A new look at the atomic level virial stress: on continuum-molecular system equivalence

The numerical modelling of particulate processes in environmental science increasingly requires an ability to represent the properties of individual natural particles. Considerable advances have been made in discontinuum modelling using spheres to represent particles. In this paper, we discuss recent developments that illustrate a way forward for tackling the complexity of realistically shaped bodies such as those exhibited by rock fragments. To address the validation of such approaches, we present a comparison of cube-packing experiments and their equivalent numerical simulation. Sensitivity to initial conditions, highlighted for non-spherical bodies, enters the discussion of problems with validation of numerical simulation. The algorithmic details behind these advances in modelling large systems of realistically shaped particles are summarized in our companion paper in this volume.

A micromechanical dislocation model of frictional slip between two asperities is presented. The model suggests that when the contact radius is smaller than a critical value, the friction stress is constant, of the order of the theoretical shear strength, in agreement with reported atomic force microscope (AFM) friction experiments. However, at the critical value there is a transition beyond which the friction stress decreases with increasing area, until it reaches the second transition where the friction stress gradually becomes independent of the contact size. This is in contrast to previous theories, which assume that the friction stress is always independent of the size. The present model also predicts that the mechanisms of slip are size dependent. Before the first transition, the constant friction stress is associated with concurrent slip without the aid of dislocation motion. The first transition corresponds to the minimum contact size at which a single dislocation loop is nucleated and sweeps through the whole contact interface, resulting in a single–dislocation–assisted (SDA) slip. This mechanism is predicted to prevail for a wide range of contact sizes, from 10 nm to 10 µm in radius for typical dry adhesive contacts; however, there are no available experimental data in this size range. The second transition is found to be caused by the effective Peierls stress which stabilizes the dislocation loop within the contact region, resulting in dislocation pile–ups. Beyond the second transition, slip is assisted by cooperative glide of dislocations in the pile–up. For sufficiently large contacts the mechanism of cooperative glide induces a size–independent friction stress, in agreement with observations in surface force apparatus (SFA) friction experiments. This paper (Part I) addresses the first transition: from concurrent slip to SDA slip. The second transition is analysed in a companion paper (Part II).

The mobility of simple ions such as alkali–metal and halide ions at room temperature shows two anomalies. Firstly, there are maxima in mobilities as a function of ion size for both positive and negative ions and, secondly, the maximum for negative ions occurs at a larger ionic radius than the maximum for positive ions. Theoretical treatments of this problem are reviewed and it is concluded that a molecular treatment of the system is needed to understand the results. Computer simulation using the simple point charge model (SPC/E) for water reproduced the observations and is used to discuss the application of theories. In particular, the nature of the first solvation shell is correlated with ion mobility. Simulation reveals a further anomaly, namely that if the charge is removed from a large ion, then it moves more slowly. This is interpreted as the result of formation of a solvent cage around the hydrophobic solute. The changes in local structure resulting from changes in charge and size also affect the solvation thermodynamics. Simulations show that the solvation entropy has a double maximum when viewed as a function of charge. The local minimum near zero charge is interpreted as being due to hydrophobic order, and the maxima as the result of structure breaking. This double maximum in the entropy of solvation is a signature of the hydrophobic cage effect. Comparisons are made between ion mobilities in liquid water at ambient and supercritical conditions.

