a series of ReaxFF- Molecular Dynamics (MD) simulations, the generation path of ethanol at the atomic level was studied. Because the molecular system has hydrogen bonding, force-bias Monte Carlo (fbMC) is mixed into ReaxFF to reduce the cost of calculation by reducing the sampled data. In order to ensure the reliability of the simulation, a model composed of 20 cellobioses and a model composed of 40 cellobioses were respectively established for repeated simulation in the range of 500–3000 K. The results show that insulating paper produced ethanol at extreme thermal fault, and the intermediate product of vinyl alcohol is the key to the aging process. It is also basically consistent with others’ previous experiment results. So it can provide an effective reference for the use of ethanol as an indicator to evaluate the aging condition of transformers. read less

Abstract: Improving the adhesion properties of carbon nanotubes (CNTs) at the molecular scale can significantly enhance dispersion of CNT fibers in polymer matrix and unleash the dormant extraordinary mechanical properties of CNTs in CNT-polymer nanocomposites. Inspired by the outstanding adhesion, dispersion, mechanical, and surface functionalization properties of crystalline nanocellulose (CNC), this paper studies the mechanical and adhesion properties of CNT wrapped by aligned cellulose chains around CNT using molecular dynamic simulations. The strength, elastic modulus, and toughness of CNT-cellulose fiber for different cellulose contents are obtained from tensile and compression tests. Additionally, the effect of adding cellulose on the surface energy, interfacial shear modulus, and strength is evaluated. The result shows that even adding a single layer cellulose wrap (≈55% content) significantly decreases the mechanical properties, however, it also dramatically enhances the adhesion energy, interfacial shear strength, and modulus. Adding more cellulose layers, subsequently, deceases and increases mechanical properties and adhesion properties, respectively. In addition, analysis of nanopapers of pristine CNT, pristine CNC, and CNT-wrapped cellulose reveals that CNT-wrapped cellulose nanopapers are strong, stiff, and tough, while for CNT and CNC either strength or toughness is compromised. This research shows that cellulose wraps provide CNT fibers with tunable mechanical properties and adhesion energy that could yield strong and tough materials due to the excellent mechanical properties of CNT and active surface and hydrogen bonding of cellulose. read less

Abstract: Reactive molecular dynamics (MD) simulation makes it possible to study the reaction mechanism of complex reaction systems at the atomic level. However, the analysis of MD trajectories which contain thousands of species and reaction pathways has become a major obstacle to the application of reactive MD simulation in large-scale systems. Here, we report the development and application of the Reaction Network Generator (ReacNetGenerator) method. It can automatically extract the reaction network from the reaction trajectory without any predefined reaction coordinates and elementary reaction steps. Molecular species can be automatically identified from the cartesian coordinates of atoms and the hidden Markov model is used to filter the trajectory noises which makes the analysis process easier and more accurate. The ReacNetGenerator has been successfully used to analyze the reactive MD trajectories of the combustion of methane and 4-component surrogate fuel for rocket propellant 3 (RP-3), and it has great advantages in terms of efficiency and accuracy compared to traditional manual analysis. read less

Abstract: Pyrolysis of styrene-butadiene rubber receives renewed attention due to its application in tackling the waste tire disposal problem while allowing energy recovery. The density functional theory calculation (DFT) and ReaxFF molecular dynamics simulation (MD) are adopted to study the pyrolysis process with the variation of temperature and pressure. The bond dissociation energies of intramonomer and intermonomer bonds in trimers with different linking methods are calculated by DFT, where the bond with low energy tends to break during the pyrolysis process. The following MD simulation shows the pyrolysis product distribution of chain segments in styrene-butadiene rubber, where bond breaking positions in MD agree well with corresponding results in DFT and experiment. The next nearest neighbor bonds (single bonds) connected with double bond or benzene usually have lower dissociation energies than other single bonds and prone to break during the pyrolysis process. And thus, the intermonomer bonds tend to break at relatively low temperatures (around 650 K in experiment) prior to intramonomer bonds, which result in the emergence of monomers. With the temperature increase, intramonomer bonds are broken and thus large fragments are further pyrolyzed into small ones (e.g., C2 and C). Besides, the pressure strongly influences the product distribution, where high pressures promote the occurrence of secondary reactions. read less

Abstract: Nanoporous graphene was proposed as an efficient material for reverse osmosis water desalination membranes as it allows water molecules to pass at high fluxes while rejecting hydrated salt ions. Nevertheless, from an experimental point of view it is still difficult to control the pore size. A scalable method to generate pores is urgently required for the diffusion of this technology. We propose, by theoretical calculations, an innovative and scalable strategy to better control the dimension of the pores in graphene-based membranes by reduction of a single layer graphene oxide (GO). The latter is first annealed at a controlled mild temperature to induce the aggregation of its randomly distributed oxygen containing functional groups into small nanometric clusters. The layer then undergoes a high temperature reducing treatment that causes the desorption of the functional groups along with carbon removal only in the oxidized areas producing sub-nanometric pores while leaving unchanged the remaining pristine graphene areas. read less

Abstract: There is a great deal of attention given to spiral carbon-based nanostructures (SCBNs) because of their unique mechanical, thermal and electrical properties along with fascinating morphology. Dispersing SCBNs inside a polymer matrix leads to extraordinary properties of nanocomposites in diverse fields. However, the role of the interfacial mechanical properties of these nanocomposites remains unknown. Here, using molecular dynamics simulations, the characteristics of interfacial load transfer of SCBN-polyethylene nanocomposites are explored. Considering the geometric characteristics of SCBNs, new insight into the separation behavior of nanoparticles in normal and sliding modes is addressed. Interestingly, the results show that the maximum force and the separation energy of the SCBNs are much larger than those of graphene because of interlocking of the coils and polymer. The heavy influence of changes in the geometric characteristics of SCBNs on the separation behavior is observed. Pullout tests reveal that the influence of parameters such as the length and number of polyethylene chains, temperature, and functionalization of the SCBNs on the interfacial mechanical properties is also significant. This study sheds new light in understanding the crucial effect of the interaction of SCBNs with polymer chains on the interfacial mechanical properties, which can lead to better performance of nanocomposites. read less

Abstract: Dielectric barrier discharge (DBD) is an effective method for treating volatile organic compounds (VOCs). In the presence of a photocatalyst, photocatalytic technology can be used to generate a variety of reactive oxygen species (ROS). Numerous experiments have demonstrated that DBD–photocatalyst synergism is superior to the use of either approach individually. In this study, the degradation mechanism of VOCs under the DBD–photocatalyst system was investigated via the ReaxFF reaction molecular dynamics method. Acetaldehyde, toluene, 1,2,4-trimethylbenzene, cresol, and phenol were selected as representative VOCs and · O, · OH, HO2, and H2O2 were chosen as representative ROS to construct the DBD and DBD–photocatalyst reaction systems. A concentration control group and a component control group were established. Comparison of the various ROS revealed that · O and · OH possess higher activities and are more conducive to cracking VOC molecules. Among the various VOCs, the reaction rate was faster for highly reductive reactants. The carbon conversion rate was only dependent on the molecular complexity and was higher for simpler structures. To simulate the DBD–photocatalyst synergistic conditions, we established concentration control simulation systems. When · OH is used as the ROS, a large number of oxidative adsorption and hydrogen abstraction processes can occur. Increasing the · OH concentration promotes the VOC removal reactions to afford complete cracking of the VOCs into the small-molecule product CO2.Dielectric barrier discharge (DBD) is an effective method for treating volatile organic compounds (VOCs). In the presence of a photocatalyst, photocatalytic technology can be used to generate a variety of reactive oxygen species (ROS). Numerous experiments have demonstrated that DBD–photocatalyst synergism is superior to the use of either approach individually. In this study, the degradation mechanism of VOCs under the DBD–photocatalyst system was investigated via the ReaxFF reaction molecular dynamics method. Acetaldehyde, toluene, 1,2,4-trimethylbenzene, cresol, and phenol were selected as representative VOCs and · O, · OH, HO2, and H2O2 were chosen as representative ROS to construct the DBD and DBD–photocatalyst reaction systems. A concentration control group and a component control group were established. Comparison of the various ROS revealed that · O and · OH possess higher activities and are more conducive to cracking VOC molecules. Among the various VOCs, the reaction rate was faster for highly re... read less

Abstract: Increased applications of nanoporous graphene in nanoelectronics and membrane separations require ordered and precise perforation of graphene, whose scalablility and time/cost effectiveness represent a significant challenge in existing nanoperforation methods, such as catalytical etching and lithography. A strain-guided perforation of graphene through oxidative etching is reported, where nanopores nucleate selectively at the bulges induced by the prepatterned nanoprotrusions underneath. Using reactive molecular dynamics and theoretical models, the perforation mechanisms are uncovered through the relationship between bulge-induced strain and enhanced etching reactivity. Parallel experiments of chemical vapor deposition (CVD) of graphene on SiO2 NPs/SiO2 substrates verify the feasibility of such strain-guided perforation and evolution of pore size by exposure of varied durations to oxygen plasma. This scalable method can be feasibly applied to a broad variety of 2D materials (e.g., graphene and h-boron nitride) and nanoprotrusions (e.g., SiO2 and C60 nanoparticles), allowing rational fabrication of 2D material-based devices. read less

Abstract: Natural carbonaceous materials (NCMs) have recently emerged as promising organic semiconducting materials for electronics and catalysis, although the fundamental picture of charge transport within NCM systems is still incomplete. Morphologically, NCMs exhibit reminiscence of disordered organic solids, yet the experimental measurements demonstrate a transport regime that surprisingly follows Mott's formula derived for variable‐range hopping in inorganic noncrystalline materials. With ab initio and kinetic Monte Carlo simulations, a temperature scaling is revealed between the Gaussian‐defect model log(σ) ∼ T−2 typical for organic matter and the Mott‐like log(σ) ∼ T−1/4 for a wide spectrum of intermolecular connectivity. As dominant transport descriptors, energy levels and coupling strengths are screened among 30 small molecules with varying sizes, shapes, sp2/sp3 ratios, side chains, and functional groups. These analyses provide insight for the design of NCM electronics, and should also be applicable to disordered molecular materials in general. read less

Abstract: With the aim of designing an efficient procedure for producing biocompatible drug delivery systems based on nanoparticle carriers for in situ controlled antibiotic release, we have defined a novel computational approach resorting to a reactive force field capable of realistically describing hybrid systems. The modeling procedure was focused on well-known components, namely gold nanoparticles, citrate, chitosan and gentamicin, and the experiments tuned on purpose. On the one hand, gold nanoparticles were synthesized, fuctionalized with chitosan, loaded with gentamicin and characterized by means of transmission electron microscopy (TEM), scanning electron microscopy (SEM), dynamic light scattering (DLS), UV-visible (UV-vis) spectroscopy, and Fourier transform infrared spectroscopy (FTIR). On the other hand, an effective model of a functionalized gold nanoparticle was created and its structure and dynamics were explored by classical reactive molecular dynamics simulations in solution based on the ReaxFF atomistic description. The structure, dynamics and drug release were reproduced realistically disclosing the motion of all the molecular components, their adsorption on the metal support, desorption, intermolecular interactions and self-assembly. The system size was very close to the experimental conditions and all the calculations could efficiently identify the most probable binding modes, the locations of the adsorbed molecules, the characteristic arrangements of the chains and the effects due to the surrounding environment. The role played by the substrate and water molecules in the releasing process was described in detail. In line with the literature it was found that the antibiotic activity was preserved and the drug release from the carrier could be tuned by changing the chitosan/getamicin weight ratio and the deposition pattern of the adsorbed layers. read less

Abstract: The oxidation behavior of the synthetic ester oils di‐isooctyl adipate (DOA) and tri‐isodecyl trimellitate (TDTM) was investigated by analysing the oxidation induction time and oxidation onset temperature via pressure differential scanning calorimetry tests, and the variation in viscosity after oven accelerated oxidation tests. Moreover, theoretical calculations of the fractional free volumes and oxygen diffusion coefficients of DOA and TDTM were performed, and atomistic‐scale insights into the oxidative mechanisms of both oils were proposed based on reactive molecular dynamic (RMD) simulations. Better oxidation resistance for TDTM was confirmed with experimental observations. RMD results indicated that the C―O bonds of the alcohol chain and ester group of DOA were susceptible to oxidation. However, only the dissociation of the C―O bond of the alcohol chain initiated the oxidation of TDTM. Additionally, more degradation fragments for DOA were identified, along with the formation of a polymerized product, while no large molecules formed for TDTM. read less

Abstract: In the present study, the ReaxFF reactive molecular dynamics simulation method was applied to investigate the effect of a small nickel cluster (Ni13) on the formation of nascent soot from polycyclic aromatic hydrocarbon (PAH) precursors. A series of NVT simulations was performed for systems of a Ni13 cluster and various PAH monomers, namely, naphthalene, anthracene, pyrene, coronene, ovalene, and circumcoronene, at temperatures from 400 to 2500 K. At low temperatures, the PAHs form soot particles via binding and stacking around nickel clusters. Larger soot particles are formed due to the early initiation of clustering provided by nickel compared to those observed in homogenous PAH systems. At 1200-1600 K, the PAH monomers show a chemisorption tendency onto the nickel surface, which results in incipient soot particles. Chemical nucleation was observed at 2000 K where nickel-assisted dehydrogenation and chemisorption of PAH led to the growth of stable soot particles, which did not occur in the absence of Ni-clusters. At a high temperature (2500 K), nickel significantly accelerates the ring-opening and graphitization of PAH molecules and increases the size of the fullerene-type soot as compared to that of homogenous systems. read less

Abstract: A series of laboratory experiments was performed to determine the carbon stable isotopic composition of different combustion/pyrolysis (B/P) products. Variation in the δ13C values of the products was observed, up to 4‰. The differences in the carbon isotopic compositions of the B/P products were dependent on temperature, time and wood type. Comparison of the results for fresh and fossil oak wood suggested that the δ13C differences were the effect of selective decomposition of some wood components during the fossilization process. The temperature dependence of the carbon isotopic composition was linked to variation in the carbon isotopic composition of the main wood components, which each had different levels of thermal stability. Isotopes exchange reactions in between different products can be also considered as possible source of variation of δ13C on temperature. Both these hypotheses were supported by molecular simulations of cellulose and lignin B/P. The results confirm that B/P should be treated as a continuous process, where the results depend on the degree of process development. Natural burning processes are dynamic and burning conditions change rapidly and it is necessary to take care when using combustion products as a paleoenvironmental proxy or as an isotopic characteristic for the identification of source material. read less

Abstract: Phase separation has a considerable effect on the detonation performances of explosives, but its mechanism has seldom been studied in terms of the interatomic interaction through molecular modeling. The binary mixtures of molecular N2, CO2, and H2O, which are the key components of detonation products of common explosives, with high density and at high temperature were investigated by using the reactive force fields-based molecular dynamics simulations. The mixing and demixing behaviors of N2/H2O and CO2/H2O systems were compared to distinguish the driven forces of phase separation. The N2/H2O mixtures with high density exhibit a remarkable phase separation at low temperature, while the CO2/H2O mixtures are mixing in a wide range of density and temperature. Similar changes in the repulsive van der Waals energy were found for all the studied systems. However, the corresponding changes in the attractive Coulomb energy are quite different for the mixing and demixing systems. Moreover, the polarization effect ... read less

Abstract: The unique physicochemical properties and high solubility of a wide range of biomass-derived feedstocks make sub- and supercritical alcohols promising media for thermochemical conversion to liquid fuels and value-added chemicals. Short-chain alcohols (C1–C3) not only hydrogenolyse a variety of recalcitrant feedstocks by donating in situ hydrogen, but also suppress the char formation by capping reactive intermediates. However, the beneficial features of supercritical alcohols also bring some demerits, such as their excessive decomposition and high consumption, which has been given cursory attention to date. Consequently, the aim of this study was to elucidate the role of sub- and supercritical alcohols as a hydrogen donor, their self-reactivity, their reactivity with the feedstock, the extent of their conversion under catalytic and non-catalytic conditions, and the detailed pathways to byproduct formation. Based on the solvent reactivity, the optimum conditions were investigated for the solvothermal liquefaction of recalcitrant alkali lignin to give a high yield of aromatic monomers with careful emphasis on the solvent consumption. The addition of formic acid instead of the more commonly used hydrodeoxygenation catalysts (e.g., CoMo/Al2O3, Ru/Al2O3) can not only suppress ethanol consumption significantly (from 42.3–46.8 wt% to 7 wt%), but can also result in complete lignin conversion by providing an excess amount of active hydrogen. The reaction at 350 °C for a short duration of 60 min led to the complete decomposition of alkali lignin and afforded a high yield of aromatic derivatives (36.7 wt%), while at the same time, suppressing ethanol consumption (11.8 wt%) and the formation of ethanol-derived liquid products. The alkylation of lignin-derived phenolic intermediates at the expense of the solvent is a time-dependent reaction, instead of the primary stabilization reaction. Molecular dynamics simulations using dilignol molecules revealed that the ethanol–formic acid mixture reduced the activation and thermal energies required for the dissociation of C–C and C–O bonds in the lignin structure. read less

Abstract: The aim of this article is to study the effect of oxide functionalisation on the failure morphology of bicrystalline graphene. Molecular dynamics based simulations in conjunction with reactive force field were performed to study the mechanical properties as well as failure morphology of different configurations of bicrystalline graphene oxide. Separate simulations were performed with hydroxyl and epoxide functionalisation, and later on the same simulations were extended to study the graphene oxide as a whole. The authors have predicted that epoxide functionalisation helps in transforming the catastrophic brittle behaviour into ductile. Failure morphologies depict that epoxide groups tend to boost the ductility through altering the fracture path and not affecting the grain boundaries either. Also, the epoxide to ether transformations were found to be the decisive mechanism behind the plastic response shown by epoxide groups. Simulations help in concluding a ductile failure for bicrystalline graphene in conjunction with oxidation of selective atoms in the nanosheet, which further opens new avenues for the application of these graphene sheets in nanodevices and nanocomposites.The aim of this article is to study the effect of oxide functionalisation on the failure morphology of bicrystalline graphene. Molecular dynamics based simulations in conjunction with reactive force field were performed to study the mechanical properties as well as failure morphology of different configurations of bicrystalline graphene oxide. Separate simulations were performed with hydroxyl and epoxide functionalisation, and later on the same simulations were extended to study the graphene oxide as a whole. The authors have predicted that epoxide functionalisation helps in transforming the catastrophic brittle behaviour into ductile. Failure morphologies depict that epoxide groups tend to boost the ductility through altering the fracture path and not affecting the grain boundaries either. Also, the epoxide to ether transformations were found to be the decisive mechanism behind the plastic response shown by epoxide groups. Simulations help in concluding a ductile failure for bicrystalline graphene in con... read less

Abstract: The earliest stages of annealing of graphitizable anthracene coke and non-graphitizable sucrose char were observed by rapid heating with a CO2 laser. Structural transformations were observed with transmission electron microscopy. Anthracene coke and sucrose char were laser heated to 1200 °C and 2600 °C for 0.25–300 s. The transformations are compared to traditional furnace heating at matching temperatures for a 1 h duration. Traditional furnace and CO2 laser annealing followed the same pathway, based upon equivalent end structures. Graphitizable anthracene coke annealed faster than non-graphitizable sucrose char. Sucrose char passed through a structural state of completely closed shell nanoparticles that opened upon additional heat treatment and gave rise to the irregular pore structure found in the end product. The observed curvature in sucrose char annealed at 2600 °C results from shell opening. The initial presence of curvature and loss by heat treatment argues that odd membered rings are present initially and not formed upon heat treatment. Thus, odd membered rings are not manufactured during the annealing process due to impinging growth of stacks, but are likely present in the starting structure. The observed unraveling of the closed shell structure was simulated with ReaxFF. read less

Abstract: The aim of this article is to study the effects of functional groups such as hydroxyl, epoxide and carboxyl on the fracture toughness of graphene. These functional groups form the backbone of the intrinsic atomic structure of graphene oxide (GO). Molecular dynamics based simulations were performed in conjunction with reactive force field parameters to capture the Mode-I fracture toughness of functionalised graphene. Simulations were performed in stages, to study the effect of these functional groups, individually as well as all together on the fracture toughness of GO nanosheets. The molecular dynamics based simulations performed in this article helps us to conclude that the spatial distribution and concentration of functional groups significantly affects the fracture behavior of GO nanosheets. read less

Abstract: Chemical vapor deposition (CVD) on Cu foils emerged as an important method for preparing high-quality and large-area graphene films for practical applications. However, to date it remains challenging to rapidly identify the structural features, especially the layer numbers, of CVD-graphene directly on Cu substrate. Herein, we report an O2-plasma-assisted approach for identifying the coverage, wrinkles, domain size, and layer number of large-area graphene films on Cu foils by optical microscopy. The wrinkles and grain boundaries of five-layer graphene can be observed with a grayscale increment of ∼23.4% per one graphene layer after O2-plasma treatment for only 15 s, which allows for checking graphene on Cu foils with a sample size of 17 cm × 20 cm in a few minutes. The Raman spectroscopy and X-ray photoelectron spectroscopy presents a strong layer number dependence of both the plasma induced graphene defects and Cu oxides, which, as indicated by molecular dynamic simulation, is responsible for the improved... read less

Abstract: Macroscopic properties of reacting mixtures are necessary to design synthetic strategies, determine yield, and improve the energy and atom efficiency of many chemical processes. The set of time-ordered sequences of chemical species are one representation of the evolution from reactants to products. However, only a fraction of the possible sequences is typical, having the majority of the joint probability and characterizing the succession of chemical nonequilibrium states. Here, we extend a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation over a range of temperatures. We demonstrate an information-theoretic methodology to identify typical sequences under the constraints of mass conservation. Including these constraints leads to an improved ability to learn the chemical sequence mechanism from experimentally accessible data. From these typical sequences, we show that two quantities defining the variational typical set of sequences-the joint entropy rate and the topological entropy rate-increase linearly with temperature. These results suggest that, away from explosion limits, data over a narrow range of thermodynamic parameters could be sufficient to extrapolate these typical features of combustion chemistry to other conditions. read less

Abstract: We studied dependency of toluene oxidation-blended n-decane on blending ratio and temperature using the reactive molecular dynamics (RMD) simulations with the newly developed reactive force field (ReaxFF). Different initial reaction pathways of toluene were observed between pure and blended toluene, while that of n-decane showed little contrast. The differences in toluene oxidation paths are related to radical pool, which is largely influenced by H/C ratio. We analysed the influence of H/C ratio on the consumption of intermediate species, and found different dependencies of HCHO consumption on H/C ratio for different temperatures. The difference is attributed to the large active energy difference between the two main HCHO consumption reactions by OH and O2. For the production part, the OH producing pathway was analysed carefully and shows H/C ratio influences OH production via H production and H abstract reactions. Our RMD simulations show that H/C ratio plays an important role in the oxidation of fuel. read less

Abstract: We present a generalization of Tolman's concept of activation energy applicable to thermal and non-thermal reactions in molecular dynamics simulations of reactions in bulk gases. To illustrate the applicability of the method, molecular dynamics calculations were carried out for the NVT ensemble to determine the activation energies of O2 + H2 → H + HO2 and 2O2 + H2 → 2HO2 from MD simulation results for [H2]/[O2] = 1 at 3000 K using the reactive force field, ReaxFF. Assuming local thermodynamic equilibrium, we define the reaction cluster local energy, the energy of the atoms participating in an individual reaction, which is conserved. The generalized Tolman activation energy (GTEa) approach is applicable to reactions of any molecularity. Although we have applied GTEa for thermal conditions, it is applicable to chemistry occurring under non-thermal conditions because it rests upon local rather than global equilibrium. We have defined the transition configurations, unique points that define a seam separating reactants and products at which the local energies of the reactants and products become equal. read less

Abstract: The equation of state and the structure of liquid carbon are studied by molecular simulation. Both classical and quantum molecular dynamics (QMD) are used to calculate the equation of state and the distribution of chemical bonds at 6000 K in the pressure range 1-25 GPa. Our calculations and results of other authors show that liquid carbon has a fairly low density on the order of 1.2-1.35 g/cm3 at pressures about 1 GPa. Owing to the coordination number analysis, this fact can be attributed to the high content of sp1-bonded atoms (more than 50% according to our ab initio computations). Six empirical potentials have been tested in order to describe the density dependence of pressure and structure at 6000 K. As a result, only one potential, ReaxFF/lg, was able to reproduce the QMD simulations for both the equation of state and the fraction of sp1, sp2, sp3-bonded atoms. read less

Abstract: Radial deformation of boron nitride nanotubes (BNNTs) plays a significant role in the performances of BNNT-based applications. By performing molecular dynamics simulations, the radial deformation of armchair single-walled BNNTs was investigated. The deformation energy barrier was found to follow a decreasing trend with increasing tube diameter. Two threshold diameters were identified that demarcate three stability regimes for the deformed single-walled BNNTs. Whereas the van der Waals interaction was simply favorable for radial deformation, the electrostatic interaction had a complex effect; it prevented deformation from the initial cylindrical shape but promoted collapse when the opposing tube wall came into proximity. read less

Abstract: Using molecular dynamics (MD) simulations, we investigate the elastic–plastic mechanical performances of monolayer graphene oxide (GO) under uniaxial tension. The brittle–ductile–brittle transition and nonlinear–linear–nonlinear elastic transition is found in the uniaxial tension of GO, which displays strong correlations to the content, distribution and proportion of oxygen functional groups. In principle, the tensile behavior of graphene with epoxy groups exhibits ductile fracture features due to the unique epoxy-to-ether transformation in structural evolution. Our simulation results also reveal that wrinkling could cause a competing mechanism of strain-hardening or -softening, and in turn, the nonlinear–linear elasticity transition. Moreover, we propose a continuum mechanical model with a modified stress–strain relation to understand the unique deformation performances, which is consistent with the MD results. These findings might provide valuable insight and design guidelines for optimizing the specific mechanical properties and deformation behaviors of graphene and its derivatives. read less

Abstract: Reactive molecular dynamics simulation was employed to compare the damage mitigation efficacy of pristine and polyimide (PI)-grafted polyoctahedral silsesquioxane (POSS), graphene (Gr), and carbon nanotubes (CNTs) in a PI matrix exposed to atomic oxygen (AO) bombardment. The concentration of POSS and the orientation of Gr and CNT nanoparticles were further investigated. Overall, the mass loss, erosion yield, surface damage, AO penetration depth, and temperature evolution are lower for the PI systems with randomly oriented CNTs and Gr or PI-grafted POSS compared to those of the pristine POSS or aligned CNT and Gr systems at the same nanoparticle concentration. On the basis of experimental early degradation data (before the onset of nanoparticle damage), the amount of exposed PI, which has the highest erosion yield of all material components, on the material surface is the most important parameter affecting the erosion yield of the hybrid material. Our data indicate that the PI systems with randomly oriented Gr and CNT nanoparticles have the lowest amount of exposed PI on the material surface; therefore, a lower erosion yield is obtained for these systems compared to that of the PI systems with aligned Gr and CNT nanoparticles. However, the PI/grafted-POSS system has a significantly lower erosion yield than that of the PI systems with aligned Gr and CNT nanoparticles, again due to a lower amount of exposed PI on the surface. When comparing the PI systems loaded with PI-grafted POSS versus pristine POSS at low and high nanoparticle concentrations, our data indicate that grafting the POSS and increasing the POSS concentration lower the erosion yield by a factor of about 4 and 1.5, respectively. The former is attributed to a better dispersion of PI-grafted POSS versus that of the pristine POSS in the PI matrix, as determined by the radial distribution function. read less

Abstract: In this work we have investigated, by fully atomistic reactive (force field ReaxFF) molecular dynamics simulations, some aspects of impact dynamics of water nanodroplets on graphdiyne-like membranes. We simulated graphdiyne-supported membranes impacted by nanodroplets at different velocities (from 100 up to 1500 m/s). The results show that due to the graphdiyne porous and elastic structure, the droplets present an impact dynamics very complex in relation to the ones observed for graphene membranes. Under impact the droplets spread over the surface with a maximum contact radius proportional to the impact velocity. Depending on the energy impact value, a number of water molecules were able to percolate the nanopore sheets. However, even in these cases the droplet shape is preserved and the main differences between the different impact velocities cases reside on the splashing pattern at the maximum spreading. read less

Abstract: Electrochemical double layer capacitors, or supercapacitors, are high-power energy storage devices that consist of large surface area electrodes (filled with electrolyte) to accommodate ion packing in accordance with classical electric double layer (EDL) theory. Nanoporous carbons (NPCs) have recently emerged as a class of electrode materials with the potential to dramatically improve the capacitance of these devices by leveraging ion confinement. However, the molecular mechanisms underlying such enhancements are a clear departure from EDL theory and remain an open question. In this paper, we present the concept of ion reorganization kinetics during charge/discharge cycles, especially within highly confining subnanometer pores, which necessarily dictates the capacitance. Our molecular dynamics voltammetric simulations of ionic liquid immersed in NPC electrodes (of varying pore size distributions) demonstrate that the most efficient ion migration, and thereby largest capacitance, is facilitated by nonuniformity of shape (e.g., from cylindrical to slitlike) along nanopore channels. On the basis of this understanding, we propose that a new structural descriptor, coined as the pore shape factor, can provide a new avenue for materials optimization. These findings also present a framework to understand and evaluate ion migration kinetics within charged nanoporous materials. read less

Abstract: Silicon carbide (SiC) ceramics have been widely used in industry due to its high thermal conductivity. Understanding the relations between the microstructure and the thermal conductivity of SiC ceramics is critical for improving the efficiency of heat removal in heat sink applications. In this paper, a multiscale model is proposed to predict the thermal conductivity of SiC ceramics by bridging atomistic simulations and continuum model via a materials genome model. Interatomic potentials are developed using ab initio calculations to achieve more accurate molecular dynamics (MD) simulations. Interfacial thermal conductivities with various additive compositions are predicted by nonequilibrium MD simulations. A homogenized materials genome model with the calculated interfacial thermal properties is used in a continuum model to predict the effective thermal conductivity of SiC ceramics. The effects of grain size, additive compositions, and temperature are also studied. The good agreement found between prediction results and experimental measurements validates the capabilities of the proposed multiscale genome model in understanding and improving the thermal transport characteristics of SiC ceramics. read less

Abstract: We studied the degradation of a perfluoropolyether lubricant, i.e., D4OH, in the presence of different components present in hard disks including diamond-like carbon (DLC), using ReaxFF reactive force field based molecular dynamics simulations. To generate the DLC structure, a carbon-diamond structure was melted in an Ar-filled head space box at 7500 K, and was slowly cooled down to 3000 K. Then, a constant pressure (NPT) simulation was performed to adjust the sample volume and reduce the internal stress. Similarly, for growth of functionalized DLC, ethylene molecules were used as the carbon source and they were pyrolyzed in the presence of Ar atoms to make H-functionalized DLC (DLC:H). This DLC:H structure was subsequently heated in the presence of nitrogen molecules to make H/N functionalized DLC (DLC:H:N). The results indicate that, by controlling number of Ar atoms and N2 molecules, it is possible to achieve the experimental H/N/C composition and sp2/sp3 ratio composition targets. Final DLC and DLC:H:... read less

Abstract: The adsorption and dynamics of cystine, which is the oxidized dimer of cysteine where the monomers are connected through a disulfide bond, on the Au(110) surface, in water solution, is characterized by means of classical molecular dynamics simulations based on a recently developed reactive force field (ReaxFF). The adopted computational procedure and the force field description are able to give a complete and reliable picture, in line with experiments, of the molecule behavior in solution and in close contact with the metal support. Many different aspects, which have never been explored computationally at this level of theory, are disclosed, namely, physisorption, chemisorption, disulfide bridge breaking/creation, and formation of staples. It is demonstrated that all these events are connected with the specific orientation and location of cystine on the substrate. Simulations in pure water reveal that the disulfide bridge is stable, whereas dissociation is observed on gold. This is favored at low coverage, whereas at high coverage both intact and dissociated forms can be observed depending on local arrangements. The computed photoemission spectra at different K-edges for the predicted adsorbate structures satisfactorily agree with the experimental measurements extracted from literature. read less

Abstract: When at equilibrium, large-scale systems obey thermodynamics because they have microscopic configurations that are typical. "Typical" states are a fraction of those possible with the majority of the probability. A more precise definition of typical states underlies the transmission, coding, and compression of information. However, this definition does not apply to natural systems that are transiently away from equilibrium. Here, we introduce a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation. While a gaseous mixture of hydrogen and oxygen combusts, reactant molecules transform through a variety of ephemeral species en route to the product, water. Out of the exponentially growing number of possible sequences of chemical species, we find that greater than 95% of the probability concentrates in less than 1% of the possible sequences. Overall, these results extend the notion of typicality across the nonequilibrium regime and suggest that typical sequences are a route to learning mechanisms from experimental measurements. They also open up the possibility of constructing ensembles for computing the macroscopic observables of systems out of equilibrium. read less

Abstract: The kinetics and thermodynamics of thermal decomposition of naphthalene and several mono- and dimethylnaphathalene derivatives have been established through reactive molecular dynamics simulations using ReaxFF. These results were compared to previous theoretical and experimental studies and also compared to density functional theory calculation results. This work demonstrates that the kinetics and thermodynamics of the initial activation reaction is directly impacted by the position and number of methyl substituents. Subsequently, the activated molecules react to form either small organic or large char molecules. The char formation mechanism is shown to occur in three steps: activation, dimerization/trimerization, and condensation. Finally, temperature effects on the char formation reaction were also studied. read less

Abstract: We developed a ReaxFF reactive force field for Al/C interactions to investigate carbon coating and its effect on the oxidation of aluminum nanoparticles (ANPs). The ReaxFF parameters were optimized against quantum mechanics-based (QM-based) training sets and validated with additional QM data and data from experimental literature. ReaxFF-molecular dynamics (MD) simulations were performed to determine whether this force field description was suitable to model the surface deposition and oxidation on complex materials (i.e., carbon-coated ANPs). Our results show that the ReaxFF description correctly reproduced the Al/C interaction energies obtained from the QM calculations and qualitatively captured the processes of the hydrocarbons’ binding and their subsequent reactions on the bare ANPs. The results of the MD simulations indicate that a carbon coating layer was formed on the surface of the bare ANPs, while H atoms were transferred from the hydrocarbons to the available Al binding sites typically without bre... read less

Abstract: Amorphous carbon is used as coating material for computer hard-disks magnetic media and recording heads. There has been significant improvement in understanding amorphous carbon's properties based on experimental observations. High data storage density requirement in the coming years necessitates the use of an ultrathin carbon overcoat while maintaining or enhancing its tribological, thermal, optical, and corrosion properties for better recording performance and reliability. Along with experimental techniques, atomistic simulations can be a useful tool to provide fundamental understanding, especially in the cases where experiments are not adequate. This review gives an overview of how atomistic modeling can provide insights into amorphous carbon properties and discuss challenges for such modeling. read less

Abstract: Transient, macroscopic states of chemical disequilibrium are born out of the microscopic dynamics of molecules. As a reaction mixture evolves, the temporal patterns of chemical species encodes some of this dynamical information, while their statistics are a manifestation of the bulk kinetics. Here, we define a chemically-informed symbolic dynamics as a coarse-grained representation of classical molecular dynamics, and analyze the sequences of chemical species for a model of hydrogen combustion. We use reactive molecular dynamics simulations to generate the sequences and derive probability distributions for sequence observables: the reaction time scales and the chain length - the total number of reactions between initiation of a reactant and termination at products. The time scales and likelihood of the sequences depend strongly on the chain length, temperature, and density. Temperature suppresses the uncertainty in chain length for hydrogen sequences, but enhances the uncertainty in oxygen sequence chain lengths. This method of analyzing a surrogate chemical symbolic dynamics reduces the complexity of the chemistry from the atomistic to the molecular level and has the potential for extension to more complicated reaction systems. read less

Abstract: Ion bombardment is a key physical process in the ion implantation and irradiation of graphene, with important implications for tuning graphene’s electronic properties and for understanding the material’s behavior in irradiative environment. Using molecular dynamics with a reactive force field, this work systematically investigates the influence of the incident angle on the generation of defects and vacancies during the bombardment process. It is found that larger incident angles (between the incident line and the surface of graphene) ranging from 70° to 90° are desired for substitution and single vacancy, whereas smaller incident angles ranging from 30° to 50° are favored for forming double vacancies, multiple vacancies, and in-plane disorder. Oxygen ions with the incident angle of 70° produce the highest probability of ion substitution, and the ions at 40–60 eV and 70° yield the highest quality of doping with minimum other defects. These results demonstrate that bombarding graphene along oblique directio... read less

Abstract: In the current work, polycrystalline silicon microdevices are treated with a 1H,1H,2H,2H-Perfluorodecyltrichlorosilane (FDTS) self-assembled monolayer (SAM) film. Using a microelectromechanical systems-based tribometer, the adhesion characteristics of the FDTS-treated surfaces are compared to those of untreated surfaces over a range of approximately 10 × 106 impact cycles. FDTS-treated surfaces showed a lower zero-hour adhesion force compared to untreated surfaces under identical environmental conditions. The presence of the monolayer did not have a discernible effect on the number of cycles to initiate the surface degradation that was manifested as an increase in the adhesion force. Based on trends in degradation, it is concluded that similar chemical and physical wear mechanisms dominate the evolution of adhesion in both treated and untreated devices. The qualitative results of the experiment are reinforced by molecular dynamics (MD) simulations of a single nanoasperity contact coated with an octadecyltrichlorosilane (ODTS) SAM. MD simulations show cleavage of bonds along the aliphatic chains of ODTS resulting in adhesion fluctuations. In agreement with experimental observations, the MD simulation shows a logarithmic increase in adhesion force with increasing number of cycles. MD simulations also predict a logarithmic decrease in adhesion energy with increasing cycles. These results provide insight into the physicohemical changes occurring during repetitive impact of surfaces coated with low surface energy films. read less

Abstract: Molecular simulation is a promising tool for the study of zeolite formation. However, sufficient sampling remains a grand challenge for the practical use of molecular simulation for this purpose. Here, we investigate the initial stage of zeolite synthesis under realistic conditions by using the replica-exchange method and the ReaxFF reactive force field. After a total simulation time of 480 ns, both energetic and structural properties approach convergence. Analyses of data collected at 600 K show that the inorganic structure directing agent NaOH promotes the aggregation of silicate, the formation of branched Si atoms and the formation of 5-membered rings. With the trajectories collected simultaneously at different temperatures, the effect of temperature is discussed. read less

Abstract: Ionic liquids based on the dicyanamide anion (DCA) are of interest as replacements for current hypergolic fuels, which are highly toxic. To better understand the reaction dynamics of these ionic liquid fuels, this study reports the results of molecular dynamics simulations performed for two predicted intermediate compounds in DCA-based ionic liquids/nitric acid (HNO3) combustion, i.e. protonated DCA (DCAH) and nitro-dicyanamide-carbonyl (NDC). Calculations were performed using a ReaxFF reactive force field. Single component simulations show that neat NDC undergo exothermic decomposition and ignition. Simulations with HNO3 were performed at both a low (0.25 g ml−1) and high (1.00 g ml−1) densities, to investigate the reaction in a dense vapor and liquid phase, respectively. Both DCAH and NDC react hypergolically with HNO3, and increased density led to shorter times for the onset of thermal runaway. Contrary to a proposed mechanism for DCA combustion, neither DCAH nor NDC are converted to 1,5-Dinitrobiuret (DNB) before thermal runaway. Details of reaction pathways for these processes are discussed. read less

Abstract: In this work, we study diffusion of gases in porous amorphous carbon at high temperatures using equilibrium molecular dynamics simulations. Microporous and mesoporous carbon structures are computationally generated using liquid quench method and reactive force fields. Motivated by the need to understand high temperature diffusivity of light weight gases like H2, O2, H2O, and CO in amorphous carbon, we investigate the diffusion behavior as function of two important parameters: (a) the pore size and (b) the concentration of diffusing gases. The effect of pore size on diffusion is studied by employing multiple realizations of the amorphous carbon structures in microporous and mesoporous regimes, corresponding to densities of 1 g/cm(3) and 0.5 g/cm(3), respectively. A detailed analysis of the effect of gas concentration on diffusion in the context of these two porosity regimes is presented. For the microporous structure, we observe that predominantly, a high diffusivity results when the structure is highly anisotropic and contains wide channels between the pores. On the other hand, when the structure is highly homogeneous, significant molecule-wall scattering leads to a nearly concentration-independent behavior of diffusion (reminiscent of Knudsen diffusion). The mesoporous regime is similar in behavior to the highly diffusive microporous carbon case in that diffusion at high concentration is governed by gas-gas collisions (reminiscent of Fickian diffusion), which transitions to a Knudsen-like diffusion at lower concentration. read less

Abstract: Reactive molecular dynamics simulations were performed to study the polycondensation of alkoxysilane in solution with alcohol and water. The dynamic formation of siloxane clusters and rings was observed with simulation time. Two mechanisms for the growth of siloxanes were observed: monomer addition and cluster-cluster aggregation. The impacts of the alkoxysilane monomer chemical structure and solution composition on the rates of hydrolysis and condensation were explored. The polycondensation of different precursor alkoxysilane monomers (tetramethoxysilane, trimethoxysilane, methyltrimethoxysilane, or tetraethoxysilane) was modeled. The steric bulk of chemical groups attached to the monomer, such as silyl or alkoxy groups, were found to impact reaction rates. The influence of solution composition was investigated by simulating multiple systems with different concentrations of tetramethoxysilane, methanol, and water. Reactive molecular dynamics is used for the first time to study the polycondensation of alkoxysilanes, creating opportunities for future theoretical studies of the sol-gel process. read less

Abstract: The reactive force field (ReaxFF) method is employed in the molecular dynamics (MD) simulation of oleic-type triglyceride (OTG) pyrolysis for the first time. The complex pyrolysis mechanism of OTG at high temperature, especially focusing on the multichannel pyrolysis pathways of OTG and radical-related evolution mechanisms of products, is intensively investigated at the atomistic level by performing a series of ReaxFF MD simulations. On the basis of simulation trajectory analysis, we find that the initiation decomposition of OTG pyrolysis is through C–O bond fission to release the straight oleic acid radical (C18H33O2•). The decomposition of C18H33O2• radical is mainly started through multichannel pathways: the decarboxylation reaction to form long-chain hydrocarbon radical (C17H33•) and CO2, and C–C bond cleavages at α, β-C position to form hydrocarbon radicals and ester radicals. C–C bond β-scissions and conjugation reactions play important roles in the subsequent decomposition of the C18H33O2• radical.... read less

Abstract: We have developed a reactive force-field of the ReaxFF type for stoichiometric ceria (CeO2) and partially reduced ceria (CeO2–x). We describe the parametrization procedure and provide results validating the parameters in terms of their ability to accurately describe the oxygen chemistry of the bulk, extended surfaces, surface steps, and nanoparticles of the material. By comparison with our reference electronic structure method (PBE+U), we find that the stoichiometric bulk and surface systems are well reproduced in terms of bulk modulus, lattice parameters, and surface energies. For the surfaces, step energies on the (111) surface are also well described. Upon reduction, the force-field is able to capture the bulk and surface vacancy formation energies (Evac), and in particular, it reproduces the Evac variation with depth from the (110) and (111) surfaces. The force-field is also able to capture the energy hierarchy of differently shaped stoichiometric nanoparticles (tetrahedra, octahedra, and cubes), and ... read less

Abstract: We provide a methodology for deducing quantitative reaction models from reactive molecular dynamics simulations by identifying, quantifying, and evaluating elementary reactions of classical trajectories. Simulations of the inception stage of methane oxidation are used to demonstrate our methodology. The agreement of pathways and rates with available literature data reveals the potential of reactive molecular dynamics studies for developing quantitative reaction models. read less

Abstract: The pyrolysis and combustion mechanisms of benzene under different chemical environments and temperatures were investigated by a reactive force field based molecular dynamics (ReaxFF MD) simulation using two systems, pure benzene and a mixture of benzene and oxygen gas. The chemical behaviors of this system were investigated under an ultrahigh temperature that can be induced by a high-energy density laser and compared to those at high temperature. According to some experimental data, we assume that an ultrahigh temperature can be used to mimic laser irradiation. The conclusions of this simulation are as follows. First, the ReaxFF MD simulations showed that the decomposition rates of benzene were significantly accelerated by laser irradiation or in the presence of oxygen. Second, additional initiation pathways were opened up by these two factors. The primary initiation pathway involves only the hydrogen atom loss in the pyrolysis of benzene at 3000 K, and the initiation pathways become much more complicated after laser irradiation or the involvement of oxygen. Third, the ReaxFF MD simulations formed a reasonable carbon black (CB) texture of various sizes in the pyrolysis of benzene, and we also focused on the evolution of the texture of CB. The calculation results of the final gaseous products, hydrocarbons, and the formation of CB are in a good agreement with the literature. This study provides a better understanding of the initiation mechanisms of the pyrolysis and combustion of benzene under extreme conditions. read less

Abstract: Carbyne is a chain of C atoms held together by double or alternating single and triple chemical bonds, and has twice the tensile stiffness of carbon nanotubes (CNTs) and graphene sheets (GSs). In this study, we propose a nano-mechanical mass sensor using a tensioned carbyne resonator. The carbyne resonator is modeled as an equivalent continuum circular cross section beam with diameter 0.772 Å, Young’s modulus 32.71 TPa, shear modulus 11.8 TPa, Poisson’s ratio 0.386 and density 32.21 g cm−3. We analyze the resonant frequency of the proposed sensor carrying with a concentrated mass based on the Timoshenko beam theory and verify the theoretical approach using Rayleigh’s energy method and molecular dynamics simulation. The results show that the proposed mass sensor can measure a tiny mass with weight below 10−5 zg, and provide much higher sensitivity than CNTs- and GSs- based nano-mechanical mass sensors. In addition, the effects of carbyne length, mass position and tensile load on the frequency shift are also analyzed in detail, and it is preferred to use shorter carbyne and higher tensile load in the proposed mass sensor. read less

Abstract: 2,4,6-Trinitrotoluene (TNT), as a representative component of explosive wastewater, is treated in supercritical water gasification (SCWG) and supercritical water oxidation (SCWO) using molecular dynamic simulations based on ReaxFF reactive force field as well as density functional theory (DFT). The detailed reaction processes, important intermediates and products distribution, and kinetic behaviors of SCWG and SCWO systems have been analyzed at the atomistic level. For the SCWG system, TNT is activated by water cluster or H radical and the N atom is mainly converted into NH3 more than N2 through two significant intermediates NOH and C–N fragment. In addition to water cluster and H radical, the TNT is activated by O2 in the SCWO system. Besides, the N atom is transferred into N2 more than other N-containing products after 750 ps simulation. Combined with the calculated cracking energy of the bonds in TNT, SCWG can accelerate its degradation and is easier for C–N bond breaking or changing through other reac... read less

Abstract: Recent studies of single-walled carbon nanotubes (CNTs) in aqueous media have showed that water can significantly affect the tube mechanical properties. CNTs under hydrostatic compression can preserve their elastic properties up to large pressure values, while exhibiting exceptional resistance to mechanical loadings. It was experimentally observed that CNTs with encapsulated linear carbon chains (LCCs), when subjected to high hydrostatic pressure values, present irreversible red shifts in some of their vibrational frequencies. In order to address the cause of this phenomenon, we have carried out fully atomistic reactive (ReaxFF) molecular dynamics (MD) simulations for model structures mimicking the experimental conditions. We have considered the cases of finite and infinite (cyclic boundary conditions) CNTs filled with LCCs (LCC inside CNTs) of different lengths (from 9 up to 40 atoms). Our results show that increasing the hydrostatic pressure causes the CNT to be deformed in an inhomogeneous way due to the LCC presence. The LCC-CNT interface regions exhibit convex curvatures, which results in more reactive sites, thus favoring the formation of covalent chemical bonds between the chain and the nanotube. This process is irreversible with the newly formed bonds continuing to exist even after releasing the external pressure and causing an irreversibly red shift in the chain vibrational modes from 1850 to 1500 cm$^{-1}$. read less

Abstract: In order to understand the intrinsic effect mechanism of water addition on gas explosions, the methane explosion systems with water addition of different mole fractions were systematically studied by reactive force field and first-principles molecular dynamics (MD) simulations. The results show that the effects of water addition on a gas explosion process greatly depend on the system temperature at different reaction stages. Although the water can effectively suppress the methane oxidation process at the initial reaction stage, the same amount of water addition will obviously promote the gas explosion at the later reaction process. The ab initio MD simulations reveal that the water molecules can induce the reactions between ˙HO2 and ˙H with ˙OH radicals at the initial reaction stage. These reactions consume the reactive radicals, causing the reaction activity of the methane oxidation system to decrease. However, at a higher temperature (about 3000 K), water molecules react with ˙O and ˙H radicals to form extra ˙OH free radicals, and these ˙OH free radicals can be transferred rapidly to interact with the methane molecules by the water molecules. All these processes lead to a better reactive performance at the later reaction stage. These results not only identify the intrinsic interaction mechanism of water addition on the gas explosion system, but also provide a significant theoretical guide for the development of a highly efficient suppression method for gas explosions. read less

Abstract: A combination of computational and experimental methods was implemented to understand and confirm that conformational changes of a polymer [specifically polyacrylonitrile (PAN)] vary with the dispersion quality and confinement between single-wall carbon nanotubes (SWNT) in the composite fibers. A shear-flow gel-spinning approach was utilized to produce PAN-based composite fibers with high concentration (i.e., loading of 10 wt %) of SWNT. Dispersion qualities of SWNT ranging from low to high were identified in the fibers, and their effects on the structural morphologies and mechanical properties of the composites were examined. These results show that, as the SWNT dispersion quality in terms of distribution in the fiber and exfoliation increases, PAN conformations were confined to the extended-chain form. Full atomistic computational results show that the surface interaction energy between isolated PAN and SWNT was not preferred, leading to the self-agglomeration of PAN. However, confinement of the polymer chains between SWNT bundles or individual tubes (i.e., molecular crowding) resulted in large increases in the PAN-SWNT interaction energy. In other words, the crowding of polymer chains by the SWNT at high concentrations can promote extended-chain conformational development during fiber spinning. This was also evidenced experimentally by the observance of significantly improved PAN orientation and crystallization in the composite. Ultimately this work provides fundamental insight toward the specific structural changes capable at the polymer/nanotube interface which are important toward improvement of the effective contribution of the SWNT to the mechanical performance of the composite. read less

Abstract: Like filled pasta, rolled or folded graphene can form a large nanocapsule surrounding a hollow interior. Use as a molecular carrier, however, requires understanding of the opening of such vessels. Here, we investigate a monolayer sheet of graphene as a theoretical trial platform for such a nanocapsule. The graphene is bonded to itself via aligned disulfide (S-S) bonds. Through theoretical analysis and atomistic modeling, we probe the critical nonbonded length (free length, Lcrit) that induces fracture-like progressive unfolding as a function of folding radius (Ri). We show a clear linear scaling relationship between the length and radius, which can be used to determine the necessary bond density to predict mechanical opening/closing. However, stochastic dissipated energy limits any exact elastic formulation, and the required energy far exceeds the dissociation energy of the S-S bond. We account for the necessary dissipated kinetic energy through a simple scaling factor (Ω), which agrees well with computat... read less

Abstract: Adsorption of diglycine on the Cu(110) interface in the gas phase at medium coverage is investigated by means of classical all-atom reactive molecular dynamics simulations (ReaxFF) with a focus on preferential binding arrangements and peptide dynamics. Differently from earlier studies, where the slab model was frozen during all calculations, the constraints on the substrate have, in this investigation, been removed, and the atoms can readjust their location in response to the local environment and to the characteristics of the chosen copper face. Relaxation and reconstruction are indeed observed. The results are compared with the data sampled for the perfect slab where the position of every atom of the interface is kept fixed at the bulk geometry. In line with previous studies, the most stably adsorbed molecules are connected to the copper layer through all their oxygen atoms and the terminus nitrogen, adopting an on-top position at an average distance of about 2 A from the interface. In the case of surfa... read less

Abstract: Nitrogen doping in carbon nanostructures has attracted interest for more than a decade, and recent implementation of such structures in energy conversion systems has boosted the interest even more. ... read less

Abstract: Reactive force field methods such as AIREBO, ReaxFF and COMB, are extremely useful for studying physical and chemical interactions between molecules and materials. However, many chemical reactions have relatively high activation energies, putting them beyond the times-scale of conventional molecular dynamics (MD) at modest temperatures. To capture the low-temperature long-lived radical chemistry in atomistic simulations, we have developed a new transition detection scheme for performing Reactive Parallel Replica Dynamics (RPRD) simulation enabling an extended MD time-scales, essentially up to a microsecond using ReaxFF. In the newly implemented event detection scheme, the transition events are identified whenever there is a change in connectivity of any atom. 1-Heptene pyrolysis is chosen as a model system, and RPRD simulations are performed at temperatures as low as 1350K for up to 1 μs for a system consisting of 40 heptene molecules. The chemical mechanism and the product distribution that were obtained... read less

Abstract: Hydrocarbon foams are versatile materials extensively used in high energy-density physics (HEDP) experiments. However, little data exist above 100 GPa, where knowledge of the behavior is particularly important for designing, analyzing, and optimizing HEDP experiments. The complex internal structure and properties of foam call for a multi-scale modeling effort validated by experimental data. We present results from experiments, classical molecular dynamics simulations, and mesoscale hydrodynamic modeling of poly(4-methyl-1-pentene) (PMP) foams under strong shock compression. Experiments conducted using the Z-machine at Sandia National Laboratories shock compress ∼0.300 g/cm3 density PMP foams to 185 GPa. Molecular dynamics (MD) simulations model shock compressed PMP foam and elucidate behavior of the heterogeneous foams at high pressures. The MD results show quantitative agreement with the experimental data, while providing additional information about local temperature and dissociation. Three-dimensional ... read less

Abstract: The study of adsorption of glycine and glycylglycine (or diglycine) on a copper surface is an important step for the comprehension of mechanisms that determine the stability of biological functionalizers on metal substrates. These two molecules can be considered as prototypes and essential models to investigate, theoretically and experimentally, the adaptability of flexible short peptide chains to a definite interface. In this work, we have improved and updated earlier molecular dynamics simulations by including reactivity of the various species and the comparison of ab initio calculated C, N, and O core photoelectron chemical shifts with the ones found in previous studies. New diglycine-copper bonding is predicted, and the results of the chemical shift analysis are, in all cases, fully compatible with structural information obtained through experimental measurements. Moreover, we have found that the process of proton transfer, which is fundamental in the dynamics of amino acids and peptides, occurs mainly by intermolecular interaction between the first and second layer of the adsorbate. read less

Abstract: In order to investigate the initiation mechanisms associated with the pyrolysis of triglyceride that could potentially be used as petrochemical replacements, we carried out 500 ps molecular dynamics simulations employing the ReaxFF reactive force field using tripalmitin as the model molecule at 1500 and 2000 K. We find that the primary decomposition reactions of tripalmitin initiate with the successive scission of the alkyl-oxygen bond to form three straight chain C16H31O2˙ (RCOO˙) radicals and C3H5˙ radical. The deoxygenated alkyl chain is produced through the decarboxylation of the RCOO˙ radical with concurrent production of CO2. The resulting alkyl and C3H5˙ radicals further undergo recombination and decomposition to yield mainly alkanes and alkenes, with the actual product distribution being dependent on reaction temperature. β-Scission plays an important role in alkyl chain decomposition with a concomitant release of C2H4. Compared to 1500 K, this reaction is accelerated at 2000 K. In addition, the formation of cyclic hydrocarbon is also observed at 2000 K. As opposed to previous proposed Diels–Alder reactions or intramolecular cyclizations of alkenyl radicals mechanisms, it is found that cyclopentane could be produced by intramolecular cyclization of a biradical. read less

Abstract: Space vehicles often encounter very high temperature and harsh oxidative environments. To ensure proper thermal protection, layers composed of SiC and EPDM polymer are placed on the outer surface of the space vehicle. The O2 and H2O molecules are able to oxidize the SiC network, creating SiO2-type structures that may form a protective layer, while also pyrolyzing and burning the EPDM polymer, causing ablation. Reactive molecular dynamics simulations nicely complement experiment, as they provide direct observation and information to calculate physical parameters such as transport diffusivities and reaction constants. In this study, rate models were developed and molecular dynamics simulated trajectories were used to extract Arrhenius parameters that describe the initial stages of transport and kinetics of SiC oxidation by O2 and H2O and the combustion and pyrolysis of EPDM. The simulations showed that O2 was able to oxidize SiC more efficiently than H2O, with the transport activation barrier of O2 in the r... read less

Abstract: The process of mono- and multilayer adsorption of glycine on copper surface Cu(110) and the preferred binding modes of the molecule were studied theoretically by means of classical reactive (ReaxFF) molecular dynamics simulations. Starting from glycines in gas phase in the neutral nonzwitterionic form, the most stably adsorbed structures are found to be the molecules which release their carboxyl protons (anionic form) to molecules in the second layer and place both the carboxyl oxygens and the nitrogen atom on top of copper sites, at an average distance of about 2 A. The surface binding mechanism consists of different phases during which major conformational rearrangements and several intermediate adsorption configurations are observed. The overall stability of the glycine adlayers is essentially due to the combination of different intermolecular forces, namely chemical bonds with the copper top layer and intermolecular hydrogen bonds within the adsorbed molecular units. At low coverage the molecules are ... read less

Abstract: Forced crumpling of graphene and graphene oxides sheets and their reversibilities are explored here by performing molecular dynamics (MD) simulations, with focus on the stabilizing mechanisms and properties of crumples. We find that to balance strain energy stored in crumpled sheets, dangling bonds in graphene show significant chemical activity in forming covalent crosslinks. Interlayer van der Waals cohesion helps also to maintain the crumpled conformation after the compressive load is released. A distinct size-dependent behavior of the process is observed, implying competition between these driven forces. These results suggest possibilities in controlling the reversibility in crumpling graphene sheets into nanoparticles and highlight the effects of chemically active graphene edges, defective sites, van der Waals and hydrogen-bond cohesion in defining microstructures of graphene-based materials. read less

Abstract: To investigate the detailed mechanisms for brown coal oxidation at high temperatures, a ReaxFF reactive forcefield was used to perform a series of molecular dynamics simulations from 1000 K to 2500 K. Analyses indicated that the chemical system tend to be more reactive with increasing temperature. It was found that the oxidation process of brown coal primarily initiates from hydrogen abstraction reactions by O2 and related oxygenated radicals from phenolic hydroxyl groups, methyl groups, especially carboxyl groups in lower temperature to form peroxygen species, or by either thermal decomposition of brown coal backbone in higher temperature. These peroxygen species usually could chemically adsorb on the C-centered radicals of brown coal backbone. The weak O–O bond in peroxygen makes them easier to break into oxygenated radical, which could also chemically adsorb on the C-centred radical to form hydroxyl group and other oxygenated compounds. In the oxidation process of brown coal, the decomposition and oxidation of aliphatic chain is easier than aromatic ring. The chemisorption of peroxygen radical induces the breakage of aromatic ring and accelerates the depth oxidation of brown coal. An increasing number of products are observed with increasing temperature. read less

Abstract: A novel carbon allotrope consisting of parallel zigzag and armchair chains alternatively each other (10 atoms/cell, named pza-C10) was discovered. The calculated band gap of pza-C10 is 0.31 (0.71) eV with PBE (HSE06), and thus the new member of carbon family is a semiconductor. The pza-C10 sheet not only is thermodynamically more stable than the other known semiconducting carbon sheets, but also it can perfectly graft with graphene. The unprecedented properties of pza-C10 provide a new approach of modulating intrinsic band gap through forming graphene-based monolayer carbon superlattices (GSLs). The band gaps of GSLs with zigzag type of interface oscillate between semiconducting and semimetallic (mostly at the Dirac point) states as the number of zigzag chains increases, showing quantum size effect. The 2D superlattice achieved in GSLs opens a new strategy to design the crystal structures and modulate the electronic properties of 2D materials, nanoribbons, and nanotubes. read less

Abstract: A methodology is described for atomistic simulations of shock-compressed materials that incorporates quantum nuclear effects on the fly. We introduce a modification of the multiscale shock technique (MSST) that couples to a quantum thermal bath described by a colored noise Langevin thermostat. The new approach, which we call QB-MSST, is of comparable computational cost to MSST and self-consistently incorporates quantum heat capacities and Bose-Einstein harmonic vibrational distributions. As a first test, we study shock-compressed methane using the ReaxFF potential. The Hugoniot curves predicted from the new approach are found comparable with existing experimental data. We find that the self-consistent nature of the method results in the onset of chemistry at 40% lower pressure on the shock Hugoniot than observed with classical molecular dynamics. The temperature shift associated with quantum heat capacity is determined to be the primary factor in this shift. read less

Abstract: Aromatic hydrocarbon fuels, such as toluene, are important components in real jet fuels. In this work, reactive molecular dynamics (MD) simulations employing the ReaxFF reactive force field have been performed to study the high-temperature oxidation mechanisms of toluene at different temperatures and densities with equivalence ratios ranging from 0.5 to 2.0. From the ReaxFF MD simulations, we have found that the initiation consumption of toluene is mainly through three ways, (1) the hydrogen abstraction reactions by oxygen molecules or other small radicals to form the benzyl radical, (2) the cleavage of the C-H bond to form benzyl and hydrogen radicals, and (3) the cleavage of the C-C bond to form phenyl and methyl radicals. These basic reaction mechanisms are in good agreement with available chemical kinetic models. The temperatures and densities have composite effects on toluene oxidation; concerning the effect of the equivalence ratio, the oxidation reaction rate is found to decrease with the increasing of equivalence ratio. The analysis of the initiation reaction of toluene shows that the hydrogen abstraction reaction dominates the initial reaction stage at low equivalence ratio (0.5-1.0), while the contribution from the pyrolysis reaction increases significantly as the equivalence ratio increases to 2.0. The apparent activation energies, E(a), for combustion of toluene extracted from ReaxFF MD simulations are consistent with experimental results. read less

Abstract: The adsorption of glycine (Gly) on titania in water solution and its preferred binding modes are studied by means of classical reactive (ReaxFF) and nonreactive molecular dynamics simulations. A small cluster made of a few glycine molecules, surrounded by water molecules, is placed close to the TiO2(110) surface and its initial motion toward the substrate is described through classical reactive dynamics. Glycine appears to be less easily and strongly adsorbed on the surface in solution than in the gas phase due to its competition with the surrounding water molecules. Indeed, in line with the experimental observations, the preferential binding mode of glycine in solution is found to be a monodentate coordination of one of its carboxyl oxygens to a Ti surface site. The potential of mean constraint force (PMF) method, combined with the classical nonreactive molecular dynamics simulations, was used to calculate the change in free energy upon glycine adsorption and the results obtained through exhaustive sampl... read less

Abstract: Graphdiyne, a recently synthesized one-atom-thick carbon allotrope, is atomistically porous - characterized by a regular "nanomesh"- and suggests application as a separation membrane for hydrogen purification. Here we report a full atomistic reactive molecular dynamics investigation to determine the selective diffusion properties of hydrogen (H(2)) amongst carbon monoxide (CO) and methane (CH(4)), a mixture otherwise known as syngas, a product of the gasification of renewable biomass (such as animal wastes). Under constant temperature simulations, we find the mass flux of hydrogen molecules through a graphdiyne membrane to be on the order of 7 to 10 g cm(-2) s(-1) (between 300 K and 500 K), with carbon monoxide and methane remaining isolated. Using a simple Arrhenius relation, we determine the energy required for permeation on the order of 0.11 ± 0.03 eV for single H(2) molecules. We find that addition of marginal applied force (approximately 1 to 2 pN per molecule, representing a controlled pressure gradient, ΔP, on the order of 100 to 500 kPa) can successfully enhance the separation of hydrogen gas. Addition of larger driving forces (50 to 100 pN per molecule) is required to selectively filter carbon monoxide or methane, suggesting that, under near-atmospheric conditions, only hydrogen gas will pass such a membrane. Graphdiyne provides a unique, chemically inert and mechanically stable platform facilitating selective gas separation at nominal pressures using a homogeneous material system, without a need for chemical functionalization or the explicit introduction of molecular pores. read less

Abstract: Water microdroplets containing graphene oxide and a second solute are shown to spontaneously segregate into sack-cargo nanostructures upon drying. Analytical modeling and molecular dynamics suggest the sacks form when slow-diffusing graphene oxide preferentially accumulates and adsorbs at the receding air-water interface, followed by capillary collapse. Cargo-filled graphene nanosacks can be nanomanufactured by a simple, continuous, scalable process and are promising for many applications where nanoscale materials should be isolated from the environment or biological tissue. read less

Abstract: Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures. read less

Abstract: The mechanical properties of pristine graphene oxide paper and paper-like films of polyvinyl alcohol (PVA)-graphene oxide nanocomposite are investigated in a joint experimental-theoretical and computational study. In combination, these studies reveal a delicate relationship between the stiffness of these papers and the water content in their lamellar structures. ReaxFF-based molecular dynamics (MD) simulations elucidate the role of water molecules in modifying the mechanical properties of both pristine and nanocomposite graphene oxide papers, as bridge-forming water molecules between adjacent layers in the paper structure enhance stress transfer by means of a cooperative hydrogen-bonding network. For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the modulus of the paper without saturating the gallery space. Introducing PVA chains into the gallery space further enhances the cooperativity of this hydrogen-bonding network, in a manner similar to that found in natural biomaterials, resulting in increased stiffness of the composite. No optimal water concentration could be found for the PVA-graphene oxide nanocomposite papers, as dehydration of these structures continually enhances stiffness until a final water content of ~7 wt % (additional water cannot be removed from the system even after 12 h of annealing). read less

Abstract: The adsorption of glycine (Gly) on TiO2 in the gas phase and the behavior of a set of preadsorbed diglycine (Gly-Gly) molecules in solution are studied by using classical nonreactive and reactive (ReaxFF) simulations. The initial dynamic phase of Gly adsorption is rendered through the nonreactive evaporation of a droplet followed by reactive dynamics of the deposited peptide layer. Gly adsorbs strongly on the surface in a wide variety of orientations which are dominated by a carboxyl bidentate coordination to two titanium ions. The binding mode involves mainly anionic species, which are formed after transferring a proton to the surface. Gly zwitterions are present in the second layer. In the time scale explored, water activity does not perturb substantially the orientation of preadsorbed Gly-Gly molecules which remain strongly bound to the substrate through their carboxyl groups. The results of this investigation are in satisfactory agreement with previous theoretical studies and available experimental data. read less

Abstract: In this work, we have investigated the hyperthermal collisions of atomic oxygens with graphene through molecular dynamics simulations using the ReaxFF reactive force field. First, following Paci et al. (J. Phys. Chem. A 2009, 113, 4677 - 4685), 5-eV energetic collisions of atomic oxygen with a 24-atom pristine graphene sheet and a sheet with a single vacancy defect, both functionalized with oxygen atoms in the form of epoxides, were studied. We found that the removal of an O(2) molecule from the surface of the graphene sheet occurs predominantly through an Eley-Rideal-type reaction mechanism. Our results, in terms of the number of occurrences of various reactive events, compared well with those reported by Paci et al. Subsequently, energetic collisions of atomic oxygen with a 25-times-expanded pristine sheet were investigated. The steady-state oxygen coverage was found to be more than one atom per three surface carbon atoms. Under an oxygen impact, the graphene sheet was always found to buckle along its diagonal. In addition, the larger sheet exhibited trampoline-like behavior, as a result of which we observed a much larger number of inelastic scattering events than those reported by Paci et al. for the smaller system. Removal of O(2) from the larger sheet occurred strictly through an Eley-Rideal-type reaction. Investigation of the events leading to the breakup of a pristine unfunctionalized graphene sheet and the effects of the presence of a second layer beneath the graphene sheet in an AB arrangement was done through successive impacts with energetic oxygen atoms on the structures. Breakup of a graphene sheet was found to occur in two stages: epoxide formation, followed by the creation and growth of defects. Events leading to the breakup of a two-layer graphene stack included epoxide formation, transformation from an AB to an AA arrangement as a result of interlayer bonding, defect formation and expansion in the top layer, and finally erosion of the bottom layer. We observed that the breakup of the two-layer stack occurred through a sequential, layer-by-layer, erosion process. read less

Abstract: The mechanical behavior and properties of multilayer graphene sheets and nanoribbons have been a subject of intensive research in recent years, due to their potential in electronic, structural and thermal applications. Calculations of effective properties range from molecular dynamic simulations to use of structural mechanical continuum models. Here, structural and elastic parameters are obtained via full atomistic simulations, and a two-dimensional mesoscopic model for a sheet of graphene is developed utilizing coarse-grain bead-spring elements with rotational-spring potentials. The assertion of energy conservation between atomistic and mesoscale models through elastic strain energy is enforced to arrive at model parameters, incorporating normal and shear strains, out-of-plane bending and intramolecular interactions. We then apply our mesoscopic model to investigate the structure and conformational behavior of twisted ultralong multilayer graphene ribbons with lengths of hundreds of nanometers, representing several millions of individual atoms, beyond the accessible regime of full atomistic molecular dynamics. We find a distinct transition from a twisted (saddle-like) configuration to a helical (coil-like) configuration as a function of imposed rotation and number of graphene layers. Further, for single layer graphene ribbons, multiple, stable configurations occur at discrete rotations due to the surface adhesion. The model developed and applied here can be more generally used to investigate properties of other two-dimensional membrane and ribbon-like systems for mesoscale hierarchical material design. read less

Abstract: We study the mechanisms involved in Au nanocluster deposition on thiol self-assembled monolayer modified Au(111) surfaces. Molecular dynamics simulations reveal a wide range of cluster-surface binding configurations within a very narrow deposition energy range (0.2–0.6 eV/atom for ∼2.5 nm diameter clusters). These go from noncovalent to full contact and include surprising intermediate cases in which the clusters are bound to the underlying Au(111) surface via molecular links and nanowires. Experiments show that, subsequently, the clusters are covered by thiols and slightly flattened. read less

Abstract: A multilayered composite structure formed by a random stacking of graphene oxide (GO) platelets is an attractive candidate for novel applications in nanoelectromechanical systems and paper-like composites. We employ molecular dynamics simulations with reactive force fields to elucidate the structural and mechanical properties of GO paper-like materials. We find that the large-scale properties of these composites are controlled by hydrogen bond networks that involve functional groups on individual GO platelets and water molecules within the interlayer cavities. Water content controls both the extent and collective strength of these interlayer hydrogen bond networks, thereby affecting the interlayer spacing and elastic moduli of the composite. Additionally, the chemical composition of the individual GO platelets also plays a critical role in establishing the mechanical properties of the composite--a higher density of functional groups leads to increased hydrogen bonding and a corresponding increase in stiffness. Our studies suggest the possibility of tuning the properties of GO composites by altering the density of functional groups on individual platelets, the water content, and possibly the functional groups participating in hydrogen bonding with interlayer water molecules. read less

Abstract: Graphane is a two-dimensional system consisting of a single layer of fully saturated (sp3 hybridization) carbon atoms. In an ideal graphane structure C–H bonds exhibit an alternating pattern (up and down with relation to the plane defined by the carbon atoms). In this work we have investigated, using ab initio and reactive molecular dynamics simulations, the role of H frustration (breaking the H atoms’ up and down alternating pattern) in graphane-like structures. Our results show that a significant percentage of uncorrelated H frustrated domains are formed in the early stages of the hydrogenation process leading to membrane shrinkage and extensive membrane corrugations. These results also suggest that large domains of perfect graphane-like structures are unlikely to be formed, as H frustrated domains are always present. read less

Abstract: EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4—a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor’s structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor’s structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development. read less

Abstract: The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiO2 crystallines. To observe the adsorption and dissociation behavior of H2O, the reaction force field (ReaxFF) is used to investigate the dynamic behavior of H2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed H2O (H2Oad) and the bridging oxygen (Obr) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Ti5c) and Obr of the rutile and anatase TiO2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of H2O on the TiO2 surface. To describe interfacial water structures between TiO2 and bulk water, the double-layer model is proposed. The first layer is the dissociated H2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Obr or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the H2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted. read less

Abstract: MXenes, which have good reinforcing and toughening effects, can serve as excellent polymer additives. However, the mechanism whereby MXenes act has not been revealed. In this study, to understand the reinforcement effect of Tin+1Cn on polymethyl methacrylate (PMMA) from an atomistic perspective, we used molecular dynamics to conduct unidirectional tensile simulations of PMMA composites reinforced with monolayer Ti2C and Ti3C2 sheets. The results showed that Ti3C2 can more significantly improve the mechanical properties of the PMMA polymer than Ti2C, and the yield stress and Young's modulus of the Ti3C2/PMMA complexes were respectively 54.39% and 73.46% higher than the Ti2C/PMMA complexes. To further reveal the interaction mechanism between Tin+1Cn and PMMA, different separation speeds were used to simulate the pull‐out of Tin+1Cn from the PMMA matrix. The results showed that, in addition to the enhancement of interfacial strength by non‐bonding van der Waals forces, there were TiO and CTi bonds between Tin+1Cn and PMMA, which further increased the interfacial strength. Ti3C2 formed a denser interfacial region with PMMA, it could more effectively resist the formation and expansion of cracks. These findings may provide an important theoretical basis to design new type of MXene/polymer composites with excellent mechanical properties. MXene greatly improved the mechanical properties of the PMMA matrix. Formation of chemical bonds improved connection between the MXene and PMMA. The addition of MXene slows down the rate of crack propagation in PMMA. read less

Abstract: The thermal decomposition mechanism of n-hexane is investigated by using density functional theory and ReaxFF force field. The initial decomposition reactions, the effect of temperature on thermal decomposition and first-order kinetics are analyzed. The results show that the C-C bonds in n-hexane molecule are more easily decomposed than that of C-H bonds, and the breakage of C3-C4 bond is the main initial decomposition reaction. The main decomposition products of n-hexane are H2, CH4, C2H2, C2H4, C2H6, and C3H6. The decomposition rate of n-hexane is accelerated by temperature. The apparent activation energy and pre-exponential factor of n-hexane thermal decomposition are 209.8 kJ mol−1 and 1.1 × 1013 s−1, respectively. read less

Abstract: Phase formation by pulsed laser irradiation of suspended nanoparticles has recently been introduced as a promising synthesis technique for heterostructures. The main challenge still lingers regarding the exact mechanism of particle formation due to the non‐equilibrium kinetic by‐products resulting from the localized alternative, fast, high‐temperature nature of the process. Here, the authors analyze the bond breaking/formation of copper or copper (II) interfaces with ethanol during the absorption of pulses for Cu‐CuO‐Cu2O formation applicable as an electrocatalyst in ethanol oxidation fuel cells. This study includes but is not limited to, a comprehensive discussion of the interaction between nano‐laser pulses and suspension for practical control of the synthesis process. The observed exponential and logarithmic changes in the content of heterostructures for the CuO‐ethanol and Cu‐ethanol samples irradiated with different fluences are interpreted as the dominant role of physical and chemical reactions, respectively, during the pulsed laser irradiation of suspensions synthesis. It is also shown that the local interface between dissociated ethanol and the molten sphere is responsible for the oxidative/reductive interactions resulting in the formation of catalytic‐augmented Cu3+ by‐product, thanks to the reactive bond force field molecular dynamics studies confirmed by ab‐initio calculations and experimental observations. read less

Abstract: Biochar is a carbon-rich solid produced during the thermochemical processes of various biomass feedstocks. As a low-cost and environmentally friendly material, biochar has multiple significant advantages and potentials, and it can replace more expensive synthetic carbon materials for many applications in nanocomposites, energy storage, sensors, and biosensors. Due to biomass feedstock species, reactor types, operating conditions, and the interaction between different factors, the compositions, structure and function, and physicochemical properties of the biochar may vary greatly, traditional trial-and-error experimental approaches are time consuming, expensive, and sometimes impossible. Computer simulations, such as molecular dynamics (MD) simulations, are an alternative and powerful method for characterizing materials. Biomass pyrolysis is one of the most common processes to produce biochar. Since pyrolysis of decomposing biomass into biochar is based on the bond-order chemical reactions (the breakage and formation of bonds during carbonization reactions), an advanced reactive force field (ReaxFF)-based MD method is especially effective in simulating and/or analyzing the biomass pyrolysis process. This paper reviewed the fundamentals of the ReaxFF method and previous research on the characterization of biochar physicochemical properties and the biomass pyrolysis process via MD simulations based on ReaxFF. ReaxFF implicitly describes chemical bonds without requiring quantum mechanics calculations to disclose the complex reaction mechanisms at the nano/micro scale, thereby gaining insight into the carbonization reactions during the biomass pyrolysis process. The biomass pyrolysis and its carbonization reactions, including the reactivity of the major components of biomass, such as cellulose, lignin, and hemicellulose, were discussed. Potential applications of ReaxFF MD were also briefly discussed. MD simulations based on ReaxFF can be an effective method to understand the mechanisms of chemical reactions and to predict and/or improve the structure, functionality, and physicochemical properties of the products. read less

Abstract: In order to study the role of metal sodium in the spray pyrolysis of biomass tar, this paper designs a sodium-containing naphthalene pyrolysis system (NSS) and a pure naphthalene pyrolysis system (PNS) using naphthalene as the carbon source and sodium chloride as the sodium metal donor for comparison. This enables an exploration of the effect of sodium on the initial nucleation of carbon fumes formed by naphthalene pyrolysis using reaction molecular dynamics (ReaxFF MD). The simulation results show that NSS undergoes pyrolysis reactions earlier and faster than PNS at the same temperature. Simulated at 3250 K temperature for 2 ns, the naphthalene pyrolysis consumption rate of the NSS was faster than that of the PNS, and the addition of sodium atoms during the condensation process provided more active sites and accelerated the condensation of macromolecular products. Moreover, Na+ and carbon rings form a Na+-π structure to promote the bending of graphite lamellae to facilitate the formation of carbon nuclei. Molecular dynamics simulations were used to simulate the formation of carbon nuclei during the initial stage of naphthalene pyrolysis, revealing that the mechanism of sodium salt catalyzed the acceleration of organic matter pyrolysis from a microscopic visualization perspective. read less

Abstract: This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals, leading to the chain scission and crosslinking of polymer chains. In this study, we integrate a thermal oxidation kinetic model in the oxygen excess regime into the Kremer-Grest model, thereby enabling a reactive coarse-grained molecular dynamics simulation to capture the process of oxidative degradation. Our simulation reveals that when the timescale of the characteristic reaction step of oxidative degradation is shorter than the longest relaxation time of polymer chains, the scission sites exhibit spatial heterogeneity. This innovative simulation model possesses the potential to enhance our comprehension of polymer aging phenomena, thus making noteworthy contributions to the realm of polymer science and degradation chemistry. read less

Abstract: Understanding the mechanics behind knee joint injuries and providing appropriate treatment is crucial for improving physical function, quality of life, and employability. In this study, we used a hybrid molecular dynamics-finite element-musculoskeletal model to determine the level of loads the knee can withstand when landing from different heights (20, 40, 60 cm), including the height at which cartilage damage occurs. The model was driven by kinematics–kinetics data of asymptomatic subjects at the peak loading instance of drop landing. Our analysis revealed that as landing height increased, the forces on the knee joint also increased, particularly in the vastus muscles and medial gastrocnemius. The patellar tendon experienced more stress than other ligaments, and the medial plateau supported most of the tibial cartilage contact forces and stresses. The load was mostly transmitted through cartilage-cartilage interaction and increased with landing height. The critical height of 126 cm, at which cartilage damage was initiated, was determined by extrapolating the collected data using an iterative approach. Damage initiation and propagation were mainly located in the superficial layers of the tibiofemoral and patellofemoral cartilage. Finally, this study provides valuable insights into the mechanisms of landing-associated cartilage damage and could help limit joint injuries and improve training programs. read less

Abstract: In the era of low carbon and environmental protection, sustainable development ideas win support among the people. Vegetable oils have excellent environmental performance compared with traditional mineral insulating oils. The aging characteristics of insulating paper in vegetable oil have been discussed in experiments, but the deterioration mechanism at the microscopic level is still lacking. In this article, the microscopic deterioration mechanism of insulating paper in vegetable oil and mineral oil is investigated by molecular dynamics. In addition, the intermolecular properties of insulating paper under different insulating oils are compared. It is found that the cellulose cleavage in insulating paper is divided into three ways: glycosidic bond breaking, pyran ring opening, and dehydroxylation. The number of hydrogen bonds, binding energy, and electrostatic energy between insulating paper and vegetable oil are higher than those of mineral oil. It proves that there is a stronger interaction between insulating paper and vegetable oil. Finally, the change rules of characteristic products CO, $\text{H}_{{2}}\text{O}$ , $\text{H}_{{2}}$ , and formic acid are counted. It is found that vegetable oil can delay the deterioration and prolong the life of insulating paper compared to mineral oil. The above study reveals the microscopic influence law of vegetable oil and mineral oil on the degradation of insulating paper. It provides theoretical support for the large-scale application of vegetable oil in oil-immersed transformers. read less

Abstract: Aluminum oxide layer affects the integrity of electrical contact and can contribute adversely to passive intermodulation (PIM) behavior in radio frequency (RF) devices, necessitating a need for understanding its formation mechanism and realistic estimation of its thickness. Using ReaxFF molecular dynamics simulation technique, this study investigated the impact of surface defects on aluminum oxide layer formation. Results reveal that crystallographic orientation did not affect the kinetics of oxidation process of aluminum. However, the reaction kinetics increased significantly with surface inhomogeneities such as cracks, scratches, and grain boundaries. A non-uniform oxide layer with thickness variation in the range of 72-77% was observed due to surface imperfections. Concurrent crack healing and oxidation was observed, where the crack tips acted as sites for oxygen diffusion, thus increasing oxidation kinetics. The observations from this simulation agree with experimental reports and have important implications for optimizing the contact integrity in RF devices and for PIM control. read less

Abstract: Energy storage and renewable energy sources are critical for addressing the growing global energy demand and reducing the negative environmental impacts of fossil fuels. Carbon nanomaterials are extensively explored as high reliable, reusable, and high‐density mechanical energy storage materials. In this context, machine learning techniques, specifically machine learning potentials (MLPs), are employed to explore the elastic properties of 1D carbon nanowires (CNWs) as a promising candidate for mechanical energy storage applications. The study focuses on the elastic energy storage properties of these CNWs, utilizing MLPs trained with data from first‐principles molecular dynamics simulations. It is found that these materials exhibit an exceptionally high tensile elastic energy storage capacity, with a maximum storage density ranging from 2262 to 2680 kJ kg−1. Furthermore, it is discovered that some CNWs exhibit a superior torsional energy storage capacity compared to their tensile energy storage capacity. Overall, this research demonstrates the effectiveness of machine learning‐based computational approaches in accelerating the exploration and optimization of novel materials. It also highlights the potential of CNWs as promising candidates for future energy storage applications. read less

Abstract: Through molecular dynamics (MD) simulations with ReaxFF potential, the effects of chemical contaminants on the mechano-chemical properties and tribological performance of perfluoropolyether (PFPE) lubricants were investigated. For the two types of contaminants, i.e., silicon dioxide (SiO2) nanoparticles and water (H2O), their molecular interactions with the two different PFPE lubricants, i.e., Ztetraol and ZTMD, were evaluated at the two different temperatures, i.e., 300 K and 700 K. Contaminants were adsorbed onto the PFPE lubricants at a controlled temperature. Then, air shear simulations were conducted to examine the mechano-chemical behaviors of the contaminated lubricants. Sliding contact simulations were performed to further investigate the tribological performance of the contaminated lubricants, from which the resulting friction and surface contamination were quantified. Lastly, chemical reactions between PFPE lubricants and contaminants were studied to investigate the degradation of PFPE lubricants. It was observed that SiO2 nanoparticles stiffened the PFPE lubricant, which decreased its shear displacement and increased friction. In the case of the H2O contaminant, it weakened and decreased the PFPE lubricant’s viscosity, increasing its shear displacement and lowering friction. However, the decreased viscosity by H2O contaminants can weaken the lubricity of the PFPE lubricant, leading to a higher chance of direct solid-to-solid contact under high contact force conditions. read less

Abstract: Understanding how hydrogen plasma etches various potential products during the diamond growth process can contribute to improving the knowledge of diamond growth. However, due to the absence of an in situ characterization technique during the etching process, the complex chemical reactions involved in the process obscure the atomic‐scale etching mechanisms. In this paper, the etching mechanisms of diamond (001), graphite (0001), and amorphous carbon substrates irradiated by hydrogen plasmas are investigated and compared using molecular dynamics simulations based on ReaxFF. When the incident energy of H atoms is 1 eV, the rate of carbon loss from graphite and amorphous carbon are far higher than that from diamond. As the incident energy of H atoms increases, the etching rate of diamond shows a slow increase, while the etching rates of amorphous carbon and graphite exhibit more significant increases. It can be concluded that the etching rate of diamond is significantly lower than that of graphite and amorphous carbon under H plasma. In the Chemical Vapor Deposition (CVD) process of diamond growth, the generated graphite and amorphous carbon are rapidly etched, leaving only diamond. This offers a plausible explanation for the growth mechanism of diamond through CVD. read less

Abstract: High-ash coal, also known as low-grade coal, has becomes a viable alternative in recent years to high-quality coal because available resources have become increasingly scarce due to extensive mining activity. This work aims to provide a comprehensive understanding of the structural characteristics of high-ash coal and construct a plausible molecular structure to elucidate its chemical reactivity in future applications. Its properties were investigated using Solid-state 13C nuclear magnetic resonance (13C NMR), X-ray photoelectron spectroscopy analysis (XPS), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR). The molecular structure was constructed and validated using Material Studio, LAMMPS Software Package, and MATLAB program. The characterization results revealed that high-ash coal contains 72.15% aromatic carbon, significantly surpassing the percentage of aliphatic carbon (27.85%). The ratio of bridgehead carbon to peripheral aromatic carbon was calculated as 0.67, indicating that the pentacene is the main carbon skeleton form in the high-ash coal structure. Furthermore, oxygen-containing functional groups presented as C=O/O–C–O, C–O, and COO– within the structure along with pyridine and pyrrolic structures. Consequently, the molecular structure comprises pentacene with aliphatic carbon chains, such as methylene, that connect the benzene rings and form a three-dimensional network. The results of a simulated IR spectrum and contact angle simulation aligned with the experimental results, validating the molecular structure of high-ash coal. The chemical formula for the high-ash coal model was determined as C203H189N7O61S with a molecular weight of 3734.79. read less

Abstract: Over the past few years, graphene grown by chemical vapor deposition (CVD) has gained prominence as a template to grow transition metal dichalcogenide (TMD) overlayers. The resulting two-dimensional (2D) TMD/graphene vertical heterostructures are attractive for optoelectronic and energy applications. However, the effects of the microstructural heterogeneities of graphene grown by CVD on the growth of the TMD overlayers are relatively unknown. Here, we present a detailed investigation of how the stacking order and twist angle of CVD graphene influence the nucleation of WSe2 triangular crystals. Through the combination of experiments and theory, we correlate the presence of interlayer dislocations in bilayer graphene with how WSe2 nucleates, in agreement with the observation of a higher nucleation density of WSe2 on top of Bernal-stacked bilayer graphene versus twisted bilayer graphene. Scanning/transmission electron microscopy (S/TEM) data show that interlayer dislocations are present only in Bernal-stacked bilayer graphene but not in twisted bilayer graphene. Atomistic ReaxFF reactive force field molecular dynamics simulations reveal that strain relaxation promotes the formation of these interlayer dislocations with localized buckling in Bernal-stacked bilayer graphene, whereas the strain becomes distributed in twisted bilayer graphene. Furthermore, these localized buckles in graphene are predicted to serve as thermodynamically favorable sites for binding WSex molecules, leading to the higher nucleation density of WSe2 on Bernal-stacked graphene. Overall, this study explores synthesis-structure correlations in the WSe2/graphene vertical heterostructure system toward the site-selective synthesis of TMDs by controlling the structural attributes of the graphene substrate. read less

Abstract: A novel 2D carbon allotrope, pentagraphyne (PG-yne), was introduced in a recent theoretical study. This unique structure is derived from pentagraphene by incorporating acetylenic linkages between sp3 and sp2 hybridized carbon atoms. Given its intriguing electronic and structural properties, it is imperative to investigate the mechanical characteristics and thermal responses of PG-yne in both monolayer and nanotube configurations, which encompass different chiralities and diameters. We conducted fully atomistic reactive molecular dynamics (MD) simulations employing the ReaxFF potential to address these aspects. Our findings reveal that Young’s modulus of PG-yne monolayers stands at approximately 51 GPa at room temperature. In contrast, for the studied nanotubes, regardless of their chirality, it hovers around 45 GPa. Furthermore, our observations indicate that PG-yne-based systems feature an extensive and relatively flat plastic region before reaching the point of total fracture, irrespective of their topology. Regarding their thermal properties, we identified a melting point at approximately 3600 K, accompanied by a phase transition around 1100 K. read less

Abstract: An original 2.5 technology based on vertically aligned Carbon Nanotubes (VACNTs) to produce millimeter-waves Air-Filled WaveGuide (AFWG) structures is described in this paper. The design of AFWG is based on bundle of VACNTs acting as WG’s metallic lateral walls. A CMOS compatible CNTs process is developed to fabricate the WG using a dedicated assembly process. Raman spectroscopy and molecular dynamics are applied to study the effects of the CNTs compression during the fabrication process. An example of the realization of a V band AFWG is presented together with S-parameters measurements which validate the concept of VACNTs-based AFWG. In addition, the experimental attenuation constant is estimated at 0.5 dB/mm between 81–86 GHz. read less

Abstract: Atomic oxygen (AO) collision is one of the most serious threats to polymeric materials exposed to the space environment, yet understanding the structural changes and degradation of materials caused by AO impact remains a tremendous issue. Herein, we systematically evaluate the erosion collision and mechanical degradation of polyether ether ketone (PEEK) resin under hypervelocity AO impact using reactive molecular dynamics simulations. The interaction process and local evolution mechanism between high-speed AO and PEEK are investigated for the first time, suggesting that AO will either be scattered or adsorbed by PEEK, which is strongly correlated with the main degraded species evolution including O2, OH, CO, and CO2. Different AO fluxes and AO incidence angle simulations indicate that high-energy AO collision on the surface transfers kinetic energy to PEEK's thermal energy, thus inducing mass loss and surface penetration mechanisms. Vertically impacted AO causes less erosion on the PEEK matrix, rather than obliquely. Furthermore, PEEK chains modified with functional side groups are comprehensively investigated by 200 AO impact and high strain rate (1010 s-1) tensile simulations, demonstrating that the spatial configuration and stable benzene functionality of phenyl side groups can significantly improve the AO resistance and mechanical properties of PEEK at 300 and 800 K. This work revealed useful insights into the interaction mechanisms between AO and PEEK at the atomic scale and may provide a protocol for screening and designing new polymers of high AO tolerance. read less

Abstract: In order to further understand the high-temperature reaction process and pyrolysis mechanism of hydrocarbon fuels, the high-temperature pyrolysis behavior of n-tetracosane (C24H50) was investigated in this paper via the reaction force field (ReaxFF) method-based molecular dynamics approach. There are two main types of initial reaction channels for n-heptane pyrolysis, C–C and C–H bond fission. At low temperatures, there is little difference in the percentage of the two reaction channels. With the temperature increase, C–C bond fission dominates, and a small amount of n-tetracosane is decomposed by reaction with intermediates. It is found that H radicals and CH3 radicals are widely present throughout the pyrolysis process, but the amount is little at the end of the pyrolysis. In addition, the distribution of the main products H2, CH4, and C2H4, and related reactions are investigated. The pyrolysis mechanism was constructed based on the generation of major products. The activation energy of C24H50 pyrolysis is 277.19 kJ/mol, obtained by kinetic analysis in the temperature range of 2400–3600 K. read less

Abstract: Graphene and its allotropes have attracted attention due to their special electronic, mechanical, and thermal properties. Numerous studies investigate their wetting behavior. Tetrahexcarbon (THC) is a new carbon allotrope and is obtained from pentagraphene. This research, examines THC's wettability properties using reactive molecular dynamics (MD) and density functional theory (DFT) simulations. The results of molecular dynamics simulation reveal that THC is a hydrophobic substrate with a contact angle of 113.4° ± 2.8°. Using molecular dynamics, this research also evaluates quantities such as contact diameter, dipole moment, and density profile of water droplet. In addition, hydrogen and oxygen atoms' distribution functions, hydrogen bonds, path of the droplet's center of mass, and potential energy surface are presented. According to the simulation results, the droplet's structure on THC is slightly layered. Also, the water molecules' orientations in the interface are such that they do not allow the hydrogen bonds to form between water molecules and the THC substrate. The results of MD show that there are two different behavioral patterns for the hydrogen bonds between and within the water droplet's layers. Furthermore, this research utilizes DFT and AIMD in order to show how a water molecule interacts with THC. DFT exhibits that the water molecule's hydrogen atoms are toward the substrate. But an opposite configuration happens in the droplet-THC interface. The results of the atoms-in-molecules (AIM) theory indicate that there is a weak interaction between the water molecules and the THC substrate. The thermochemical results reveal that water molecules' adsorption is within the range of physical adsorption. Finally, NBO analysis shows that the THC's carbon atoms have a permanent partial charge. These results confirm that the THC is a hydrophobic material. read less

Abstract: Lithium metal anode attracts great attention because of its high specific capacity and low redox potential. However, the uncontrolled dendrite growth and its infinite volume expansion during cycling are extremely detrimental to the practical application. The formation of a solid electrolyte interphase (SEI) plays a decisive role in the behavior of lithium deposition/dissolution during electrochemical processing. Clarifying the essential relationship between SEI and battery performance is a priority. Research in SEI is accelerated in recent years by the use of advanced simulation tools and characterization techniques. The chemical composition and micromorphology of SEIs with various electrolytes are analyzed to clarify the effects of SEI on the Coulombic efficiency and cycle life. In this review, the recent research progress focused on the composition and structure of SEI is summarized, and various advanced characterization techniques applied to the investigation of SEI are discussed. The comparisons of the representative experimental results and theoretical models of SEI in lithium metal batteries (LMBs) are exhibited, and the underneath mechanisms of interaction between SEI and the electrochemical properties of the cell are highlighted. This work offers new insights into the development of safe LMBs with higher energy density. read less

Abstract: At present, most high-performance cellulose matrix composites only use cellulose as reinforcement material, which is an obstacle to maximize the advantages of nanocellulose in structure and properties. The development of new functional nanocomposites with cellulose as the main component can better meet people’s needs for high-performance and degradable composites, which requires a comprehensive and thorough understanding of cellulose. Considering the limitations of physical experiments, we performed molecular dynamics simulation of the uniaxial tensile behavior of the cellulose system at three different strain rates (10−4/ps, 10−5/ps, and 10−6/ps), and the stress-strain responses of cellulose systems at different strain rates are obtained. The effect of the strain rate on the mechanical properties of amorphous cellulose system during the tensile processes is analyzed. The deformation mechanism of cellulose amorphous system during the tensile processes is characterized by the energy changes of the different terms including dihedral angle torsion term, bond tensile term, angle bending term, and nonbond term. Structural evolution of the cellulose crystal system during the tensile processes is used to explain the failure mechanism of cellulose. The kinetic simulation results show that the mechanical properties of the cellulose amorphous system increase with the increase of strain rate. Compared with the strain rate of 10−5/ps, the elastic modulus of the system increases by 6.73 GPa at the strain rate 10−4/ps. During the tensile processes, cellulose amorphous region adapts to the applied load mainly through the stretching of the cellulose macromolecular chains, i.e., the deformation of bond lengths and bond angles, without any breakage of the molecular chains. The main causes of chain lengthening at different strain rates are different. The failure of cellulose is caused by the slip and rearrangement of some molecular chains in the crystal structure. read less

Abstract: Recently, the cold atmospheric plasma (CAP) has demonstrated a satisfactory ability to inactivate severe acute respiratory syndrome CoV‐2 (SARS‐CoV‐2), but the microscopic inactivation mechanism is still unclear. This paper takes the interaction process between O atoms generated by plasma and the spike protein of coronavirus as the research object. It uses the reaction molecular dynamics simulation method to study the reaction mechanism of different numbers of O atoms and the spike protein molecules. The results show that the O atom triggers a chain reaction by taking away hydrogen atoms in the spike protein molecule, destroying the molecular structure of the spike protein and making it inactive. The severity of the reaction and the destruction of the spike protein molecule also increases with increasing O atom numbers. [ FROM AUTHOR] Copyright of Plasma Processes & Polymers is the property of John Wiley & Sons, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.) read less

Abstract: ABSTRACT In this paper, the CH4 combustion characteristics in CO2/O2/N2 atmosphere subjected to electric field were studied by the molecular dynamics simulation method. Conventional and unique pathways were obtained. The evolution law of reactants and main products and the first reaction time of main intermediates under the influence of different electric field intensities were analysed. Results showed that the addition of external electric fields increased conventional responses and species diversity. The generation of new pathways induced the production of new species, and the further reactions of new species produced other new pathways, thus accelerating the generation of new pathways and species in the electric field. It was noteworthy that, the applied external electric field could advance the reaction start time and reinforce the combustion process, but its effect on the reaction rate was highly nonlinear. The CH4 reaction with CO2 was significantly intensified at E ≥ 105 V/m, while suppressed at E = 104 V/m. Furthermore, electric fields could promote the oxidation degree of CH4, especially at E = 106 V/m. The studies provide theoretical guidance for revealing the mechanism of methane combustion under a high concentration CO2 atmosphere and promoting the efficient capture of CO2. read less

Abstract: The initial formation cycles are critical to the performance of a lithium-ion battery (LIB), particularly in the case of silicon anodes, where the high surface area and extreme volume expansion during cycling make silicon susceptible to detrimental side reactions with the electrolyte. The solid electrolyte interface (SEI) that is formed during these initial cycles serves to protect the surface of the anode from a continued reaction with the electrolyte, and its composition reflects the composition of the electrolyte. In this work, ReaxFF reactive force field simulations were used to investigate the interactions between ether-based electrolytes with high LiTFSI salt concentrations (up to 4 mol/L) and a silicon oxide surface. The simulation investigations were verified with galvanostatic testing and post-mortem X-ray photoelectron spectroscopy, revealing that highly concentrated electrolytes resulted in the faster formation and SEIs containing more inorganic and silicon species. This study emphasizes the importance of understanding the link between electrolyte composition and SEI formation. This ReaxFF approach demonstrates an accessible way to tune electrolyte compositions for optimized performance without costly, time-consuming experimentation. read less

Abstract: Two-dimensional (2D) carbon materials perforated with uniform micropores are considered ideal building blocks to fabricate advanced membranes for molecular separation and energy storage devices with high rate capabilities. However, creating high-density uniform micropores in 2D carbon using conventional perforation methods remains a formidable challenge. Here, we report a zeolite-templated bottom-up synthesis of ordered microporous 2D carbon. Through rational analysis of 255 zeolite structures, we find that the IWV zeolite having large 2D microporous channels and aluminosilicate compositions can serve as an ideal template for carbon replication. The resulting carbon is made of an extremely thin polyaromatic backbone and contains well-defined vertically aligned micropores (0.69 nm in diameter). Its areal pore density (0.70 nm−2) is considerably greater than that of porous graphene (<0.05 nm−2) prepared using top-down perforation methods. The isoporous membrane fabricated by assembling the exfoliated 2D carbon nanosheets exhibits outstanding permeance and molecular sieving properties in organic solvent nanofiltration. read less

Abstract: Short and thin pristine carbon nanotubes (CNTs) emerge as 1D emulsion stabilizers capable of replacing aquatoxic low‐molecular surfactants. However, inconsistencies in understanding of water–solid interfaces for realistic CNTs hamper their individualization‐driven functionalities, processability in benign media, and compatibility with a broad‐scale of matrices. Pristine CNT processing based on water and inexpensive n‐alkanes within a low energy regime would constitute an important step toward greener technologies. Therefore, structural CNT components are quantitatively assessed, placing various CNTs on the scale from hydrophobicity to hydrophilicity. This structural interweave can lead to amphipathicity enabling the formation of water‐in‐oil emulsions. Combining experiments with theoretical studies, CNTs and CNT emulsions are comprehensively characterized establishing descriptors of the emulsifying behavior of pristine and purified CNTs. They emerge as having hydrophilic open‐ends, small number of oxygen–functionalized/vacancy surface areas, and hydrophobic sidewalls and full caps. The interplay of these regions allows short and thin CNTs to be utilized as fully recyclable 1D surfactants stabilizing water/oil emulsions which, as demonstrated, can be applied as paints for flexible conductive coatings. It is also shown how the amphipathic strength depends on CNT size, the pristine‐to‐oxidized/vacancy domains and the oil‐to‐water ratios. read less

Abstract: ABSTRACT Graphene-based materials have been considered as reinforcement for cement-based materials due to its excellent properties. In this paper, the effects of graphene oxide (GO) and graphene nanoplatelets (GNPs) on the mechanical properties and microstructure of cement-based composites are investigated. The results reveal that the incorporation of 0.02 wt% GO and GNPs can enhance the flexural strength by 16.3% and 11.6%, respectively. In addition, GO and GNPs can fill the cracks and form a compacted microstructure in cement mortars. Furthermore, the enhanced mechanism of calcium silicate hydrate composite (C–S–H), which is the main production of cement hydration, is studied by reaction molecular dynamics. The results from simulation show that Young’s modulus and tensile strength of C–S–H are enhanced by 32.1% and 23.8% with the incorporation of GO, because the hydrogen-bonds (H-bonds) linkages and Ca2+ near the interface surface play an important role to improve the interface adhesion and transfer more loads between GO and C–S–H. Comparatively, the graphene nanosheet unremarkable enhances the mechanical behaviour of C–S–H composite due to poor binding in the interlayer region. read less

Abstract: In this work, a characterization study of the interfacial interaction between different types of graphene nanoplatelets and an epoxy matrix is computationally performed. To quantify the discrete mutual graphene–epoxy “interfacial interaction energy” (IIE) within the nanocomposite, molecular dynamics simulations with a reactive force field are performed on a localized model of the suggested nanocomposite. Pull-out molecular dynamics simulations are also performed to predict the interfacial shear strength between the two constituents. The results indicate a significant increase in interfacial adhesion of functionalized nanoplatelets with the hosting epoxy matrix relative to virgin graphene nanoplatelets. The obtained results also demonstrate a dramatic increase in the interfacial interaction energy (IIE) (up to 570.0%) of the functionalized graphene/epoxy nanocomposites relative to the unmodified graphene/epoxy nanocomposites. In the same context, the surface functionalization of graphene nanoplatelets with the polymer matrix leads to a significant increase in the interfacial shear strength (ISS) (up to 750 times). The reported findings in this paper are essential and critical to producing the next generation of lightweight and ultra-strong polymer-based nanocomposite structural materials. read less

Abstract: The evolution of oxygen functional groups (OFGs) and the associated thermic effects upon heat treatment up to 800 °C were investigated experimentally as well as by theoretical calculations. A synthetic carbon with a carbonaceous structure close to that of natural chars, yet mineral-free, was derived from cellulose and oxidized by HNO3 vapor at different temperatures and for varied durations in order to generate char samples with different concentrations and distributions of OFGs. The functionalized samples were subjected to calorimetric temperature-programmed desorption measurements in correlation with an extensive effluent gas analysis, thereby focusing on the specific heat effects of individual OFG evolution. Interpretation of the experimental results was aided by density functional theory (DFT) calculations which allowed one to infer the thermal stability of different OFGs and the reaction energy associated with their evolution upon heating. Results showed that, with increasing temperature, H2O was released due to the loss of physisorbed water, the decomposition of clusters bound to carboxylic acids, and condensation reactions. The associated heat uptake amounted to about 100 kJ mol–1. Contrarily, the release of CO2, attributed to the decomposition of condensed acids, carboxylic acids, anhydrides, and lactones, resulted in a heat release of about 40 kJ mol–1. The most strongly pronounced thermic effects were detected for the release of CO, comprising highly exothermic effects due to the decomposition of condensed acids and carbonyls/quinones as well as endothermic effects attributed to anhydrides and phenols/ethers. Notably, anhydrides can be formed during the oxidative treatment as well as during heating by condensation of adjacent carboxylic acids. In the latter case, the two-step decomposition is overall highly exothermic, indicating the associated occurrence of pronounced carbon matrix rearrangements. DFT investigations suggest that these rearrangements not only affect the immediate OFG proximity but also involve several carbon sheets. read less

Abstract: Kapton film is a polymeric material widely used on low-Earth-orbit (LEO) spacecraft surfaces. In the LEO environment, atomic oxygen (AO) is spaceflight materials’ most destructive environmental factor. The erosion mechanism of AO on Kapton films has long been an important issue, where the parameter dependence of the AO effect has received increasing attention. Studies of AO energy and cumulative flux have been extensively carried out, while the influence mechanism of the incidence angle and flux density is not fully understood. The AO incidence angle and flux density in space are diverse, which may cause different damage effects on aerospace materials. In this paper, the dependence of the incidence angle and flux density in the damaging effect of AO on Kapton films was investigated using ground-based AO test technology and the reactive molecular dynamics (ReaxFF MD) simulation technique. Firstly, the ground-based experiment obtained the mass loss data of Kapton films under the action of AO with a variable incidence angle and flux density. Then, the mass loss, temperature rise, product, and erosion yield of Kapton during AO impact with different incidence angles and dose rates were calculated using the ReaxFF MD method. The influences of the incidence angle and flux density on the damage mechanism of the AO effect were discussed by comparing the simulation and test results. The results show that the AO effect in the lower incidence angle range (0–60°) is independent of the incidence angle and depends only on the amount of impacted atomic oxygen. AO in the higher incidence angle range (60–90°) has a surface stripping effect, which causes more significant mass loss and a temperature rise while stripping raised macromolecules from rough surfaces, and the erosion effect increases with the increasing incidence angle and amount of impacted atomic oxygen. There is a critical value for the influence of flux density on the AO effect. Above this critical value, AO has a reduced erosive capacity due to a lower chance of participating in the reaction. The amount of each main product from the AO effect varies with the incidence angle and flux density. Nonetheless, the total content of the main products is essentially constant, around 70%. This work will contribute to our understanding of the incidence angle and flux density dependence of the AO effect and provide valuable information for the development of standards for ground simulation tests. read less

Abstract: ABSTRACT The nature of interaction between coal surface and collector molecule affects the yield of fine coal flotation. The interaction depends on coal surface characteristics and collector polarity as well as collector size. In this work, a detail understanding on the interaction nature of nonpolar such as dodecane (C1) and polar collectors such as tetrahydrofurfuryl oleate (C2) and 2-[2-[2-[2-[2-[2-(2-hydroxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl(Z)-octadec-9-enoate (C3) with low-rank coal is presented using density functional theory calculations and finite temperature large scale ReaxFF molecular dynamics simulations. It has been shown that collector consisting of more electronegative elements (i.e. with larger polarity) show stronger interaction with low-rank coal. Moreover, larger aliphatic chain helps to interact via van der Walls interactions and polar functional groups through electrostatic interaction (hydrogen bond formation) due to flexibility in the collector backbone. Interestingly, the collectors did not show any spike like attachment to the low-rank coal surface, rather lies along the coal surface to maximize the possible interactions. This contrasts with commonly presented picture for collector-(low-rank) coal surface interaction. Optimal requirement of aliphatic chain length and polar functional groups was discussed by analyzing structure properties relationship. GRAPHICAL ABSTRACT read less

Abstract: The paper/oil system is the main component of transformer insulation. Indicator plays a vital role in assessing the aging condition of local hot spots of transformer insulation paper. The cellulosic insulating paper is mainly composed of cellobiose. This study uses the molecular dynamics method based on reactive force field (ReaxFF) to pyrolyze the insulating paper. Various production paths of ethanol were studied at the atomic level through ReaxFF simulations. A model consisting of 40 cellobioses was established for repeated simulation at 500 K–3000 K. Besides, to explore the relationship between the intermediate products and ethanol, the combination model of intermediate products (levoglucosan, acetaldehyde, 2,2-dihydroxyacetaldehyde) was established for repeated simulation. The simulation results showed that the increase in temperature can accelerate the production of ethanol from insulating paper and its pyrolysis intermediate products, which matched the related experimental results. This study can provide an effective reference for the use of ethanol as an indicator to assess the aging condition of the local hot spots of transformers. read less

Abstract: Molecular dynamics simulation using the reactive force field was performed to investigate the stability and formation mechanisms of organic porous thin films made of 1,3,5-tris(4-carboxyphenyl) benzene (BTB) molecules fabricated at the air/water interface. A single-layer honeycomb structure is found to be unstable, whereas thicker films are stable, which is consistent with experimental findings. The slight corrugation of the existing film produces local charge variation that attracts isolated molecules via the Coulomb interaction. When the isolated molecule approaches the film, a hydrogen bond is formed, and then the molecule adjusts the adsorption configuration by itself to maximize both horizontal and vertical intermolecular interactions. The key to the initial hydrogen bond formation is suggested to be the density of the molecules provided in the system as well as the spontaneous alignment of the BTB molecules to the solution/water interface. Our study showed that the BTB film is stable, and the molecules are self-assembled without external forces in the quasi-two-dimensional system. These results suggest that the dominant factor for the film formation at the air/water interface is interactions among BTB molecules and confinement to the two-dimensional space. read less

Abstract: Focused ion beams (FIB) are a common tool in nanotechnology for surface analysis, sample preparation for electron microscopy and atom probe tomography, surface patterning, nanolithography, nanomachining, and nanoprinting. For many of these applications, a precise control of ion-beam-induced processes is essential. The effect of contaminations on these processes has not been thoroughly explored but can often be substantial, especially for ultralow impact energies in the sub-keV range. In this paper we investigate by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the simulation conditions used in this work, the adsorption of water favours the formation of defects in silicon by mixing hydrogen and oxygen atoms into the substrate. The sputtering yield of silicon is not significantly changed by the contamination, but the fraction of hydrogen and oxygen atoms that is sputtered largely depends on the incidence angle. This fraction is the largest for incidence angles between 70 and 80° defined with respect to the sample surface. Overall, it changes from 25% to 65%. read less

Abstract: Supercritical fluids exhibit peculiar inhomogeneity, which strongly affects reaction behaviors in them. However, explanations for inhomogeneity and its effect on reactions are both ambiguous so far. Here, we provide an atomic-level understanding of inhomogeneity effects on reactions via the computational method, with the example of n-decane pyrolysis under supercritical conditions. We describe the characteristic pyrolysis behaviors through collective variable-driven hyperdynamics (CVHD) simulations and explain the inhomogeneity of supercritical n-decane as the coexistence of gas-like and liquid-like atoms by a trained machine learning classifier. Due to their specific local environment, the appearance of liquid-like atoms under supercritical conditions significantly increases the type and frequency of bimolecular reactions and eventually causes changes in product distributions. Future research with this method is expected to extend the effect of inhomogeneity on other reactions under supercritical conditions or other condensed phases. read less

Abstract: A major concern in the modern cement industry is considering how to minimize the CO2 footprint. Thus, cements based on belite, an impure clinker mineral (CaO)2SiO2 (C2S in cement chemistry notation), which forms at lower temperatures, is a promising solution to develop eco-efficient and sustainable cement-based materials, used in enormous quantities. The slow reactivity of belite plays a critical role, but the dissolution mechanisms and kinetic rates at the atomistic scale are not known completely yet. This work aims to understand the dissolution behavior of different facets of β-C2S providing missing input data and an upscaling modeling approach to connect the atomistic scale to the sub-micro scale. First, a combined ReaxFF and metadynamics-based molecular dynamic approach are applied to compute the atomistic forward reaction rates (RD) of calcium (Ca) and silicate species of (100) facet of β-C2S considering the influence of crystal facets and crystal defects. To minimize the huge number of atomistic events possibilities, a generalized approach is proposed, based on the systematic removal of nearest neighbors’ crystal sites. This enables us to tabulate data on the forward reaction rates of most important atomistic scenarios, which are needed as input parameters to implement the Kinetic Monte Carlo (KMC) computational upscaling approach. The reason for the higher reactivity of the (100) facet compared to the (010) is explained. read less

Abstract: The melting thermodynamic characteristics of 2- to 20-layered onion-like fullerenes (OLF n ) (C60@C240 to C60@···@C6000···@C24000) are comprehensively explored using first-principles-based ReaxFF atomistic simulations and random forest machine learning (RF ML). It is revealed that OLF n shows lower thermal stability than the counterparts of single-walled fullerenes (SWF n ). The melting point of SWF n increases monotonically with increasing size, whereas for OLF n , an unusual size-dependent melting point is observed; OLF n with intermediate size shows the highest melting point. For small OLF n , the melting occurs from the inner to the outer, whereas for large OLF n , it nucleates from the inner to the outer and to intermediate fullerenes. The melting and erosion behaviors of both SWF n and OLF n are mainly characterized by the nucleation of non-hexagons, nanovoids, carbon chains and emission of C2. RF ML model is developed to predict the melting points of both SWF n and OLF n . Moreover, the analysis of the feature importance reveals that the Stone-Wales transformation is a critical pathway in the melting of SWF n and OLF n . This study provides new insights and perspectives into the thermodynamics and pyrolysis chemistry of fullerenic carbons, and also may shed some lights onto the understanding of thermally-induced erosion of carbon-based resources and spacecraft materials. read less

Abstract: Nanotubes made of non-concentric and multiple small layers of porous MoS2 contain inner pores suitable for membrane applications. In this study, molecular dynamics simulations using reactive potentials were employed to estimate the stability of the nanotubes and how their stability compares to macroscopic single- (1L) and double-layer MoS2 flakes. The observed stability was explained in terms of several analyses that focused on the size of the area of full-covered layers, number of layers, polytype, and size of the holes in the 1L flakes. The reactive potential used in this work reproduced experimental results that have been previously reported, including the small dependency of the stability on the polytype, the formation of S–S bonds between inter- and intra-planes, and the limit of stability for two concentric rings forming a single ring-like flake. read less

Abstract: Micro-nanobubbles (MNBs) technology has emerged as an effective means of sewage treatment, while the molecular mechanism for its pollutant degradation is still unknown. In this paper, the reactive molecular dynamics simulation technique is used to study the degradation mechanism of pollutants caused by shock-induced nanobubble collapse. We first demonstrate that the propagating shock wave can induce nanobubble collapse, and the collapsing nanobubble has the ability to focus mechanical energy via the converging motion of liquid in the interior of the bubble, leading to the formation of a high-speed jet with a much higher energy density. We also unveil the mechanical nature of long-chain pollutant degradation and the mechanism of free radical generation. Due to the impacting jet, the high-gradient flow has the ability to stretch the long-chain molecule and cause mechanical scission of the molecule in a homolytic manner. Finally, our simulation results reveal that adding ozone molecules to the collapsing bubble would introduce an additional dehydrogenation mechanism. read less

Abstract: Flue gas produced by biomass fuel combustion contains various chlorine-containing substances and is an important factor causing biomass boiler corrosion. The corrosion processes of chlorine, hydrogen chloride and water on iron covered with an intact/damaged oxide film were investigated under the high temperature of 1300 K through reactive molecular dynamics simulation. The results show that the diffusion processes of oxygen and chlorine are similar and can be divided into three stages: rapid diffusion, continuous diffusion, and no oxide film (stable). Oxygen diffusion in Fe2O3 into a pure iron layer is the main cause of gas corrosion in iron/iron oxide systems. A complete oxide film can hinder iron corrosion by chlorine and hydrogen chloride. Damage in an oxide film significantly affects oxygen and chlorine diffusion and iron corrosion. However, such influence is gradually reduced. The integrity of a protective film is the key to alleviating corrosion. Water facilitates the dissociation of chlorine and hydrogen chloride, and it reacts with iron at high temperatures to enhance corrosion. This study improves the understanding of the iron oxide/iron corrosion from chlorine-containing gases from a microscopic perspective and is of great significance to metal corrosion protection and biomass combustion technologies. read less

Abstract: Biomass has played an increasingly important role in the consumption of energy worldwide because of its renewability and carbon-neutral property. In this work, the pyrolysis mechanism of wheat straw is explored using reactive force field molecular dynamics simulations. A large-scale wheat straw model composed of cellulose, hemicellulose, and lignin is built. After model validation, the temporal evolutions of the main pyrolysis products under different temperatures are analyzed. As the temperature rises, the gas production increases and the tar yield can decrease after peaking. Relatively high temperatures accelerate the generation rates of the main gas and tar species. CO and CO2 molecules mainly come from the cleavage of CHO2 radicals, and numerous H2O molecules are generated on account of dehydration. Moreover, the evolution of six functional groups and pyran and phenyl rings as well as three types of bonds is also presented. It is observed that the phenyl rings reflect improved thermostability. Finally, the pyrolytic kinetics analysis is conducted, and the estimated activation energy of wheat straw pyrolysis is found to be 56.19 kJ/mol. All these observations can help deeply understand the pyrolytic mechanism of wheat straw biomass. read less

Abstract: As the solid waste by-product from the delayed coking process, high-sulfur petroleum coke (HSPC), which is hardly used for green utilization, becomes a promising raw material for Hg0 removal from coal-fired flue gas. The effects of the physical–chemical evolution of HSPC on Hg0 removal are discussed. The improved micropores created by pyrolysis and KOH activation could lead to over 50% of Hg0 removal efficiency with the loss of inherent sulfur. Additional S-containing and Br-containing additives are usually introduced to enhance active surface functional groups for Hg0 oxidation, where the main product are HgS, HgBr, and HgBr2. The chemical–mechanical activation method can make additives well loaded on the surface for Hg0 removal. The DFT method is used to sufficiently explain the micro-scale reaction mechanism of Hg0 oxidation on the surface of revised-HSPC. ReaxFF is usually employed for the simulation of the pyrolysis of HSPC. However, the developed mesoporous structure would be a better choice for Hg0 removal in that the coupled influence of pore structure and functional groups plays a comprehensive role in both adsorption and oxidation of Hg0. Thus, the optimal porous structure should be further explored. On the other hand, both internal and surface sulfur in HSPC should be enhanced to be exposed to saving sulfur additives or obtaining higher Hg0 removal capacity. For it, controllable pyrolysis with different pyrolysis parameters and the chemical–mechanical activation method is recommended to both improve pore structure and increase functional groups for Hg0 removal. For simulation methods, ReaxFF and DFT theory are expected to explain the micro-scale mechanisms of controllable pyrolysis, the chemical–mechanical activation of HSPC, and further Hg0 removal. This review work aims to provide both experimental and simulational guidance to promote the development of industrial application of Hg0 adsorbent based on HSPC. read less

Abstract: Microcracks inevitably appear on the SiC wafer surface during conventional thinning. It is generally believed that the damage-free surfaces obtained during chemical reactions are an effective means of inhibiting and eliminating microcracks. In our previous study, we found that SiC reacted with water (SiC–water reaction) to obtain a smooth surface. In this study, we analyzed the interfacial interaction mechanisms between a 4H-SiC wafer surface (0001-) and diamond indenter during nanoscale scratching using distilled water and without using an acid–base etching solution. To this end, experiments and ReaxFF reactive molecular dynamics simulations were performed. The results showed that amorphous SiO2 was generated on the SiC surface under the repeated mechanical action of the diamond abrasive indenter during the nanoscale scratching process. The SiC–water reaction was mainly dependent on the load and contact state when the removal size of SiC was controlled at the nanoscale and the removal mode was controlled at the plastic stage, which was not significantly affected by temperature and speed. Therefore, the reaction between water and SiC on the wafer surface could be controlled by effectively regulating the load, speed, and contact area. Microcracks can be avoided, and damage-free thinning of SiC wafers can be achieved by controlling the SiC–water reaction on the SiC wafer surface. read less

Abstract: In order to shorten the ignition delay of 2-azido-N,N-dimethylethanamine (DMAZ) and dinitrogen tetroxide (NTO), four amines [tert-butylamine, pyrrole, N,N,N′,N′-tetramethyl ethylenediamine (TMEDA), and diethylenetriamine (DABH)] with a mass fraction of 5% were added to DMAZ, and the potential energy change and the product change during the reaction of the mixture of an additive and DMAZ with NTO were analyzed by Reactive molecular dynamics (ReaxFF MD) calculation. Then, the ignition delay of the mixture of the additive and DMAZ as well as pure DMAZ with NTO was measured by a drop experiment with a photoelectric sensor and high-speed camera. The results show that the addition of pyrrole greatly reduced the time to reach the maximum system energy and greatly increased the rate of HNO2 formation. The dripping of the fuel was approximately a uniform linear motion, and the expression was y = 43.13 + 7.16x. The ignition delay time recorded by the camera was in good agreement with that of the optical signal. The measured ignition delay time for DMAZ with NTO was 261.5 ms. The mixture of pyrrole and DMAZ with NTO had the shortest ignition delay time of 100 ms, and the proportion of shortening the ignition delay time was the largest. The results of the droplet experiment were consistent with those of ReaxFF MD simulation, indicating that HNO2 plays an important role in the ignition delay, that is, the formation rate of HNO2 is positively correlated with the ignition delay. read less

Abstract: In this study, we have utilized the reactive molecular dynamics (MD) simulations to model the Atomic Layer Deposition (ALD) process that forms an ultra-thin film of a tunnel barrier made of amorphous alumina. We chose the reactive MD approach over the ab-initio molecular dynamics simulation used in previous studies due to its lower computational cost, its ability to model over a relatively longer simulation period and its capability to assess atomistic-based dynamics for a larger substrate. We have reviewed the capabilities of ReaxFF to model stable precursors and reactions paths for two surface reactions of the ALD process utilizing LAMMPS and Amsterdam Modeling Suites software. A comparison of two force field potential models is also made in an effort to determine where deficiencies in the modeling capabilities lie. read less

Abstract: To study the generation rules of organic molecules or fragments and the generation paths of some hydrocarbon gases (C2H2/C2H4) and inorganic gases (CO2/H2O/H2/H2S) in the pyrolysis process of bituminous coal at 1000–5000 K, the ReaxFF molecular dynamics module in AMS software was used to simulate the pyrolysis behavior of the Hongqingliang model, Gaojialiang model, and Wiser model. With the increase of temperature, the system potential energy decreases, the endothermic efficiency increases first and then decreases, the fragments of C1–C4 fragments increase, and the gas molecules generated increase. In the pyrolysis process, the oxygen-containing functional groups and hydrogen groups formed H2O and H2 with the increase of temperature. H2S as an intermediate product is always maintained in dynamic equilibrium. CO2 comes from the decarboxylation of the carboxyl groups. When the temperature is lower than 3000 K, C2H4 and C2H2 are mainly formed by the adjacent carbon structure in coal molecules, and C2H4 is formed from the ethyl side chain, the naphthenic structure, and the unstable aromatic rings. C2H2 is formed from naphthene structures and aromatic rings with multiple side chains. When the temperature is higher than 3000 K, C2H4 and C2H2 are mainly formed by the random combination of free radicals generated by the crushing of coal molecules. The research results are of great significance to coal pyrolysis and clean utilization of coal. read less

Abstract: Vibrational spectroscopy is one of the most important experimental techniques for the characterization of molecules and materials. Spectroscopic signatures retrieved in experiments are not always easy to explain in terms of the structure and dynamics of the studied samples. Computational studies are a crucial tool for helping to understand and predict experimental results. Molecular dynamics simulations have emerged as an attractive method for the simulation of vibrational spectra because they explicitly treat the vibrational motion present in the compound under study, in particular in large and condensed systems, subject to complex intramolecular and intermolecular interactions. In this context, first‐principles molecular dynamics (FPMD) has been proven to provide an accurate realistic description of many compounds. This review article summarizes the field of vibrational spectroscopy by means of FPDM and highlights recent advances made such as the simulation of Infrared, vibrational circular dichroism, Raman, Raman optical activity, sum frequency generation, and nonlinear spectroscopies. read less

Abstract: Solid electrolyte interphase (SEI) plays a significant role in enhancing the stability and durability of lithium metal batteries (LMBs) by separating highly reactive lithium metal anode (LMA) from the electrolyte to avoid continuous degradation. However, the underlying reaction mechanism is still far from clear. Herein, a hybrid ab initio and reactive force field (HAIR) method is employed to extend the ab initio molecular dynamics (AIMD) to 1 ns, which provides crystal information about the reaction mechanism of elementary reactions that can explain the components and morphology evolution of SEI formation. Specifically, HAIR simulation confirms the two‐electron (2e–) reduction of ethylene carbonate (EC) by releasing CO and CO2, agreeing with phenomenal experiment observation. As the unsaturated intermediates accumulate, polymerization reactions occur, producing linear polyethylene oxide (PEO), Li2OCO2CH2CH2, Li2OCO2(CH2)4, etc., which regulate the formation of outer organic layer (OOL) that consists of linear polyethylene oxide (PEO), Li2OCO2CH2CH2, Li2OCO2(CH2)4, etc., and the inner inorganic layer (IIL) mainly consists of LiF and Li2O. Simulations at low concentration (LC, 1M) and high concentration (HC, 5M) reveal significantly different reaction pathways when HC electrolyte can significantly promote the formation of homogenous LiF that has been regarded as an important component to facilitate robust SEI. read less

Abstract: Photocurable polymers are used ubiquitously in 3D printing, coatings, adhesives, and composite fillers. In the present work, the free radical polymerization of photocurable compounds is studied using reactive classical molecular dynamics combined with a dynamical approach of the nonequilibrium molecular dynamics (D-NEMD). Different concentrations of radicals and reaction velocities are considered. The mechanical properties of the polymer resulting from 1,6-hexanediol dimethacrylate systems are characterized in terms of viscosity, diffusion constant, and activation energy, whereas the topological ones through the number of cycles (polymer loops) and cyclomatic complexity. Effects like volume shrinkage and delaying of the gel point for increasing monomer concentration are also predicted, as well as the stress–strain curve and Young’s modulus. Combining ab initio, reactive molecular dynamics, and the D-NEMD method might lead to a novel and powerful tool to describe photopolymerization processes and to original routes to optimize additive manufacturing methods relying on photosensitive macromolecular systems. read less

Abstract: A neural network (NN)-based model is proposed to construct the potential energy surface of soot formation. Our NN-based model is proven to possess good scalability of O(N) and retain the ab initio accuracy, which allows the investigation of the entire evolution of soot particles with tens of nm from an atomic perspective. A series of NN-based molecular dynamics (NNMD) simulations are performed using a nanoreactor scheme to investigate critical processes in soot formation, acetylene polymerization, and inception of PAH radicals. This shows that NNMD can capture the dynamic process of acetylene polymerization into PAH precursors. The simulation of PAH radicals reveals that physical interaction enhances chemical nucleation, and such enhancement is observed for clusters of π- and σ-radicals, which is distinct from the dimer. We also observed that PAH radicals of ~ 400 Da can produce core-shell soot particles at a flame temperature, with a disordered core and outer shell of stacked PAHs, suggesting a potential physically stabilized soot inception mechanism. read less

Abstract: The current contribution proposes a multi-scale bridging modeling approach for the dissolution of crystals to connect the atomistic scale to the (sub-) micro-scale. This is demonstrated in the example of dissolution of portlandite, as a relatively simple benchmarking example for cementitious materials. Moreover, dissolution kinetics is also important for other industrial processes, e.g., acid gas absorption and pH control. In this work, the biased molecular dynamics (metadynamics) coupled with reactive force field is employed to calculate the reaction path as a free energy surface of calcium dissolution at 298 K in water from the different crystal facets of portlandite. It is also explained why the reactivity of the (010), (100), and (11¯0) crystal facet is higher compared to the (001) facet. In addition, the influence of neighboring Ca crystal sites arrangements on the atomistic dissolution rates is explained as necessary scenarios for the upscaling. The calculated rate constants of all atomistic reaction scenarios provided an input catalog ready to be used in an upscaling kinetic Monte Carlo (KMC) approach. read less

Abstract: The pyrolysis kinetics of SiHCl3 and its reaction mechanism are essential for the chemical vapor deposition process in polysilicon industries. However, due to the high temperature and lack of in situ experimental detection technology, it is difficult to carry out experimental research on the pyrolysis kinetics of SiHCl3. In this work, reactive force field molecular dynamics simulations of SiHCl3 pyrolysis were performed to investigate the effect of temperature on the pyrolysis kinetics of SiHCl3 at the atomistic scale in a wide temperature range (1000–2000 K). The lumped Si clusters containing more than five Si atoms tended to appear at the later period of the reaction under a temperature lower than 1300 K, some of which even possessed polycyclic structures; nevertheless, small ones with less than two Si atoms such as SiHCl2 and HCl tended to emerge under a high temperature. The changes of partial energy terms with time evolution under various temperatures were proved to be rooted in the distribution of intermediates based on the momentary simulation period. In general, the reaction network at a low temperature was more complicated than that at a high temperature, resulting from the fact that more chemical events and intermediates came into existence, and the maximum number of Si atoms in one single molecule/radical was observed under a low temperature than that under a high temperature. As to the variation of SiHCl3 with the progress of the reaction, the linear fitting tendency disappeared under the temperature above 1300 K, which changed in fluctuation with the further elevation of temperature, elucidating the fact that SiHCl3 can act as a product and not just as a reactant to participate in elementary chemical events frequently. read less

Abstract: In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD indicates that the ReaxFF force field is not capable of accurately describing the diffusive behaviors of water on lignite at low temperatures. The oxidations of brown coal for both fuel rich and fuel lean conditions at various temperatures were investigated using ReaxFF-MD simulations through which the generation rates of major products were obtained. In addition, it was observed that the density decrease significantly enhances the generation of gaseous products due to the entropy gain by reducing system density. Although the ReaxFF-MD simulation of complete coal combustion process is limited to high temperatures, the combined CPMD and ReaxFF-MD simulations allow us to examine the correlation between water adsorption on brown coal and the initial stage of coal oxidation. read less

Abstract: ABSTRACT Advances in graphene assembly has shown that mechanically strong 3D nano-porous graphene sponge (NGS) can potentially be used for gas separation. The objectives of this computational study are to: (i) explore the use of NGS as adsorbent for separating light gases and light hydrocarbons from methane, and (ii) assess the potential of using NGS as a membrane for methane/ethane gas separation. A 3D nano-porous graphene sponge was constructed by reacting graphene flakes in the presence of inert non-reactive particles using Reactive Force Field (ReaxFF) molecular dynamics. We performed grand canonical Monte Carlo (GCMC) simulation to determine the adsorption capacity of NGS for methane, ethane, propane, butane, carbon dioxide, and nitrogen. In addition, GCMC simulations were performed on methane/ethane, methane/carbon dioxide, and nitrogen/methane gas mixtures to determine the selectivity for these gases on NGS. Our results show that graphene sponge has high selectivity for ethane over methane and methane over nitrogen. In addition, we obtained the diffusion coefficients of methane and ethane in NGS and estimated the perm-selectivity of ethane over methane. Because of its high solubility in graphene sponge, the perm-selectivity of ethane over methane is 4.76, despite its lower diffusion coefficient, suggesting that it could potentially be used as a membrane for separating ethane from methane. read less

Abstract: Platinum serves as a model electrode in solid‐state electrochemistry and as the inert electrode in redox‐based resistive random‐access memory (ReRAM) technology. Experimental work has proposed that oxygen may diffuse faster along platinum's extended defects, but quantitative, unambiguous transport data do not exist. In this study, the diffusion of oxygen atoms in crystalline platinum and along its extended defects is studied as a function of temperature by means of molecular dynamics (MD) simulations with the ReaxFF interatomic potentials. The MD simulations indicate that platinum vacancies trap oxygen atoms, inhibiting their diffusion through the platinum lattice and leading to a high activation enthalpy of diffusion of around 3 eV. This picture of trapping is supported by static density‐functional‐theory calculations. MD simulations of selected dislocations and selected grain boundaries indicate that oxygen diffusion is much faster along these extended defects than through the Pt lattice at temperatures below 1400 K, exhibiting a much lower activation enthalpy of ≈0.7 eV for all extended defects examined. Producing specific electrode microstructures with controlled densities and types of extended defects thus offers a new avenue to improve the performance of ReRAM devices and to prevent device failure. read less

Abstract: Polylactic acid (PLA) is a widely used bioresorbable polymer in medical devices owing to its biocompatibility, bioresorbability, and biodegradability. It is also considered a sustainable solution for a wide variety of other applications, including packaging. Because of its widespread use, there have been many studies evaluating this polymer. However, gaps still exist in our understanding of the hydrolytic degradation in extreme pH environments and its impact on physical and mechanical properties, especially in fibrous materials. The goal of this work is to explore the hydrolytic degradation of PLA fibers as a function of a wide range of pH values and exposure times. To complement the experimental measurements, molecular-level details were obtained using both molecular dynamics (MD) simulations with ReaxFF and density functional theory (DFT) calculations. The hydrolytic degradation of PLA fibers from both experiments and simulations was observed to have a faster rate of degradation in alkaline conditions, with 40% of strength loss of the fibers in just 25 days together with an increase in the percent crystallinity of the degraded samples. Additionally, surface erosion was observed in these PLA fibers, especially in extreme alkaline environments, in contrast to bulk erosion observed in molded PLA grafts and other materials, which is attributed to the increased crystallinity induced during the fiber spinning process. These results indicate that spun PLA fibers function in a predictable manner as a bioresorbable medical device when totally degraded at end-of-life in more alkaline conditions. read less

Abstract: Adhesion bonding of metals and polymers is attracting attention as an innovative bonding technology to realize high functionality and weight reduction of various mechanical parts and structural materials. This technology has been significantly demanded with the rapid development of multi-materials in recent years. However, it has been reported that natural oxide film and hydroxide film are formed on the metal surface, resulting in the change in adhesion, especially degradation of adhesion is sometimes accelerated by water molecules at the interface. The mechanism of adhesion degradation is still unclear. In this study, the interface between metal and resin was modeled using the molecular dynamics (MD) simulation to investigate how the moisture (water molecules) on the interfacial surface affects the adhesion. This study varied the amount of water molecules at the interface and investigated how water molecules affect the adhesive strength subjected to uni-axial tensile loading. In addition, the potential energy around the interface was calculated, and the adhesion mechanism with respected to water molecules was carefully discussed. read less

Abstract: Cryo-electron microscopy (cryo-EM) has emerged as a vital tool to reveal the native structure of beam-sensitive biomolecules and materials. Yet high-resolution cryo-EM analysis is still limited by the poorly controlled specimen preparation and urgently demands a robust supporting film material to prepare desirable samples. Here, we developed a bilayer Janus graphene membrane with the top-layer graphene being functionalized to interact with target molecules on the surface, while the bottom layer being kept intact to reinforce its mechanical steadiness. The ultraclean and atomically thin bilayer Janus membrane prepared by our protocol on one hand generates almost no extra noise and on the other hand reduces the specimen motion during cryo-EM imaging, thus allowing the atomic-resolution characterization of surface functional groups. Using such Janus membranes in cryo-EM specimen preparation, we were able to directly image the lithium dendrite and reconstruct macromolecules at near-atomic resolution. Our results demonstrate the bilayer Janus design as a promising supporting material for high-resolution cryo-EM and EM imaging. read less

Abstract: The mechanism of how a soot nucleus is impacted by polycyclic aromatic hydrocarbons (PAHs) and then grows through PAH condensation remains unclear. Using steered molecular dynamics (SMD), the non-bonding interaction between PAHs and soot was quantitatively studied using the free energy distribution during the dimerisation and condensation. The results showed that only two dimers (A7-A10 and 2 A10) remained stable at 1000 K. The simulations showed that PAH condensation on a fullerene should not be ignored in soot mass growth. For fullerenes with a diameter not less than 1.8 nm (C540), even A4 condenses at temperatures of 1500 K, and A10 condenses stably on the surface of fullerenes even at 2000 K. The effects of multilayers and hydrogenated fullerenes on the free energy of PAH condensation are different. The stability of PAH dimers and PAH condensation pairs was discussed through free energy and chemical equilibrium. The results show that larger dimers are more stable than small ones at flame temperatures. Condensation is far more important than nucleation in mass growth at flame temperatures. Furthermore, the larger the PAH is, the higher the transformation ratio of the PAH in condensation on soot and thus the more stable the condensation product is. Finally, both the stability analysis of an upper temperature limit for condensation and simulation results of ReaxFF-MD cross-confirm that pyrene stably condensates on a simplified nascent soot (C540) and a simulated soot (C658H319O9), respectively, at 1500 K, but not at higher temperatures over 1800 K. read less

Abstract: The pervasive use of portable electronic devices, powered from rechargeable batteries, represents a significant portion of the electricity consumption in the world. A sustainable and alternative energy source for these devices would require unconventional power sources, such as harvesting kinetic/potential energy from mechanical vibrations, ultrasound waves, and biomechanical motion, to name a few. Piezoelectric materials transform mechanical deformation into electric fields or, conversely, external electric fields into mechanical motion. Therefore, accurate prediction of elastic and piezoelectric properties of materials, from the atomic structure and composition, is essential for studying and optimizing new piezogenerators. Here, we demonstrate the application of harmonic-covalent and reactive force fields (FF), Dreiding and ReaxFF, respectively, coupled to the polarizable charge equilibration (PQEq) model for predicting the elastic moduli and piezoelectric response of crystalline zinc oxide (ZnO) and polyvinylidene difluoride (PVDF). Furthermore, we parametrized the ReaxFF atomic interactions for Zn-F in order to characterize the interfacial effects in hybrid PVDF matrices with embedded ZnO nanoparticles (NPs). We capture the nonlinear piezoelectric behavior of the PVDF-ZnO system at different ZnO concentrations and the enhanced response that was recently observed experimentally, between 5 and 7 wt % ZnO concentrations. From our simulation results, we demonstrate that the origin of this enhancement is due to an increase in the total atomic stress distribution at the interface between the two materials. This result provides valuable insight into the design of new and improved piezoelectric nanogenerators and demonstrates the practical value of these first-principles based modeling methods in materials science. read less

Abstract: Using the molecular dynamics (MD) simulations with ReaxFF potential, two different types of PFPE lubricants (Ztetraol and ZTMD) are prepared on a-C film, and SiO2 particles are adsorbed onto the lubricants at room temperature. From the simulation results, it is observed that the adsorbed SiO2 particles increase the stiffness of PFPE lubricants leading to less airshear displacement. Since Ztetraol has higher mobility with lower viscosity than ZTMD, the adsorbed SiO2 particles penetrate deeper into the Ztetraol lubricants. Accordingly, the effect of SiO2 on the airshear displacement is more obvious to Ztetraol than ZTMD. In addition, the adsorbed SiO2 particles increase the friction force and the amount of lubricant pick-up during the sliding contact with a nanosized a-C tip. read less

Abstract: Molecular dynamics simulations modeled the aramid poly( p -phenylene terephtha-lamide) (PPTA) and a related aromatic-aliphatic polyamide derived from a five-carbon aliphatic diacid (PAP5) with nine different reactive and non-reactive force fields. The force fields were evaluated based on crystal structures as well as intermolecular H-bonding and π -molecular interactions. The optimum force field was then used to simulate stress-strain behavior in the chain and transverse-to-chain directions. In the chain direction, PAP5 had higher ultimate stress and failure strain than PPTA; however, the stiffness of PAP5 was lower than PPTA at low strain (0-2%) while the reverse was observed at high strain (last 5% before failure). This contrast, and differences in the transverse direction properties, were explained by the methylene segments of PAP5 that confer conformational freedom, enabling accommodation of low strain without stretching covalent bonds. The simulation approach demonstrated here for two poly-1 read less

Abstract: The biphenylene network with periodically arranged four-, six-, and eightmembered rings has been successfully synthesized in very recent experiments. This novel two-dimensional (2D) carbon allotrope has potentials in applications of lithium storage and carbon-based circuitry. Understanding the thermal transport properties of biphenylene network is of critical importance for the performance and reliability of its practical applications. To this end, the thermal transport in biphenylene network is comprehensively investigated in this paper with the aid of molecular dynamics simulations together with first-principles calculations. For the sake of comparison, the thermal conductivities of other 2D sp2-hybridized carbon allotropes including graphene and pentaheptite are also investigated using the same method. It is found that the thermal conductivities of biphenylene network and pentaheptite are, respectively, only about one-thirteenth and one-eighth of graphene. Through the analysis of phonon property, mechanical property and electron density distribution, it is demonstrated that the great reduction in the thermal conductivity of biphenylene network and pentaheptite arises from the decline in their structural symmetry, which leads to the decrease of phonon group velocity and the reduction of phonon mean free path. read less

Abstract: Recent work on printed graphene ink has shown the importance of ethyl cellulose (EC) as a stabilizing polymer in ink formulation and a source of decomposed aromatic species that increase the conductivity of the graphene film. In this work, a reactive molecular dynamic simulation is implemented to study the decomposition of EC in the presence of a pristine graphene and a defective graphene sheet. High temperature annealing simulations revealed that the main reaction pathway of EC polymers is through the decomposition of the cellulose unit backbone into linear chain polymers containing carbon-carbon double bonds. The interactions between EC species and graphene sheets are shown to be maintained through van der Waals forces and the decomposed EC polymers were not observed to undergo chemical reactions with graphene basal-plane defect sites. The results in this paper present the first atomistic study in graphene-EC interactions and lead the way to future computational studies to optimize the electronic properties of printable graphene ink. read less

Abstract: Microwave is of promising applications in various chemical and material pro-cesses, however, the interactions between the microwave and the molecules from atomistic scales are lack of understanding. ReaxFF reactive molecular dynamics simulations were carried out to get insights into the interactions between the microwave and polyacrylonitrile (PAN) during microwave heating. It was found that the temperature evolution of the system was dependent on the electric field strength and frequency of the microwave. The alternate change of the electric field of the microwave leads to the alternate fluctuation of the temperature. We surprisingly predicted the atomistic hot-spot effect of microwave heating of PAN that the cyano groups were selectively heated. With an electric field intensity of 0.6 V Å -1 and a frequency of 60 GHz, the temperature of the hot-spot atoms was 300 and 500 K higher than the carbon and hydrogen atoms in the PAN backbone, respectively. We also analyzed the thermal runaway behavior of the system during microwave irradiations and found that it was attributed to the decomposition of PAN into smaller polar molecules. This work suggests that it is possible to selectively and effectively activate the cyano groups of PAN to improve their reactivity. read less

Abstract: Disordered graphene networks (DGNs) can be regarded as the three-dimensional (3D) assembly of graphene-like fragments at the nanoscale, in which some intrinsic topological features are usually hidden in these formless fragments without clear understanding. Although some high-resolution structural patterns have been observed in pyrolytic carbons and flash graphene experimentally, it is still hard to characterize the topology and texture of DGNs considering continuous 3D connectivity. Toward this end, starting from the annealing process, we herein performed molecular dynamics simulations to investigate the formation and topological structure of DGNs. Three typical stages are found during the formation of DGNs, that is, the formation of polyaromatic fragments, formation of a disordered framework, and further graphitization. The topology of the obtained DGNs was then investigated, including topological defects, stacking behavior, and global curvature. Several typical in-plane and out-of-plane topological defects are found to connect the 3D network of graphene-like layers. The computed X-ray diffraction and angular defects demonstrate that a high-density DGN tends to form a randomly stacked structure with more connections, while a low-density DGN exhibits more bowl-shaped layers and a less distorted curvature. At low annealing temperatures, the local curvature of DGNs is highly distorted, and the structure seems to lack graphitization compared to high-temperature ones. read less

Abstract: In computational catalysis, density-functional theory (DFT) calculations are usually utilized, although they suffer from high computational costs. Thus, it would be challenging to explicitly predict the catalytic properties of nanoparticles (NPs) at the nanoscale under solvents. Using molecular dynamics (MD) simulations with a reactive force field (ReaxFF), we investigated the catalytic performance of Ni-Pt NPs for the direct synthesis of hydrogen peroxide (H2O2), in which water solvents were explicitly considered along with the effects of the sizes (1.5, 2.0, 3.0, and 3.5 nm) and compositions (Ni90Pt10, Ni80Pt20, and Ni50Pt50) of the NPs. Among the Ni-Pt NPs, 3.0 nm NPs show the highest activity and selectivity for the direct synthesis of H2O2, revealing that the catalytic performance is not well correlated with the surface areas of NPs. The superior catalytic performance results from the high H2 dissociation and low O2 dissociation properties, which are correlated with the numbers of NiNiPt-fcc and NiNi-bridge sites on the surface of Ni-Pt NPs, respectively. The ReaxFF-MD simulations propose the optimum composition (Ni80Pt20) of 3.0 nm Ni-Pt NPs, which is also explained by the numbers of NiNiPt-fcc and NiNi-bridge sites. Furthermore, from the ReaxFF-MD simulations, the direct synthesis of H2O2 for the Ni-Pt NPs can be achieved not only with the Langmuir-Hinshelwood mechanism, which has been conventionally considered, but also with the water-induced mechanism, which is unlikely to occur on pure Pd and Pd-based alloy catalysts; these results are supported by DFT calculations. These results reveal that the ReaxFF-MD method provides significant information for predicting the catalytic properties of NPs, which could be difficult to provide with DFT calculations; thus, it can be a useful framework for the design of nanocatalysts through complementation with a DFT method. read less

Abstract: Graphene-based nanofolds (GNFs) are edge-connected 2D stacked monolayers that originate from single-layer graphene. Graphene-based nanoscrolls (GNSs) are nanomaterials with geometry resembling graphene layers rolled up into a spiral (papyrus-like) form. Both GNS and GNF structures induce significant changes in the mechanical and optoelectronic properties of single-layer graphene, aggregating new functionalities in carbon-based applications. Here, we carried out fully atomistic reactive (ReaxFF) molecular dynamics simulations to study the self-folding and self-scrolling mechanisms of edge-deformed graphene sheets. We adopted initial armchair edge-scrolled graphene (AESG(φ, θ)) structures with similar (or different) twist angles (φ, θ) in each edge, mimicking the initial configuration that was experimentally developed to form biscrolled sheets. The results showed that AESG(0, 2π) and AESG(2π, 2π) evolved to single-folded and two-folded fully stacked morphologies, respectively. As a general trend, for twist angles higher than 2π, the self-deformation process of AESG morphologies yields GNSs. Edge twist angles lower than π are not enough for triggering the self-deformation processes. In the AESG(0, 3π) and AESG(3π, 3π) cases, after a relaxation period, their morphology transition towards GNSs occurred rapidly. In the AESG(3π, 3π) dynamics, a metastable biscroll was formed by the interplay between the left- and right-sided partial scrolling while forming a unique GNS. At high-temperature perturbations, the edge folding and scrolling transitions to GNFs and GNSs occurred within an ultrafast time-period. Remarkably, the AESG(2π, 3π) evolved to a dual state that combines folded and scrolled structures in a temperature-independent process. read less

Abstract: We investigate the melting process of polycrystalline copper doped with hydrogen atoms by using the newly developed Cu/H ReaxFF force field. Hydrogen atoms are found to effectively promote the melting of copper, and even make it happen at temperatures below the equilibrium melting temperature of copper during rapid heating. The enhanced melting is closely relevant to the interaction of hydrogen atoms with the grain boundary. We find that host Cu atoms perform cooperative vibration around the grain boundaries as the precursor of premelting. The doping of hydrogen atoms is shown to drive the vibration more violent so that the grain boundary becomes broader and the premelting is prematurely triggered. Meanwhile, hydrogen atoms segregated in grain boundaries massively diffuse into the bulk region with increasing temperature, resulting in intensification of lattice distortion of the bulk phase. This facilitates the rapid advancement of the liquid-solid interface during melting in contrast to the slow and discontinuous interface advancement in hydrogen-free polycrystalline copper. Our results suggest that even a small amount of hydrogen atoms is expected to significantly affect the thermodynamic properties of metals with the existence of structural defects. read less

Abstract: The structure of organic matter in anthracite samples of different ranks and coal-derived natural graphites was investigated using XRD, micro-Raman spectroscopy, and HRTEM to determine XRD and Rama... read less

Abstract: ABSTRACT A conceptually accurate method to connect the free energy multicanonical sampling to meso-scale kinetic Monte Carlo (kMC) dynamics is proposed. The required input parameters for kMC simulation are the attempt frequency and activation energy for each event, and the free energy multicanonical sampling enables to obtain the kinetic parameters as a function of temperature, which is the most significant difference from a conventional kMC approach that is based on fixed attempt frequency and activation energy. The present approach is applied to oxygen diffusion in single crystal BaTiO3 including Zn dopant (160 ppm) where an anomaly in the oxygen diffusion is experimentally confirmed; the oxygen diffusion coefficient is slightly dropped at around 1080 K. We carried out 1 μs kMC dynamics in the temperature range of 1020 to 1120 K, and obtained a diffusion anomaly at around 1060 K, which is not obtained in conventional kMC calculations. In addition, the calculated diffusion coefficients using the present approach are in the same order as those of experimental ones, whereas the calculated diffusion coefficients using the conventional method are larger than those of experiment by one order of magnitude at least. The results indicate the advantages of the present approach in comparison with the conventional ones because any assumption and fixation of kinetic parameters are not required in the dynamics simulation. read less

Abstract: Polytetrafluoroethylene (PTFE) has been studied as a low friction surface coating since its discovery. The high wear-rate of PTFE reduces the usefulness of the polymer for mechanical purposes; however, combining PTFE with polydopamine (PDA) has been shown to greatly reduce the film wear-rate. During rubbing tests involving PDA/PTFE thin films, a tenacious layer of PTFE remains intact after substantial testing even though pure PTFE film layers are destroyed quickly. Understanding the interface mechanics that allow PTFE and PDA to adhere so well during experimental rubbing tests is necessary to improve the wear-rate of PDA/PTFE thin films. In this study, we use density functional theory (DFT) and molecular dynamics (MD) simulations to investigate the adhesive properties and interface deformation mechanisms between PDA and PTFE molecules. Steered molecular dynamics (SMD) is then performed on isolated pairs of PDA and PTFE molecules to investigate different modes of deformation from equilibrium. PDA trimer oligomers were identified as the most adhesive to PTFE and selected to use in a PDA/PTFE thin film, where nano-indentation and scratch tests are performed. Our results indicate that a combination of the unique deformation mechanisms of PDA molecules and the penetration of PTFE molecules into the PDA substrate provide the PTFE/PDA interface with its wear resistance. read less

Abstract: The modeling of low-temperature plasma synthesis of low-dimensional carbon coatings remains a challenge, since the long-time spans must be simulated for structural relaxation. A proper theoretical method should be chosen to address possible charge-transfer processes. Considering the possibility of linear-chained carbon (LCC) synthesis simulation, a numerical study of the C-C bond breaking under slow argon-ion irradiation is performed for the model molecules of 2,2,3,3-tetramethylbutane (sp3 hybridization), 1,2,3-butatriene (sp2), and 2-butyne (sp). Threshold energies of bond breaking are calculated for the carbon atoms in all three hybridizations. Three levels of theory are applied, and the results are compared with experiment. Based on the accuracy of the values obtained, an approach is proposed for modeling the ion-assisted plasma synthesis. read less

Abstract: Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. We also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics read less

Abstract: Studies on nitrocellulose (NC) mixtures with little solubilities were neglected in many cases previously. This investigation was performed to provide supplemental characterizations of NC and its soaked state with pure liquid ethanol or diethyl ether by simulations and practical methods. Above all, a short-chained NC model (polymerisation degree: 8) and a dried NC specimen were characterized for their substitution of nitrate and microstructure. It was confirmed that both the numerical model and practical specimen belonged to low-nitrated NC. The bonding information of a glycosyl unit and nitrate ester were summarized via first-principle calculations. Then, ReaxFF potential based Molecular Dynamic (MD) simulations and soaking tests on binary organic mixtures demonstrated that both ethanol and diethyl ether had limited solubility for our specified NC. However, potential energies and diffusion coefficients of both computational models showed that the interactions from ethanol molecules were relatively stronger than diethyl ether molecules. The viscosities of saturated NC solutions also proved this consequence, as the difference between pure ether and its filtered NC solution was only 0.02 mm2 s−1. Finally, the strong volatility of diethyl ether itself could keep the wetness of NC upper surface shortly, because this was an upward volatilization effect. Due to this effect, the penetration of NC-diethyl ether mixture was higher in the early period of penetration tests. read less

Abstract: In order to form a SiGe thin film by chemical vapor deposition (CVD) with a suitable quality for advanced devices, the relationships between materials/process and structure/composition are needed to be clarified at the atomic level. We simulated SiGe CVD by using reactive force-field (ReaxFF) molecular dynamics simulations, especially on binary systems of SiHx + GeHx, and derived the influence of the substrate temperature and these ratios of gaseous species on the crystallinity and compositions in the thin films. The crystallinity increases as the substrate temperature increases, and the lowest crystallinity is obtained at the ratios of gaseous species 0.5 and 0.7 for the SiH3 and SiH2, respectively. As the substrate temperature increases, the hydrogen content decreases while Si and Ge content tend to increase. These trends can be seen in relevant studies. Through this simulation we successfully observe that the reactivity of gaseous species greatly affects the crystallinity and compositions in the thin films. read less

Abstract: A method based on the combination of in situ small-angle X-ray scattering (SAXS) and reactive molecular dynamics (MD) simulation is proposed to investigate the nucleation and initial growth of nano... read less

Abstract: As an environmental vegetable insulation oil, camellia oil will be decomposed into dissolvable gases in the presence of electric field. In this work, the characteristic gases of camellia oil were m... read less

Abstract: In this paper, nanoscale mechanical properties and failure behavior of graphene with Stone-Wales defect concentration were investigated using molecular dynamics simulations with the latest ReaxFFC-2013 potential that can accurately capture bond breakages of graphitic compounds. The choice of interatomic potential plays an essential role in capturing the deformation mechanism accurately. Stable configuration of two-dimensional graphene experiences out-of-plane deformation leading to ripples and wrinkles in graphene. It is observed that the mechanical properties such as Young’s modulus, ultimate tensile strength, and the fracture strain are dependent on the out-of-plane deformation, temperature, defect concentration, defect orientation, defect layout and loading configuration. It is observed that the post transient phase non-homogenous ripples and wrinkles influence the mechanical properties at low and high defect concentrations, respectively. read less

Abstract: Experiments and simulations were used to demonstrate that decorating functionalized graphene sheets (FGSs) with platinum nanoparticles (Pt@FGS) stabilized these particles. Addition of these particles to liquid hydrocarbon fuels was observed to significantly affect decomposition under supercritical conditions at a pressure of 4.75 MPa and temperatures from 753 to 803 K. The suspension of only 50 ppmw Pt@FGS in the fuel (equivalent to adding 10 ppmw Pt) enhanced fuel conversion rates (by up to 24%) with a major effect on specific product yields. The production of low-molecular-weight species increased in the pyrolysis products (with the hydrogen yield increasing by a factor of 12.5). ReaxFF molecular dynamics (MD) simulations supported a mechanism in which synergy between Pt and FGS catalyzed dehydrogenation during n-C12H26 pyrolysis. The highest conversion rates and greatest yields of hydrogen and low-molecular-weight species were observed for fuels containing Pt@FGS particles rather than those containing either FGSs or Pt-clusters alone. Analysis of the platinum decorated FGSs post reaction indicated no deterioration of the composite particles. read less

Abstract: It is reported that a three-dimensional cross-linked macromolecular structure with heterogeneous inorganic and organic compositions widely exists in coal particles. The macromolecules usually represent the rank transition of more than 75% of the carbon (C) content of coal particles. In order to know the coal combustion process better, it is important to specifically study the evolution of the coal macromolecule during combustion. In this paper, the structural evolution and the detailed oxidization reactions of a coal macromolecule during the process of combustion are numerically studied with the reactive force field (ReaxFF) molecular dynamics (MD) method, in which the carbon (C) and hydrogen (H) atoms are fully oxidized to CO2 and H2O, respectively. It is found that the coal macromolecule experiences three main stages sequentially: the cleavage, the ring opening, and the oxidation. The heteroatoms (O, N, and S) inside the coal macromolecule are found to play important roles throughout the whole combustion process. The detailed chemical reactions with their occurrence frequencies show that the chemical reactions with O2 mainly occur in C1–4 fragments, and the C1–2–H–O fragments widely exist in the system before they are finally oxidized to CO or CO2. read less

Abstract: The dynamics of neutral diglycine collision with highly oriented pyrolytic graphite (HOPG) were studied by molecular dynamics simulations using a reactive force field. The simulations were performed at an initial incident energy of 481.5 kJ/mol for four different initial incident polar angles of 0°, 20°, 45°, and 70°, and a surface temperature of 677 K. The angular, translational and internal energy, and residence time distributions of the scattered products were determined and analyzed. As a polyatomic molecule, diglycine has several low frequency vibrational modes and shows a rather strong attraction to HOPG, which leads to a long residence time on the surface and facile energy loss, particularly along the normal surface. Since there is significant normal momentum lost while parallel momentum is partially conserved, the scattering angular distribution is found to be generally superspecular and the final translational energies are much lower than the values predicted by the so-called hard-cube model. This study extends our knowledge of collisional energy transfer during collisions of polypeptide molecules with HOPG, which is expected to help the design of a neutral-gas concentrator for the fly-by collection of such molecules in rarefied atmospheres. read less

Abstract: The solid-electrolyte interphase (SEI) formed through the reductive decomposition of solvent molecules plays a crucial role in the stability and durability of lithium-ion batteries (LIBs). Here, we... read less

Abstract: A mechanism to achieve super-low friction in water lubrication is still in debate because friction is accompanied by complex mechanochemical processes at sliding interfaces. Here, we experimentally... read less

Abstract: In this study, we modeled and analyzed a critical aspect of the synthesis process for a-BxC:Hy i.e. the argon bombardment from the ortho-carborane precursor. Utilizing the reactive molecular dynamics simulations, we identified and evaluated the formation of free radicals as a result of ion bombardment. We found that increasing kinetic energy of ions releases an increasing amount of hydrogen. Thus, hydrogen content in the product can be tuned by varying the ion energy. Overall, our approach allows for a better understanding of the mechanism of Ar bombardment and the role of radical species toward the formation of ortho-carborane network. read less

Abstract: In this paper, thermal diffusion states of pure diethyl ether and its mixture with cellulose dinitrate tripolymer were uncovered by LAMMPS-based Molecular Dynamic (MD) simulations. Those MD simulations were generally performed through specified ReaxFF reactive force field to obtain the properties of the chemical system such as molecular energy, density, mean square displacement (MSD) and molecular coordinate. The result of MD simulations presented the clear superheating phenomenon of pure liquid diethyl ether system in the studied environment. The obtained phase transition point was much higher than the reported one. The deviation between two temperatures was about 132.369[Formula: see text]K. It was also demonstrated that the transition process was associated with the sharp increment of potential energy, volume, diffusion coefficient and cohesive energy. However, the split of these diethyl ether molecules was not uniform. The cluster-like transition state was observed before the end of the vaporing process (460[Formula: see text]K). As for the addition of cellulose dinitrate tripolymer, these molecules were not agglomerated in the simulated organic mixture. However, the diffusion of cellulose dinitrate tripolymer was much weaker than those diethyl ether molecules. While the concentration of cellulose dinitrate tripolymer was higher, molecular interactions of this organic mixture were consequently improved, and this further limited the diffusion behavior of the entire chemical system. It could be concluded that the diffusion behavior of the entire organic system was decreased with more amount of cellulose dinitrate tripolymer molecules. read less

Abstract: The pyrolysis processes of a coal particle containing 19,638 atoms in different atmospheres are studied with a reactive force field molecular dynamics (ReaxFF MD) method. The detailed chemical reactions with the corresponding occurrence frequencies are obtained. The generation paths of the main products are disclosed, including CO, H2, H2O, and CH4. The nonuniform effect of temperature on the pyrolysis production is analyzed, among which the productions of CH4 and CO nonmonotonically vary with temperature, while the H2 production increases linearly with temperature. The kinds of atmospheres can significantly influence the coal pyrolysis. Hydrogen atmosphere can apparently improve the CH4 production, which results from the enhancement of the C–H bond generation. read less

Abstract: We have developed a reactive force field (ReaxFF), which is able to reproduce accurately the physical and chemical properties of a comprehensive Fe/Na/P/O system. This ReaxFF was trained systematic... read less

Abstract: As a primary component of cell walls of plants, algae, bacteria, and other natural biomaterials, cellulose has attracted research attention and is the key to effective conversion of natural biomate... read less

Abstract: The ReaxFF molecular dynamics simulations, which can predict chemical reactions, were performed on integral asphalt and individual asphalt molecules at different temperatures and oxygen levels to i... read less

Abstract: The lack of reliable predictive modeling methods and robust experimental techniques has hindered the rational design of hierarchical materials with desired structure–property–performance attributes... read less

Abstract: In this paper, the oxidation behavior of H–Si(100) surface under different humidities (i.e., water environment and air environment) and temperatures (such as 300 and 500 K) was studied by molecular... read less

Abstract: Thermal reduction of graphene oxide (GO) is an essential technique to produce low-cost and higher quality graphene-based materials and composites used today in a plethora of applications. However, despite a demonstrated efficiency of high-temperature annealing in reducing the oxygen content of GO, the impact of the morphology of the initially oxidized samples on the restored sp2 graphene plane versus remaining sp3 imperfections remains unclear and out-of-control. Here using classical molecular dynamics, we simulate the process of thermal reduction on several GO samples for a variety of initial conditions and elucidate how both the concentration of oxygen functional groups and their spatial distribution jeopardize the reduction process efficiency. Our simulations suggest thermal annealing strategies to further optimize the crystallinity of reduced GO, enhancing their transport properties and hence making the resulting composites even more performant for electronic applications. read less

Abstract: Triboemission of hydrocarbon molecules such as methane and ethylene induces chemical and mechanical wear of diamond-like carbon. Understanding atomic-scale wear is crucial to avoid device failure. Atomic-scale wear differs from macroscale wear because chemical reactions and interactions at the friction interface are dominant in atomic-scale tribological behaviors, instead of macroscale properties, such as material strength and hardness. It is particularly challenging to reveal interfacial reactions and atomic-scale wear mechanisms. Here, our operando friction experiments with hydrogenated diamond-like carbon (DLC) in vacuum demonstrate the triboemission of various hydrocarbon molecules from the DLC friction interface, indicating its atomic-scale chemical wear. Furthermore, our reactive molecular dynamics simulations reveal that this triboemission of hydrocarbon molecules induces the atomic-scale mechanical wear of DLC. As the hydrogen concentration in hydrogenated DLC increases, the chemical wear increases while mechanical wear decreases, indicating an opposite effect of hydrogen concentration on chemical and mechanical wear. Consequently, the total wear shows a concave hydrogen concentration dependence, with an optimal hydrogen concentration for wear reduction of around 20%. read less

Abstract: Reactions of linkages and monomer rings in hardwood, softwood, and kraft lignin pyrolysis were investigated using reactive force field (ReaxFF) molecular dynamics (MD) simulations. Four large ligni... read less

Abstract: This work compares pyrolysis reactions of 3- and 4-component surrogate models of RP-3 aviation fuel by a ReaxFF molecular dynamics (MD) simulation method. To evaluate the reactivity of the two RP-3 surrogate models, a multi-component baseline model that consists of 45 components was constructed as a representative of real RP-3 fuel. Reactive MD simulations of RP-3 fuel pyrolysis were performed for the two simple surrogate models and the multi-component baseline model using the GPU code of GMD-Reax. Reaction pathways were analyzed with aid of the unique software of VARxMD. The main product yield and the initial reaction pathways in heat-up pyrolysis simulations of the two RP-3 surrogate models are found different from those in the 45-component model. In comparison to the 45-component baseline model, the weight fraction of C2H4 generated can be 15% higher for the 4-component surrogate model and 10% higher for the 3-component surrogate model. Because the C2H4 molecules in RP-3 pyrolysis are mainly produced t... read less

Abstract: The presence of leachable ions in multicomponent silicate glasses complicates the understanding of their surface structure and chemistry under a humid or aqueous environment, in particular when com... read less

Abstract: Oxygenated treatment is considered to be an effective chemical water treatment method and is widely used in supercritical power plants. Previous isotope tracer experiments reported that dissolved o... read less

Abstract: A new graphene allotrope, penta-graphene (PG), has been proposed recently with unique electronic properties. However, the mechanical behaviors have not been fully explored yet. In this work, we performed classic molecular dynamics (MD) simulations to evaluate the fundamental mechanical properties of PG under uniaxial tension. The effects of strain rate and hydrogenation on the mechanical properties and deformation mechanism of PG were also systematically investigated. Our simulations show that unlike brittle graphene, PG behaves plastically during tensile deformation, which is inherently originated from the irreversible pentagon-to-polygon structural transformation. Higher strain rate generally leads to lower Young’s modulus but higher yield and ultimate strength and strain of PG. In addition, it is also found that fully hydrogenated PG (HPG) exhibits brittle fracture characteristics and does not undergo structural transformation under tension, while HPG with lower H-coverages possess similar mechanical behaviors to that of pristine PG. Moreover, we demonstrate that temperature can trigger pentagon-to-hexagon structural reconstruction for free-standing pristine PG and partially HPG, but cannot for fully HPG. These findings are expected to provide important guidelines for the practical applications of PG in nanodevices and nanoelectronics. read less

Abstract: Molecular dynamics simulations of dry oxidation of bicrystals with incoherent and coherent grain boundaries (GBs) in 3C–SiC are performed at 2000 K and the results are compared to oxidation of single-crystal SiC. Oxidation near incoherent GBs is found faster than that in single crystals and in coherent GBs, whereas oxidation of coherent GBs is comparable to that of single crystals. The accelerated oxidation near incoherent GBs is attributed to strain and the presence of under-coordinated Si within the GB region, both of which reduce the positive charge on silicon atoms, making them more reactive with oxygen. Although atoms with similar properties are found in dislocation cores of coherent GBs, dislocation cores are isolated from each other by crystalline regions, which in turn control the rate of oxidation. read less

Abstract: Amorphous semiconductors with tailored ionic and electronic conductivities are central to the operation of emerging resistive memory. However, because of the large amount of potential candidates and compositions, only limited numbers of materials have been tested experimentally. To accelerate the search of efficient solid electrolytes for resistive switching devices, we developed parameters to describe copper-doped germanium sulfides based on ReaxFF, a reactive molecular dynamics framework. The force field was optimized against a training set of first-principle calculations including crystals, amorphous structures, some small molecules, and clusters to describe the atomic interactions among Ge, S, and Cu elements. Based on this novel atomistic model, we studied the mobility of Cu as a function of the ternary composition of amorphous GexSyCuz, and we investigated the corresponding atomic and electronic structures of each solid electrolyte in details. Our analysis led to semiconducting compositions with hig... read less

Abstract: We report on the self-assembly of a conformational flexible organic compound on Au(111) using scanning tunneling microscopy and low-energy electron diffraction measurements. We observed different conformers of the compound upon adsorption on the reconstructed Au(111) surface. Increasing the molecular coverage enhanced the lateral pressure, that is, parallel to the surface, favoring a coverage-controlled transition from a supramolecular network displaying only one molecular organization, into a polymorphic array with two coexisting arrangements. Our results give insights into the role of substrate-induced conformational changes on the formation of polymorphic supramolecular networks. read less

Abstract: The irradiation healing process of defective graphene was studied by reactive molecular dynamics simulation of injecting C atoms on a multi-vacancy graphene sheet. We studied the effect of environment temperature and incident energy of injected atoms on healing process of defective graphene. Our simulations show that a relatively high temperature (about 1600 K) is prerequisite for perfect healing of defective graphene. Moreover, an appropriate incident energy for injected atoms (0.16 eV/atom for ∼1800 K) is also necessary for perfect healing, even under a suitable temperature for perfect healing. Defect structures, such as carbon chains and blister-like structures, will occur and hinder the healing process, if the adsorption process (determined basically by incident energy) is faster than the reorganization process (dominated by temperature). In addition, the temperature dependence of reorganization capability of graphene was further studied by molecular dynamics simulation of relaxing an intact graphene sheet with adsorbed atoms. The analysis of the evolution of various micro-structures, emerged during the reorganization simulations, is helpful for deeply understanding the healing mechanism of defective graphene sheet under carbon irradiation. read less

Abstract: The dynamics of H2O, CO2, and glycine (GLY) colliding with highly oriented pyrolytic graphite (HOPG) have been explored with beam-surface scattering techniques and molecular dynamics (MD) simulations that were carried out using a reactive force field. A supersonic, continuous molecular beam containing H2O, CO2, and GLY with incidence translational energies of 38.9, 87.5, and 149.5 kJ mol–1, respectively, was directed at an HOPG surface held at a temperature of 677 K. Angular and translational energy distributions of the inelastically scattered molecules were derived from time-of-flight distributions collected with a rotatable mass spectrometer employing electron bombardment ionization. The experimental results indicated that H2O and CO2 retained their incident parallel energy during the gas–surface interaction. The scattering dynamics of GLY were more complicated, as a substantial fraction of the molecules exchanged a significant amount of energy during the gas–surface interaction but did not come into th... read less

Abstract: We use molecular dynamics (MD) simulations with the ReaxFF reactive force field to investigate the thermomechanical, chemical, and spectroscopic response of nitromethane (NM) to shock loading. We simulate shocks using the Hugoniostat technique and use four different parametrizations of ReaxFF to assess the sensitivity of the results with respect to the force field. The predicted shock states, for both the unreacted and reacted materials, are in good agreement with experiments, and two of the force fields capture the increase in shock velocity due to exothermic reactions in excellent agreement with experiments. The predicted detonation velocities with these two force fields are also in good agreement with experiments, and the differences in predicted values are linked to the differences in the reaction products. Across all force fields, NM decomposes predominantly via bimolecular reactions and the formation of nitrosomethane (CH3NO) is found as a dominant initiation pathway. We elucidate the mechanisms of ... read less

Abstract: The synergistic mechanism of Ni catalyst and supercritical water (SCW) during the treatment of dibutyl phthalate (DBP), a representative component of refractory phthalic acid esters, has been investigated using the ReaxFF molecular dynamic simulations. During the catalytic SCW gasification process, Ni catalyst could facilitate the bond cleavage while the roles of SCW were to promote cracking and serve as H sources. As for the evolution of dissociated side chains, the cooperative effects greatly enhanced the cracking of long-chain fragments and generation of saturated products. Ni could help split H2O and the SCW accelerated β-scission as well as provided H and O atoms. For the aromatic ring-opening stage, a Ni-catalyzed process involved successive bond scission and migration of carbon chains into catalyst bulk was dominant while the SCW only offered marginal help. With regard to H2 production, the synergistic effects were supposed to improve H2 yield. Furthermore, the Ni catalyst was gradually deactivated... read less

Abstract: In the present paper, in order to create the model structure of amorphous carbon, we have performed classical molecular-dynamic calculations of liquid carbon quenching on a cold diamond substrate. For this purpose a double-layer simulation cell diamond–liquid carbon containing 90 000 atoms of carbon at a pressure of 1.2 GPa has been used. We have exploited a classical potential ReaxFFC-2013. Characteristic quenching rates versus the distance from the diamond substrate and the velocity of thermal front of quenching have been obtained. The influence of the number of particles in a simulation cell on the results has been investigated as well. read less

Abstract: Current fundamental understanding of the reaction mechanisms controlling Cu oxidation encompasses early-stage chemisorption and O surface diffusion, as well as later-stage Cu oxide nano-island nucleation and growth. This understanding cannot broadly predict preferential Cu oxide formation on competing surface defects. Improving understanding on how to control preferential oxide formation can lead to more effective corrosion mitigation and Cu/Cu2O catalyst optimization strategies. Computational methods, such as density functional theory and reactive force field molecular mechanics, linked by a multiscale approach can calculate early-stage O adsorption and diffusion energetics on simulated structures comparable to experimental surface defects. Experimental methods, like environmental transmission electron microscopy, can characterize later-stage preferential Cu oxide formation on competing surface defects. This study aspires to illustrate consistency between early- and later-stage oxidation properties, find... read less

Abstract: This study employed the reactive force field molecular dynamics to capture atomic-level heat and mass transfer and reaction processes of an aluminum nanoparticle (ANP) oxidizing in a high temperatu... read less

Abstract: The subtle and efficient manufacture of high-quality carbonaceous materials dominates their extensive applications. Meanwhile, revealing the underlying mechanism in the formation of carbonaceous materials is crucial to improving their manufacture efficiency. In the present work, we focus upon the pyrolysis mechanism for four light hydrocarbons including methane, CH4, ethane, C2H6, ethylene, C2H4, and acetylene, C2H2, to carbonaceous materials, combined with reactive molecular dynamics (RMD) simulations. The carbonaceous materials with various morphologies are observed in our simulations, and the morphologies are strongly dependent on the initial reactants; i.e., a disorderly C cluster, a crossed C multilayer, and an orderly C monolayer are made from C2H2, C2H4, and C2H6 and CH4, respectively, as ascertained partly in experiments. Tracing the RMD trajectories, we confirm that the pyrolysis of all four light hydrocarbons undergoes three stages, including the C chain elongation with generation of new small c... read less

Abstract: A fundamental understanding of the thermomechanical properties of electrode materials and Li-ion diffusion kinetics is indispensable for designing high-performance Li-ion batteries (LIBs) with high structural stability and safety. Herein, we performed both molecular dynamics (MD) simulations and density functional theory (DFT) calculations to investigate the thermomechanical properties and Li diffusion kinetics in a two-dimensional (2D) defect-filled graphene-like membrane consisting of 5-, 6-, and 7-membered rings, called psi (ψ)-graphene. Our results reveal that ψ-graphene has a negative linear thermal expansion coefficient, a high specific heat capacity, and high elastic constants that satisfy the Born's criterion for mechanical stability, which can be elucidated as the evidence of strong anharmonicity in ψ-graphene because of the soft out-of-plane bending modes. These characteristics can help prevent the thermal runaway that can occur during overheating and prevent structural damage because of the severe volume expansion of the LIBs. In addition, the Li diffusion coefficient was estimated to be 10-9 cm2/s at 300 K with a low Li migration activation energy (<0.16 eV), which suggests favorable electrode kinetics with fast Li conduction. Our DFT calculations also show that ψ-graphene can possess a fairly good theoretical capacity (339 mA h g-1) and a lower Li diffusion barrier (<0.21 eV). Our results suggest that the new fundamental insights presented here will help to stimulate further experimental work on ψ-graphene for promising future applications as a superior electrode material for LIBs. read less

Abstract: Aim of this article was to investigate the effect of chemical functionalisation on the thermal conductivity of graphene monolayer via reverse non-equilibrium molecular dynamics simulations. Separate simulations have been performed with hydroxyl and epoxide functional groups, which forms intrinsic part of graphene oxide nanostructure. Hydroxyl and epoxide functionalization of graphene has deteriorating effect on the thermal conductivity of graphene. Functionalisation of graphene alters the local structural deformation, phonon transmittance and vibrational frequency of the graphene lattice network. Spatial distribution of hydroxyl group in conjunction with tensile strain engineering plays a significant role in tailoring the thermal conductivity of functionalised graphene. Atomistic alterations such as stable flattening, formation of atomic chains network and epoxide-to-ether chemical transformation upon stretching resulted in an enhanced thermal conductivity. This improvement in thermal conductivity could enable graphene oxide as a promising candidate for thermoelectrics and thermal rectification applications. read less

Abstract: The enhancement of H2O on the carbonation reaction of CaO with CO2 is now widely recognized in the calcium-looping systems. However, the microscopic origins of steam-enhanced reactions remain unclear. A new insight into this issue from the atomic level is provided. We performed molecular dynamics (MD) simulations using a recently developed ReaxFF reactive force field to study the role of H2O on the carbonation reaction of CaO for enhancing CO2 capture. First, the effects of H2O on the carbonation reaction of CaO with CO2 were investigated by MD simulations combined with thermogravimetric analysis (TGA) experiments. Our calculation results well-supported by the TGA experiments showed that H2O just enhances CaO carbonation at the diffusion-controlled stage, whereas there is little influence on the kinetic stage. Then, we analyzed the properties of ion/gas diffusion and the solid product layer to deeply understand the role of H2O in the diffusion-controlled stage. It was found that the ion/gas diffusion coul... read less

Abstract: Sodium aluminosilicate hydrate (NASH) gel is the primary adhesive constituent in environmentally friendly geopolymer. In this study, to understand the thermal behavior of the material, molecular dynamics was utilized to investigate the molecular structure, dynamic property, and mechanical behavior of NASH gel subjected to temperature elevation from 300 K to 1500 K. The aluminosilicate skeleton in NASH gel provides plenty of oxygen sites to accept H-bond from the invading water molecules. Upon heating, around 18.2% of water molecules are decomposed and produce silicate and aluminate hydroxyls. About 87% of hydroxyls are associated with the aluminate skeleton, which weakens the Al-O bonds and disturbs the O-Al-O angle and the local structure, transforming it from an aluminate tetrahedron to a pentahedron and octahedron. With increasing temperature, both Al-O-Si and Si-O-Si bonds are stretched to be broken and the network structure of the NASH gel is gradually transformed into a branch and chain structure. Furthermore, the self-diffusivity of water molecules and sodium dramatically increases with the elevation of temperature, because the decrease in connectivity of the aluminosilicate network reduces the chemical and geometric restriction on the water and ions in NASH gel under higher temperatures. The high temperature also contributes to around 63% of the water molecules further dissociating and hydroxyl groups forming; meanwhile proton exchange between the water molecules and aluminosilicate network frequently takes place. In addition, a uniaxial tensile test was utilized to study the mechanical behavior of the NASH gel at different temperatures. During the tensile test, the aluminosilicate network was found to depolymerize into a branch or chain structure which plays a critical role in resisting the tensile loading. In this process, the breakage of the aluminosilicate skeleton is accompanied with hydrolytic reactions that further deteriorate the structure. Due to the reduction of the chemical bond stability at elevated temperature, both the tensile strength and stiffness of the NASH gel are weakened significantly. However, the ductility of the NASH gel is improved because of the higher extent of structural arrangement at the yield stage and partly due to the lower water attack. Hopefully, the present study can provide valuable molecular insights on the design of alkali-activated materials with high sustainability and durability. read less

Abstract: We report a molecular dynamics (MD) simulation employing the reactive force field (ReaxFF), developed from various first-principles calculations in this study, on ammonia (NH3) synthesis from nitrogen (N2) and hydrogen (H2) gases over Ru nanoparticle (NP) catalysts. Using ReaxFF-MD simulations, we predict not only the activities and selectivities but also the durabilities of the nanocatalysts and discuss the size effect and process conditions (temperature and pressure). Among the NPs (diameter = 3, 4, 5, and 10 nm) considered in this study, the 4 nm NPs show the highest activity, in contrast to our intuition that the smallest NP should provide the highest activity, as it has the highest surface area. In addition, the best selectivity is observed with the 10 nm NPs. The activity and selectivity are mainly determined by the hcp, fcc, and top sites on the Ru NP surface, which depend on the NP size. Moreover, the selectivity can be improved more significantly by increasing the H2 pressure than by increasing the N2 pressure. The durability of the NPs can be determined by the mean stress and the stress concentration, and these two factors have a trade-off relationship with the NP size. In other words, as the NP size increases, its mean stress decreases, whereas the stress concentration simultaneously increases. Because of these two effects, the best durability is found with the 5 nm NPs, which is also in contrast to our intuition that larger NPs should show better durability. We expect that ReaxFF-MD simulations, along with first-principles calculations, could be a useful tool in developing novel catalysts and understanding catalytic reactions. read less

Abstract: Cementitious materials act as a diffusion barrier, immobilizing liquid and solidradioactive waste and preventing their release into the biosphere. The retention capability of hydratedcement paste and its main hydration product, C-S-H gel, has been extensively explored experimentallyfor many alkali and alkaline earth cations. Nevertheless, the retention mechanisms of these cations atthe molecular scale are still unclear. In this paper, we have employed molecular dynamics simulationsto study the capacity of C-S-H to retain Cs, Ca and Na, analyzing the number of high-affinity sites onthe surface, the type of sorption for each cation and the diffusivity of these ions. We have also exploredthe impact of aluminum incorporation in C-S-H at a constant concentration of the ions in the gel pore.We found strong competition for surface sorption sites, with notable differences in the retention of thecations under study and a remarkable enhance of the adsorption in C-A-S-H with respect to C-S-H. read less

Abstract: We proposed a thinning approximation (TA) for estimation of the two-dimensional (2D) wide-angle scattering patterns from Kremer–Grest polymer melts under shear. In the TA, extra particles are inserted at the middle of bonds for fine-graining of the coarse-grained polymers. For the case without the TA, spots corresponding to the orientation of bonds at a high shear rate are difficult to observe because the bond length of successive particles is comparable to the distance between neighboring particles. With the insertion of the extra particles, a ring pattern originating from the neighboring particles can be moved to a wide-angle region. Thus, we can observe the spots at high shear rates. We also examined the relationship between 2D scattering patterns and the Weissenberg number, which is defined as the product of the shear rate and the longest relaxation time. It is confirmed that the relationship for coarse-grained polymers with the TA is consistent with that of the all-atomistic model of polyethylene. read less

Abstract: We use molecular dynamics (MD) simulations with the reactive force field ReaxFF to investigate the response of polyvinyl nitrate (PVN), a high-energy polymer, to shock loading using the Hugoniostat technique. We compare predictions from three widely used ReaxFF versions, and in all cases, we observe shock-induced, volume-increasing exothermic reactions following a short induction time for strong enough insults. The three models predict NO2 dissociation to be the first chemical, and relatively similar final product populations; however, we find significant differences in intermediate populations indicating different reaction mechanisms due to discrepancies in the relative stability of various intermediate fragments. A time-resolved spectral analysis of the reactive MD trajectories enables the first direct comparison of shock-induced chemistry between atomistic simulations and experiments; specifically, ultrafast spectroscopy on laser shocked samples. The results from one of the ReaxFF versions are in excel... read less

Abstract: We study the role of solid-liquid interface thermal resistance (Kapitza resistance) on the evaporation rate of droplets on a heated surface by using a multiscale combination of molecular dynamics (MD) simulations and analytical continuum theory. We parametrize the nonbonded interaction potential between perfluorohexane (C6F14) and a face-centered-cubic solid surface to reproduce the experimental wetting behavior of C6F14 on black chromium through the solid-liquid work of adhesion (quantity directly related to the wetting angle). The thermal conductances between C6F14 and (100) and (111) solid substrates are evaluated by a nonequilibrium molecular dynamics approach for a liquid pressure lower than 2 MPa. Finally, we examine the influence of the Kapitza resistance on evaporation of droplets in the vicinity of a three-phase contact line with continuum theory, where the thermal resistance of liquid layer is comparable with the Kapitza resistance. We determine the thermodynamic conditions under which the Kapitza resistance plays an important role in correctly predicting the evaporation heat flux. read less

Abstract: We establish a theoretical foundation for understanding the nucleation and growth of 2D covalent organic frameworks (COFs) from solution. This foundation should make it easier to realize some of the unique properties of COFs in targeted applications by allowing us to understand how processing variables such as solvent choice and linkage chemistry lead to larger crystalline domains. We use free energy techniques to map out the reaction mechanisms and activation energies of three fundamental reactions that are responsible for the early stages of 2D COF nucleation for a prototypical and commonly used 2D boronate ester material, COF-5, in water and methanol solvents. We show that the presence of water and methanol greatly catalyzes the boronate ester formation reactions, lowering the activation energy barrier by about 10 kcal mol-1 relative to an uncatalyzed reaction pathway. This is in good agreement with experimental observations by Smith and Dichtel (JACS 2014). Our crystallization studies also conclusively eliminate certain proposed mechanisms of growth, such as polymerization of large sheets followed by stacking, while strengthening the case for templated polymerization as a likely growth mechanism for COF crystals. read less

Abstract: Growth of hBN on metal substrates is often performed via chemical vapor deposition from a single precursor (e.g., borazine) and results in hBN monolayers limited by the substrates catalyzing effect. Departing from this paradigm, we demonstrate close control over the growth of mono-, bi-, and trilayers of hBN on copper using triethylborane and ammonia as independent sources of boron and nitrogen. Using density functional theory (DFT) calculations and reactive force field molecular dynamics, we show that the key factor enabling the growth beyond the first layer is the activation of ammonia through heterogeneous pyrolysis with boron-based radicals at the surface. The hBN layers grown are in registry with each other and assume a perfect or near perfect epitaxial relation with the substrate. From atomic force microscopy (AFM) characterization, we observe a moiré superstructure in the first hBN layer with an apparent height modulation and lateral periodicity of ∼10 nm. While this is unexpected given that the moiré pattern of hBN/Cu(111) does not have a significant morphological corrugation, our DFT calculations reveal a spatially modulated interface dipole layer which determines the unusual AFM response. These findings have improved our understanding of the mechanisms involved in growth of hBN and may help generate new growth methods for applications in which control over the number of layers and their alignment is crucial (such as tunneling barriers, ultrathin capacitors, and graphene-based devices). read less

Abstract: For the first time a special force field ReaxFF is used to describe the synthesis of polymer networks and for all-atom simulations of intermolecular cross linking in polystyrene. The density, specific surface, and coefficient of thermal expansion for sample networks with different degrees of crosslinking are calculated in the all-atom model. The results are in agreement with experimental data. read less

Abstract: Energetic cocrystallization, by combining existing molecules together, is thought to be new strategy for creating energetic materials. Nevertheless, the underlying mechanism of its influences on properties and performances in comparison with their pure components remains unclear. The present work reveals the cocrystallization influence of a typical energetic cocrystal of CL-20/HMX on thermal stability, by ReaxFF molecular reactive dynamic simulations and kinetics calculations on the pure and cocrystals. As a result, we find that the cocrystal mediates the thermal stability of pure crystalsand this is in agreement with experimental observations. The initial decay steps in pure crystals remain still in the cocrystal, that is, the independent and intramolecular reactions of N–N bond cleavage governing the initial decay of the pure CL-20 and HMX crystals also dominate in the cocrystal of CL-20/HMX. Meanwhile, during the thermal decomposition of the cocrystal, CL-20 releases heat faster than HMX, thus the heat... read less

Abstract: In this paper, we present our first results in the study of the details of nucleation in the homogeneous carbon gas phase using computer calculations with molecular dynamics methods. Direct and controlled molecular-dynamics approaches are used and two reactive potentials (ReaxFF and AIREBO) are compared. The calculations have shown that the nucleation process in the AIREBO model is going more actively than in the ReaxFF one. read less

Abstract: Over the past decade, interest in leveraging subnanometer pores for improved capacitance in electrochemical double layer capacitors (EDLCs) has readily grown. Correspondingly, many theoretical studies have endeavored to understand the mechanisms that dictate the capacitance enhancement once ions are confined within nanopores, typically within quasi-equilibrium conditions. However, a kinetic-based understanding of the capacitance may be important, especially since the dynamics of ion transport can exhibit dramatic differences under confinement compared to the bulk liquid phase; ion transport is driven by the competition between the electrostatic electrode–ion and ion–ion interactions, which can be comparable as the internal surface area to volume ratio increases. In this work, we study the relationship between the dynamics of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF4) ionic liquid and the capacitance within two idealized cylindrical subnanometer pores with diameters of 0.81 and 1.22 nm using ... read less

Abstract: Understanding the interaction between polyimide and inorganic surfaces is vital in controlling interfacial adhesion behavior. Here, molecular dynamics simulations are employed to study the adhesion of polyimide on both crystalline and glassy silica surfaces, and the effects of hydroxylation, silica structure, and polyimide chemistry on adhesion are investigated. The results reveal that polyimide monomers have stronger adhesion on hydroxylated surfaces compared to nonhydroxylated surfaces. Also, adhesion of polyimide onto silica glass is stronger compared to the corresponding crystalline surfaces. Finally, we explore the molecular origins of adhesion to understand why some polyimide monomers like Kapton have a stronger adhesion per unit area (adhesion density) than others like BPDA-APB. We find this occurs due to a higher density of oxygen’s in the Kapton monomer, which we found to have the highest contribution to adhesion density. read less

Abstract: Sonochemical synthesis can lead to a dramatic increase in the kinetics of formation of polymer spheres (templates for carbon spheres) compared to the modified Stober silica method applied to produce analogous polymer spheres. Reactive molecular dynamics simulations of the sonochemical process indicate a significantly enhanced rate of polymer sphere formation starting from resorcinol and formaldehyde precursors. The associated chemical reaction kinetics enhancement due to sonication is postulated to arise from the localized lowering of atomic densities, localized heating, and generation of radicals due to cavitation collapse in aqueous systems. This dramatic increase in reaction rates translates into enhanced nucleation and growth of the polymer spheres. The results are of broad significance to understanding mechanisms of sonication induced synthesis as well as technologies utilizing polymers spheres. read less

Abstract: We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives. read less

Abstract: Determining quantitative grain boundary (GB) energies as a function of microscopic orientation parameters is essential in order to understand the population of boundaries present in polycrystalline ceramics and films, and the physical properties that result from these boundaries. Here, we investigate the use of two reactive potentials, COMB3 and ReaxFF, to predict free surface and grain boundary structures and energies in the TiO2 rutile system, and compare these results against previously reported ab initio surface and interfacial energies. We demonstrate reactive MD potentials to be generally capable of reproducing key features anticipated for GB structures and energetics, including relative GB and surface energy, charge distributions and potential for different polar and nonpolar terminations, and energy cusps at low-energy interfaces (e.g., coherent twin boundaries, coherent site lattice boundaries). This work establishes the foundation for further use of reactive MD to simulate libraries of oxide GBs... read less

Abstract: Some constructions of the molecular model for reactive molecular dynamics (RMD) simulations have neglected the effect of molecular weight on the RMD results. A computational methodology for generating structural models of amorphous ultrahigh molecular weight polyethylene (UHMWPE) with different degrees of polymerization was thus proposed. The methodology was then used in RMD simulations of three types of molecular models for UHMWPE with 20, 40, and 80 vinyl monomers. The accuracy of the model has been discussed by comparing the RMD results with experimental data previously available in the literature. Results have confirmed that the atomic model with larger molecular weight allows (i) exact calculations of the diffusion coefficient and (ii) accurate prediction of the cross-linked reaction. The RMD simulations provide the basic data for understanding and further studying the chemical reaction of other interesting macromolecules. read less

Abstract: We present a microscopic understanding of the chemical erosion due to combustion product on the nozzle throat using molecular dynamics simulations. The present erosion process consists of molecule-addition step and equilibrium step. First, either CO2 or H2O are introduced into the system with high velocity to provoke the collision with graphite surface. Then, the equilibrium simulation is followed. The collision-included dissociation and its influence on the erosion is emphasized and the present molecular observations are compared with the macroscopic chemical reaction model. read less

Abstract: As a potential building block for the next generation of devices/multifunctional materials that are spreading in almost every technology sector, one-dimensional (1D) carbon nanomaterial has received intensive research interests. Recently, a new ultra-thin diamond nanothread (DNT) has joined this palette, which is a 1D structure with poly-benzene sections connected by Stone-Wales (SW) transformation defects. Using large-scale molecular dynamics simulations, we found that this sp(3) bonded DNT can transition from brittle to ductile behaviour by varying the length of the poly-benzene sections, suggesting that DNT possesses entirely different mechanical responses than other 1D carbon allotropes. Analogously, the SW defects behave like a grain boundary that interrupts the consistency of the poly-benzene sections. For a DNT with a fixed length, the yield strength fluctuates in the vicinity of a certain value and is independent of the "grain size". On the other hand, both yield strength and yield strain show a clear dependence on the total length of DNT, which is due to the fact that the failure of the DNT is dominated by the SW defects. Its highly tunable ductility together with its ultra-light density and high Young's modulus makes diamond nanothread ideal for the creation of extremely strong three-dimensional nano-architectures. read less

Abstract: Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C60 and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside... read less

Abstract: We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link. read less

Abstract: Slip sliding away Many applications would benefit from ultralow friction conditions to minimize wear on the moving parts such as in hard drives or engines. On the very small scale, ultralow friction has been observed with graphite as a lubricant. Berman et al. achieved superlubricity using graphene in combination with crystalline diamond nanoparticles and diamondlike carbon (see the Perspective by Hone and Carpick). Simulations showed that sliding of the graphene patches around the tiny nanodiamond particles led to nanoscrolls with reduced contact area that slide easily against the amorphous diamondlike carbon surface. Science, this issue p. 1118; see also p. 1087 Nanodiamonds wrapped with graphene sheets lead to ultralow friction against a diamondlike carbon surface. [Also see Perspective by Hone and Carpick] Friction and wear remain as the primary modes of mechanical energy dissipation in moving mechanical assemblies; thus, it is desirable to minimize friction in a number of applications. We demonstrate that superlubricity can be realized at engineering scale when graphene is used in combination with nanodiamond particles and diamondlike carbon (DLC). Macroscopic superlubricity originates because graphene patches at a sliding interface wrap around nanodiamonds to form nanoscrolls with reduced contact area that slide against the DLC surface, achieving an incommensurate contact and substantially reduced coefficient of friction (~0.004). Atomistic simulations elucidate the overall mechanism and mesoscopic link bridging the nanoscale mechanics and macroscopic experimental observations. read less

Abstract: The inherent trade-off of porosity and mechanical properties in ultralow dielectric constant SiCOH materials is a critical challenge in semiconductor processing. Numerous postdeposition processes have been studied to achieve simultaneous low-k materials with adequate mechanical rigidity, including thermal annealing. Typically, these thermal anneals are characterized by times on the order of seconds to minutes at relatively low temperatures (below 500 °C). In this work, we report on potential advantages of submillisecond time frame anneals at extreme temperatures up to 1200 °C. The effects of such processing on the structure of ultralow-k materials were studied using molecular dynamics computer simulations employing a force field that facilitates the determination of bond rearrangements, coupled with direct experimental measurements during CO2 laser-induced spike annealing. Results show structural evolution with increasing temperature leading to densification of the SiOx network, reduction in the concentra... read less

Abstract: Molecular dynamics (MD) simulations using a reactive force field (ReaxFF) method for a Green River oil shale model demonstrate that the thermal decomposition of the oil shale molecule is initiated with the cleavage of the oxygen bridge (C-O bond), and the first product is formaldehyde (CH2O). The simulation results show that the C-O bond is weaker than the other bonds, agreeing with its smaller bond dissociation energy (BDE). The ring-opening position of the aliphatic ring is usually determined by the stability of free radicals formed in this process. For aromatic hydrocarbons, the long-chain substituents are found to be easier to leave and the cleavage of C-C bonds leads to a series of chain reactions and the formation of small fragments, such as ethylene and propylene. The bond cleavages are almost in accordance with the minimum bonding energy rule. NVT simulations show that the pyrolysis process progresses in two stages: the decomposition of kerogen into heavy (C40+.) species and then the generation of light compounds. Recombinations and rearrangements of different fragments are also observed via MD simulations. The main hydrocarbon fragments of C-10-C-20 are regarded as the component or precursor of diesel oil. The formation pathways of typical aromatic components are analyzed by tracking the motion trajectories of relevant structures. The intermediates and products in MD simulations are found to be similar to the gas chromatography mass spectrometry (GC-MS) results from previous experiments. read less

Abstract: C black is a class of substantial materials with a long history of applications. However, apart from some descriptions of primary reactions, subsequent processes leading up to the final formation mechanism remain unclear. This mechanism is also crucial for understanding the formation of other carbonaceous materials. In this work, we visualize C black formation by acetylene pyrolysis using molecular dynamics simulations with a molecular reactive force field named ReaxFF. We find that the formation undergoes four stages: (1) chain elongation by H abstraction and polymerization of small C species, (2) chain branching, (3) cyclization and ring densification, and (4) condensed ring folding. The simulated C black particle possesses a structure of folded graphite layers, which is in good accordance with experimental observations. Cyclization and condensation are derived from fusion between neighboring chains, significantly varying from common experimental observations at relatively low temperatures that abide by the mechanism of H abstraction and C2H2 addition. Moreover, polyyne and polyene are usually found during acetylene pyrolysis, suggesting that the pyrolysis of acetylene and other hydrocarbons may be a feasible method of obtaining carbyne, a novel carbonaceous material with a high value. read less

Abstract: Amorphous SiO 2 thin films have been studied via molecular dynamics (MD) simulations. Thin film models (with two free surfaces) have been obtained by cooling from the melt with reactive force field (ReaxFF) potential. Structural and dynamic properties of the thin films are analyzed via radial pair distribution functions (RPDFs), coordination number distributions, ring statistics and bond-angle distributions. Fraction and role of structural defects have been analyzed and discussed. We also show temperature dependence of various thermodynamic quantities of the system. We found that structure of interior of thin films is close to that of the bulk while surface region contains a large amount of structural defects including dangling bonds, undercoordinated sites, small membered rings. Small and large membered rings concentrate mainly in the surface region and their fraction has a tendency to decrease with decreasing temperature. read less

Abstract: The complex chemistry of coal pyrolysis is difficult to be captured by experimental techniques or simulated with the quantum mechanics computational methods. The emerging of both the large-scale coal models and the promising capability of reactive molecular dynamics (ReaxFF MD) motivated us to develop a new methodology by combining graphics processing unit (GPU)-enabled high performance computing with cheminformatics analysis in order to explore the coal pyrolysis mechanisms using ReaxFF MD. The methodology is rooted in two new software tools, GMD-Reax, the first GPU-enabled ReaxFF MD codes that make it practical to simulate large-scale models (∼10,000 atoms) on desktop workstations, and visualisation and analysis of reactive molecular dynamics (VARMD), the first software dedicated to analysis of detailed chemical reactions from the trajectories of ReaxFF MD simulation. With this methodology, reasonable product profiles and gas generation sequences of pyrolysis for bituminous coal models ranging from ∼1000 to ∼10,000 atoms (including the system with 28,351 atoms, one of the largest systems used in ReaxFF MD) have been obtained. The complex and detailed chemical reactions directly revealed by VARMD can provide further information on radical behaviours and their connection with pyrolysates. The methodology presented here offers a new and promising approach to systematically understand the complex chemical reactions in thermolysis of very complicated molecular systems. read less

Abstract: In order to better understand the local influence of nano-particle on the mechanical properties of the polymer, nano-scale analysis is necessary. In that context, this paper is directed towards understanding damage initiation and failure progression in advanced nanostructured composite materials using molecular dynamics. The critical value of the Jintegral (JIC) at crack initiation is related to the fracture toughness of the material, where the subscript I denotes the fracture mode (I=1, 2, 3). Therefore, the J-integral could be used as a suitable metric for estimating the crack driving force as well as the fracture toughness of the material as the crack begins to initiate. Further, the conventional isothermal definition of Jintegral does not take into account the entropic contribution to the free energy, and consequently, may lead to significant over-estimation of the J-integral at the atomistic level, especially at finite temperatures. As a case study, the feasibility of computing the dynamic atomistic J-integral over the molecular dynamics (MD) domain at finite temperature is evaluated for a graphene nano-platelet and the values are compared with results from linear elastic fracture mechanics (LEFM) for isothermal crack initiation at 0 K and at 300 K. Jintegral computations are also done using ReaxFF force field in order to simulate bond breakage during crack propagation. Good agreement is observed between the atomistic J and the LEFM results at 0 K, with predictable discrepancies at 300 K due to entropic effects. A novel cohesive-contour based methodology for computing J-integral is discussed and successfully applied to a graphene nano-platelet. Work is currently underway to compute Jintegral for nanographene modified EPON 862 at 0.1 K and 300 K using the cohesive-contour based procedure and to be able to computationally predict fracture toughness. In order to account for the high strain-rates encountered in MD simulations, scaling laws will be developed to correlate fracture toughness predicted by the MD simulations to the toughness data obtained from compact tension fracture experiments. read less

Abstract: Ammonium nitrate mixed with fuel oil (ANFO) is a commonly used blasting agent. In this paper we investigated the shock properties of pure ammonium nitrate (AN) and two different mixtures of ammonium nitrate and n-dodecane by characterizing their Hugoniot states. We simulated shock compression of pure AN and ANFO mixtures using the Multi-scale Shock Technique, and observed differences in chemical reaction. We also performed a large-scale explicit sub-threshold shock of AN crystal with a 10 nm void filled with 4.4 wt% of n-dodecane. We observed the formation of hotspots and enhanced reactivity at the interface region between AN and n-dodecane molecules. read less

Abstract: We present results of reactive molecular dynamics simulations of hotspot formation and chemical reaction initiation in shock-induced compression of pentaerythritol tetranitrate (PETN) with the ReaxFF reactive force field. A supported shockwave is driven through a PETN crystal containing a 20 nm spherical void at a sub-threshold impact velocity of 2 km/s. Formation of a hotspot due to shock-induced void collapse is observed. During void collapse, NO2 is the dominant species ejected from the upstream void surface. Once the ejecta collide with the downstream void surface and the hotspot develops, formation of final products such as N2 and H2O is observed. The simulation provides a detailed picture of how void collapse and hotspot formation leads to initiation at sub-threshold impact velocities. read less

Abstract: We simulate the impact of an Ar1000 cluster (energy 10 keV, impact angle 55°) into an amorphous l-phenylalanine target. By use of a ReaxFF potential, it is possible to model not only the emission dynamics of intact Phe molecules but also the fragmentation and reaction pathways taken. The simulated sputter yield is in close agreement with experiment. The simulated emission mass spectrum features both emission of large Phen clusters and entrainment of reaction products in the ejected flow, again in agreement with experimental observation. While H abstraction is a common fragmentation channel, the H radicals quickly combine with Phe in the amino group; no isolated H atom is ejected. read less

Abstract: We report reactive molecular dynamics simulations using the ReaxFF reactive force field to examine shock-induced hot-spot formation followed by detonation initiation in realistic (2.7 million atoms) models of polymer bonded explosives (PBX) with nonplanar interfaces. We considered here two energetic materials (EMs) pentaerythritol tetranitrate (PETN), a common EM for PBX, and silicon pentaerythritol tetranitrate (Si-PETN), which is so extremely sensitive that it has not been possible to characterize its shock properties experimentally. In each case the EM was embedded in a hydroxyl-terminated polybutadiene (HTPB) based polymer binder matrix to form a model of PBX that has a periodic sawtooth nonplanar interface. For the cases in which the shock wave propagates from the EM to polymer (EM→poly), we observed that a hot spot arises from shear localization at the convex polymer asperity. For the case in which the shock direction is inverted (shock wave propagates from the polymer to the EM, EM←poly), we find t... read less

Abstract: Tribochemical processes have profound consequences on tribological performance. In the present paper, the tribochemical mechanism of low friction state in the silica/phosphoric acid system is elucidated by reactive molecular dynamics (ReaxFF) simulations. The friction coefficient is found having strong positive correlation with the number of interfacial hydrogen bonds, which suggests that a weaker interfacial hydrogen bond network would favor a lower friction. The friction reduction mechanisms have been analyzed in two temperature regimes: For 300 ≤ T ≤ 600 K, no indication of tribochemical reaction is observed, and the friction coefficient decreases because of the accelerated molecular rotational and translational motion and the corresponding weakened hydrogen bond network. For 800 K ≤ T ≤ 1400 K, the occurrence of tribochemical reactions leads to a clustering and polymerization of the phosphoric acid molecules and generation of a considerable quantity of water molecules distributed mainly in the sliding... read less

Abstract: Two-dimensional carbon materials such as the 2D nanoweb-like graphyne membrane are promising as molecular sieves for energy and environmental applications. Based on the application of water purification - the removal of contaminants from wastewater and seawater - here we use molecular dynamics (MD) simulations to investigate the interplay between mechanical forces, filtration mechanisms, and overall performance for graphyne membranes with different pore sizes. We carry out biaxial tensile tests and verify the superior mechanical robustness and tolerance of graphyne membranes against possible deformations from the membrane installation process. A possible ultimate stress in excess of 15 GPa and an ultimate strain of 1.2-2.7% are determined. We also demonstrate their excellent filtration performance with barrier-free water permeation and perfect rejection of the representative contaminants considered here, including divalent heavy metal salts (copper sulfate), hydrophobic organic chemicals (benzene and carbon tetrachloride), and inorganic monovalent salts (sodium chloride). We find that graphtriyne, with an effective pore diameter of 3.8 Å, exhibits an optimal purification performance, because the contaminant rejection rate is more sensitive to pore size than water permeability. In addition, we find that the hydrophobic graphyne membranes exhibit higher rejection rates for hydrophilic contaminants compared to the hydrophobic ones. This size exclusion effect is a result of the larger hydrated radii of hydrophilic species due to stronger interactions between them and water molecules. Finally, we find that the maximum deformation of graphtriyne at the ultimate strain before material failure has only a minor impact on its filtration performance. One of the advantages of using graphyne for water purification is that no chemical functionalization or defects need to be introduced, which maintains the structural integrity of the membrane, and possibly, the long-term device performance. read less

Abstract: A systematic comparison of atomistic modeling methods including density functional theory (DFT), the self-consistent charge density-functional tight-binding (SCC-DFTB), and ReaxFF is presented for simulating the initial stages of phenolic polymer pyrolysis. A phenolic polymer system is simulated for several hundred picoseconds within a temperature range of 2500 to 3500 K. The time evolution of major pyrolysis products including small-molecule species and char is examined. Two temperature zones are observed which demark cross-linking versus fragmentation. The dominant chemical products for all methods are similar, but the yields for each product differ. At 3500 K, DFTB overestimates CO production (300-400%) and underestimates free H (~30%) and small C(m)H(n)O molecules (~70%) compared with DFT. At 3500 K, ReaxFF underestimates free H (~60%) and fused carbon rings (~70%) relative to DFT. Heterocyclic oxygen-containing five- and six-membered carbon rings are observed at 2500 K. Formation mechanisms for H2O, CO, and char are discussed. Additional calculations using a semiclassical method for incorporating quantum nuclear energies of molecules were also performed. These results suggest that chemical equilibrium can be affected by quantum nuclear effects at temperatures of 2500 K and below. Pyrolysis reaction mechanisms and energetics are examined in detail in a companion manuscript. read less

Abstract: We study the bombardment of a suspended monolayer graphene sheet via different energetic atoms via classical molecular dynamics based on the reactive force field (ReaxFF). We find that the probability, quality, and controllability of defects are mainly determined by the impact site, the properties of the incident atom, and the incident energy. Through comparison with density functional theory calculations, we demonstrate that defects and vacancies in graphene form only in regions of sufficiently high electron density. Furthermore, the quality of defects is influenced by the bond order of the incident atom-carbon bonds, where a higher bond order leads to lower probability of pristine defects (vacancies) but a higher probability of direct-substitution. Finally, the incident energy plays an important role on the evolution and final pattern of defects in graphene. Based on the probability, quality, and controllability analysis performed, we depict a full-range energy spectrum for atomic bombardment, where we ... read less

Abstract: The thermal decomposition of n‐heptane is an important process in petroleum industry. The theoretical investigations show that the main products are C2H4, H2, and C3H6, which agree well with the experimental results. The products populations depend strongly on the temperature. The quantity of ethylene increases quickly as the temperature goes up. The conversion of n‐heptane and the mole fraction of primary products from reactive molecular dynamic and chemical kinetic modeling are compared with each other. We also investigated the pre‐exponential factor and activation energy for thermal decomposition of n‐heptane by kinetic analysis from the reactive force field simulations, which were extracted to be 1.78×1014s−1 and 47.32 kcal/mol respectively. read less

Abstract: The research objective is to gain a better fundamental understanding of the mechanical behaviour of cellulose structure in wood microfibre for enhancing the mechanical properties of cellulosic-based composites. Molecular static and molecular dynamics simulations were used to both generate and deform the amorphous cellulose structure in a three-dimensional periodic simulation cell. The 14-b-D-glucose structure was chosen along with a reactive force field, ReaxFF, to model the atomic interactions and complex bonding of cellulose. Mechanical properties were calculated for these models and predicted geometric, energetic and elastic material properties were compared to published modelling results and experimental measurements. The significance of the research is that this sets the stage for future polymer-cellulose predictive micromechanical models. These predictive models can be used to elucidate the interfacial compatibility between the cellulose and polymer and how deposited nanoparticles and nanophases on cellulose surfaces affect this interfacial strength. read less

Abstract: The mechanical properties of metallic nanowires depend dramatically on the atmospheric conditions. Molecular-dynamics simulations with ReaxFF were conducted to study tensile elastic deformation of oxidized Al nanowires. The thin amorphous oxide shell formed around Al nanowires had a very low Young's modulus of 26 GPa, due to its low density and low Al-O coordination. Consequently, for diameters less than 100 nm, the composite Young's modulus of oxide-covered Al nanowires showed a size dependence implying that in this case “smaller is softer.” The model developed also explained the discrepancies in the reported modulus values of nanometer-scale Al thin films. read less

Abstract: The effects of stoichiometry on the atomic structure and the related mechanical properties of boron carbide (B4C) have been studied using density functional theory and quantum molecular dynamics simulations. Computational cells of boron carbide containing up to 960 atoms and spanning compositions ranging from 6.7% to 26.7% carbon were used to determine the effects of stoichiometry on the atomic structure, elastic properties, and stress–strain response as a function of hydrostatic, uniaxial, and shear loading paths. It was found that different stoichiometries, as well as variable atomic arrangements within a fixed stoichiometry, can have a significant impact on the yield stress of boron carbide when compressed uniaxially (by as much as 70% in some cases); the significantly reduced strength of boron carbide under shear loading is also demonstrated. read less

Abstract: Heat transfer through micro channels is being investigated due to its importance in micro channel cooling applications. Molecular dynamics simulation is regarded as a potential tool for studying such microscopic phenomena in detail. However, the applicability of molecular dynamics method is limited due to scarcely known inter atomic interactions involved in complex fluids. In this study we use an empirical force field (ReaxFF), which is parameterized using accurate quantum chemical simulation results for water, to simulate heat transfer phenomena through a layer of water confined between two platinum slabs. The model for water seems to reproduce the macroscopic properties such as density, radial distribution function and diffusivity quite well. The heat transfer phenomena through a channel filled with water, which is confined by two platinum (100) surfaces are studied using ReaxFF. The model accurately predicts the formation of surface mono-layer. The heat transfer analysis shows temperature jumps near the walls which are creating significant heat transfer resistances. A low bulk density in the channel creates a multi-phase region with vapor transport in the region. read less

Abstract: Asphalt derived from crude oil (or petroleum) is an important base organic material for many industrial purposes. Oxidative hardening occurs throughout the service life of asphalt materials, which could significantly change the desired physicochemical properties. The study of asphalt oxidative hardening has thus far been focused on the changes in the physical properties, mainly the viscosity and ductility of bulk asphalt. Such phenomenological approaches meet the direct engineering needs, however do not help understand the fundamental physicochemical mechanisms of asphalt hardening. From this standpoint, this paper aims at exploring the chemical basis of asphalt oxidative hardening by establishing an ab initio quantum chemistry (QC) based physicochemical environment, in which the possible chemical reactions between asphalt ingredients and oxygen, as well as the incurred changes in their physical behavior, can be readily studied. X-ray photoelectron spectroscopy (XPS) was used to validate the bulk asphalt ... read less

Abstract: Thermal cracking of n-decane and n-decane in the presence of several fuel additives are studied in order to improve the rate of thermal cracking by using reactive molecular dynamics (MD) simulations employing the ReaxFF reactive force field. From MD simulations, we find the initiation mechanisms of pyrolysis of n-decane are mainly through two pathways: (1) the cleavage of a C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding decyl radical. Another pathway is the H-abstraction reactions by small radicals including H, CH(3), and C(2)H(5). The basic reaction mechanisms are in good agreement with existing chemical kinetic models of thermal decomposition of n-decane. Quantum mechanical calculations of reaction enthalpies demonstrate that the H-abstraction channel is easier compared with the direct C-C or C-H bond-breaking in n-decane. The thermal cracking of n-decane with several additives is further investigated. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis. The different chemical structures of the fuel additives greatly affect the apparent activation energy and pre-exponential factors. The presence of diethyl ether (DEE), methyl tert-butyl ether (MTBE), 1-nitropropane (NP), 3,6,9-triethyl-3,6,9-trimethyl-1,2,4,5,7,8-hexaoxonane (TEMPO), triethylamine (TEA), and diacetonediperodixe (DADP) exhibit remarkable promoting effect on the thermal cracking rates, compared with that of pure n-decane, in the following order: NP > TEMPO > DADP > DEE (∼MTBE) > TEA, which coincides with experimental results. These results demonstrate that reactive MD simulations can be used to screen for fuel additives and provide useful information for more comprehensive chemical kinetic model studies at the molecular level. read less

Abstract: The carbonization mechanism in polyacrylonitrile (PAN) based carbon nanofibers is studied using ReaxFF molecular dynamics simulations. Simulations are performed at two carbonization temperatures, 2500 and 2800 K, and also at two densities, 1.6 and 2.1 g/cm(3), that are relevant to the experimental carbonization conditions. The results are analyzed by examining the evolution of species with time, including carbon-only ring structures and gaseous species. Formation mechanisms are proposed for species like N(2), H(2), NH(3), and HCN and five-, six-, and seven-membered carbon-only rings, along with polycyclic structures. Interestingly, the formation of five-membered rings follows N(2) formation and usually occurs as a precursor to six-membered rings. Elimination mechanisms for the gaseous molecules are found that are in agreement with previously proposed mechanisms; however, alternative mechanisms are also proposed. read less

Abstract: Carbon phenolic resin has been used as a charring ablative material in protecting the structure integrity of an object subjected to high heat loads, such as the re-entry vehicle. The composition of the pyrolysis gases generated from the charring ablator and injected into the surrounding boundary layer has a significant impact on the aerothermodynamics around the object. Recent studies revealed that the pyrolysis gas composition ejected from the charring ablator is sensitive to the incipient composition of the pyrolysis gases from material decomposition, which is not well known and thus leads to large uncertainties. We have explored the use of atomistic simulations to help understand the underlying chemistry involved in the thermal degradation of phenolic resins and determine the initial composition of the pyrolysis gases and their associated chemical evolution. In this study, reactive atomistic simulations were conducted to analyze the thermal decomposition of phenol monomers and non-crosslinked phenolic resin, as well as the propene oxidation. In addition, a numerical procedure for constructing chemically crosslinked phenolic resin based on molecular dynamics was explored and developed. The employed numerical procedures, obtained numerical results, and constructed crosslinked phenolic resin network are presented in this paper. Discussions and recommendation for future work are also included. read less

Abstract: Atomistic simulations equipped with the ab initio based classical reactive force fleld ReaxFF are used to study adsorption of oxygen on a Pt(111) surface. Molecular Dynamics (MD) simulations are used to study the adsorption dynamics of O2 on Pt(111) for both normal and oblique impacts, whereas Grand Canonical Monte Carlo (GCMC) calculations are employed to study the surface coverage of atomic oxygen on the same platinum surface. Overall, good quantitative agreement with the experimental data is found. Our MD simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF Potential Energy Surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule’s rotational energy) because of steric hindrance. In the energy range between 0.1 eV and 0.4 eV, the sticking probability increases, similarly to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3, due to an overall less attractive ReaxFF PES compared to experiments and DFT. For oblique impacts, the trapping probability does not scale with the total incident kinetic energy, but is reduced by the non-zero parallel momentum because of the PES corrugation. Furthermore, our simulations predict quasi-specular (slightly supraspecular) distributions of angles of re∞ection, in accordance with molecular beam experiments. With GCMC simulations, a coverage of about 0.25 is determined at ultra-vacuum conditions (» 10 i10 atm), reproducing the experimental observations. Further reflning of the potential parameters will be aimed to improve the agreement of sticking results at high Ei (by including direct dissociation pathways in the training set) and to reproduce the p(2£ 2) adsorbates surface structure at 0.25 coverage (by strengthening the lateral repulsion between adsorbed O atoms). read less

Abstract: By use of molecular dynamics simulations, we have studied the evolution of epoxy and hydroxyl functional groups on graphene oxide (GO) during high-temperature thermal reduction. We find that the reduced GO sheets are characterized by a large number of stable holelike defects formed by breaking of C−C bonds in the basal plane. These defects are always decorated by the carbonyl (C═O) groups and are formed due to the strain in the basal plane created by epoxy and hydroxyl functional groups that are located close to each other. With very few exceptions, the carbonyl groups that are observed in Raman spectroscopy and other experimental studies are generally attributed to the C═O terminations of the edges. However, our study using first-principles calculations and a reactive force field approach clearly shows that the formation of carbonyl groups within the graphene basal plane is energetically favorable compared to other well-known functional groups such as epoxies and ethers. We have identified the specific r... read less

Abstract: OF DISSERTATION CARBON OXIDATION AT THE ATOMIC LEVEL: A COMPUTATIONAL STUDY ON OXIDATIVE GRAPHENE ETCHING AND PITTING OF GRAPHITIC CARBON SURFACES In order to understand the oxidation of solid carbon materials by oxygen-containing gases, carbon oxidation has to be studied on the atomic level where the surface reactions occur. Graphene and graphite are etched by oxygen to form characteristic pits that are scattered across the material surface, and pitting in turn leads to microstructural changes that determine the macroscopic oxidation behavior. While this is a well-documented phenomenon, it is heretofore poorly understood due to the notorious difficulty of experiments and a lack of comprehensive computational studies. The main objective of the present work is the development of a computational framework from first principles to study carbon oxidation at the atomic level. First, the large body of literature on carbon oxidation is examined with regards to experimental observations of the pitting phenomenon as well as relevant theoretical studies on different aspects of the mechanistic details of carbon oxidation. Next, a comprehensive, atomic-scale kinetic mechanism for carbon oxidation is developed, which comprises only elementary surface reactions with reaction rates derived from first principles. The mechanism is then implemented using the Kinetic Monte Carlo (KMC) method. This framework for the first time allows the simulation of oxidative graphene etching at the atomic scale to relevant timeand lengthscales (up to seconds and hundreds of nanometers), and in a wide range of conditions (temperatures up to 2000 Kelvin, pressures ranging from vacuum to atmospheric pressure). The numerical results reveal information about the pitting process in heretofore unattained detail: Pit growth rates (and therefore intrinsic oxidation rates) are calculated and validated against a set of different experimental data at a wide range of conditions. Such information is crucial for modelling of material behavior on mesoand macroscales. The dependence of the pit geometry (hexagonal vs. circular) on temperature and gas pressure is assessed. This is important for utilizing oxidative etching as a manufacturing technique for graphene-based nanodevices. More subtle phenomena like pit inhibition at low pressures and temperatures are also discussed. Moreover, all these findings are examined with respect to the underlying reaction mechanism. This unveils the fundamental reasons for the observed reaction behavior, in particular different activation energies and reaction orders at low and high temperatures, as well as the transition of the pit geometry. The present work is a first step in an ongoing effort to develop predictive models for carbon oxidation in Thermal Protection Systems (TPS), with the ultimate goal of improved safety for hypersonic flight vehicles. read less

Abstract: It is well known, that quenching from the liquid state is the basis of many methods for creating new materials with unique properties. Liquid and amorphous carbon are a mixture of atoms with different states of hybridization (sp1, sp2, sp3) owing to polymorphism. It is claimed that there is a tendency of growth of sp1 atoms in liquid and amorphous carbon at decreasing pressure. Great interest has been shown recently to carbyne and pseudocarbynes, consisting of sp1-hybridizing atoms. These materials have unique optical and mechanical properties. In the present work a pressure dependence of the structure of amorphous carbon, quenched from liquid is studied by molecular dynamics simulation in the pressure range 1–40 GPa. The interaction between carbon atoms was determined by two bond-order potentials: Airebo and ReaxFF. These two potentials take into account the type of a chemical bond as well as breaking and formation of new chemical bonds during the modeling process. We study a bulk quenching from liquid carbon in the NPT ensemble at a constant pressure and determine the distribution of chemical bonds sp1–sp2–sp3 in amorphous carbon during the quenching. Quenched liquid structure modeling at a pressure of 1 GPa and the structure of an amorphous carbon sample obtained experimentally at a pressure of 25 MPa by Raman spectroscopy showed that the sp1 fraction of carbon was significant. read less

Abstract: Phase transformation between carbon allotropes usually requires high pressures and high temperatures. Thus, the development of low-temperature phase transition approaches between carbon allotropes is highly desired. Herein, novel amorphous carbon nanocapsules are successfully synthesized by pulsed plasma glow discharge. These nanocapsules are comprised of highly strained carbon clusters encapsulated in a fullerene-like carbon matrix, with the formers serving as nucleation sites. These nucleation sites favored the formation of a diamond unit cell driven by the self-nanoscopic local excessive pressure, thereby significantly decreasing the temperature required for its transformation into a diamond nanocrystal. Under moderate electron beam irradiation (10-20 A cm-2 ) without external heating, self-organization of the energetic carbon clusters into diamond nanocrystals is achieved, whereas the surrounding fullerene-like carbon matrix remains nearly unchanged. Molecular dynamics simulations demonstrate that the defective rings as the active sites dominate the phase transition of amorphous carbon to diamond nanocrystal. The findings may open a promising route to realize phase transformation between carbon allotropes at a lower temperature. read less

Abstract: The effect of vacancy defects on the structural properties and the thermal stability of free standing silicene – a buckled structure of hexagonally arranged silicon atoms – is studied using reactive molecular dynamics simulations. Pristine silicene is found to be stable up to 1500 K, above which the system transits to a three-dimensional amorphous configuration. Vacancy defects result in local structural changes in the system and considerably reduce the thermal stability of silicene: depending on the size of the vacancy defect, the critical temperature decreases by more than 30%. However, the system is still found to be stable well above room temperature within our simulation time of 500 ps. We found that the, stability of silicene can be increased by saturating the dangling bonds at the defect edges by foreign atoms (e.g., hydrogen). read less

Abstract: Using fully reactive molecular dynamics methodologies we investigated the structural and dynamical aspects of the fluorination mechanism leading to fluorographene formation from graphene membranes. Fluorination tends to produce significant defective areas on the membranes with variation on the typical carbon-carbon distances, sometimes with the presence of large holes due to carbon losses. The results obtained in our simulations are in good agreement with the broad distribution of values for the lattice parameter experimentally observed. We have also investigated mixed atmospheres composed by H and F atoms. When H is present in small quantities an expressive reduction on the rate of incorporation of fluorine was observed. On the other hand when fluorine atoms are present in small quantities in a hydrogen atmosphere, they induce an increasing on the hydrogen incorporation and the formation of locally self-organized structure of adsorbed H and F atoms. read less