Molecular Modeling: An Experimental Tool

This special section on molecular dynamics (MD) simulations is based on presentations at the recent conference `International Anniversary Symposium on Molecular Dynamics Simulations' which was held on 29–31 August 2005, at Osaka University Nakanoshima Center, Osaka, Japan.Fifty-six researchers including four invited speakers got together at this international symposium and presented their original studies in oral or poster format. This is part of a series of symposia which started about 10 years ago. Every year a symposium has been held at a Japanese venue, organized by members of the molecular dynamics committee, Japan Society of Materials Science (JSMS). The object of the symposia is to bring researchers together and to discuss new perspectives concerning MD simulations. Attention has been directed at (but not limited to) the following materials-engineering-science or solid-mechanics fields: the strength of materials, materials interfaces, materials design and new materials, micromechanics, microstructure, deformation process, fracture mechanics and simulation methodology. Last year, we reached the 10th anniversary milestone successfully holding the conference as planned. We appreciate the efforts of all the people involved.Owing to the rapid and expanding development of our computational environment, MD simulation which directly and solely chases atomic motions in materials has now come to be widely utilized for obtaining microscopic viewpoints and insights, not only by the pure physicist or pure chemist, but also by engineering scientists, engineers, and scientists in industry. There has been development of new algorithms or methods in MD simulation in the last decade. Also, the applicable field of MD seems to be spreading, but its basic methodology is being maintained and is still beneficial.In this special section, the subjects covered by the papers are located in the relatively broad range of material engineering and science: carbon nanotubes, phase transformation, materials interfaces, amorphous, metallic glass, dislocation, nanocrystalline structure, polymers, ceramics, semiconductors, potential function, modelling of dynamical systems and nanofluidics. All the articles in this special section have gone through the journal's peer review process with contributions from the authors, referees, and the Editorial Board of Modelling and Simulation in Materials Science and Engineering.We would like to thank all the contributors to the symposium, the authors of this special section, the co-organizers, and the Editorial Board of Modelling and Simulation in Materials Science and Engineering.

This paper examines the influence of microstructure on the quasi–static failure of PBX 9501, a polymer–bonded explosive (PBX) manufactured for the Los Alamos National Laboratory in America. Optical microscopy has been used to examine qualitatively cracked and pristine material. Consequent on the manufacturing process, the explosive crystals display angular features and natural facets. In addition, considerable growth twinning, internal defects and voidage has been observed. These defects are found significantly to alter the failure path. In common with other PBXs, failure paths tend to run around the long straight edges of the explosive filler and avoid regions of fine filler and binder. Explosive crystals were found to fracture due either to cracks propagating from another region or internal defects. These observations are confirmed by the use of high–resolution moire interferometry. This sensitive optical technique allows the deformation of the sample to be measured up to and including the point of failure. By taking white–light micrographs that are in exact registration with the measured displacement maps, the influence of the underlying microstructure can be seen.

The continuum theory of electro‐elasticity is used in order to describe the large deformations observed in gels endowed with electric properties when they are placed in electric fields. The analytical solution of the properly constructed boundary‐value problem agrees quantitatively with available experimental data.

A computational framework is developed which couples a series of models, each describing vastly different physical events, in order to characterize particle growth (agglomeration) in thermochemically reacting granular flows. The modelling is purposely simplified to expose the dominant mechanisms which control agglomeration. The overall system is comprised of relatively simple coupled submodels describing impact, heat production, bonding and fragmentation, each of which can be replaced by more elaborate descriptions, if and when they are available. Inverse problems, solved with a genetic algorithm, are then constructed to ascertain system parameters which maximize agglomeration likelihood within a range of admissible data.

Halo approach to model cracks initiation and propagation in 3D Discrete Element Method simulation of homogeneous and heterogeneous materials

In this paper we explore the second transition in the mechanism of frictional slip of single–asperity contacts, which takes place at large contact sizes. This is a transition from single–dislocation–assisted (SDA) slip to multiple–dislocation–cooperated (MDC) slip. It is found that the friction stress is controlled by dislocation nucleation for SDA slip, and by dislocation mobility for MDC slip. A model of concentric dislocation loops is introduced to analyse dislocation pile–up processes and their relationship to the friction stress. Dislocations are stabilized to be piled up as a result of the non–zero effective Peierls stress of the interface. The analysis shows that slip occurs when the condition for the nucleation of a new dislocation and the condition for destabilizing the leading dislocation of the pile–up are simultaneously satisfied. It is also shown that, as the contact size increases, the friction stress approaches asymptotically a constant value equal to the effective Peierls stress of the interface. This result is in agreement with reported experimental results in the surface force apparatus (SFA). The case of a large number of dislocations in the pile–up is studied via an asymptotic analysis, a key concept of which is the existence of a dislocation–free zone that controls the dislocation nucleation process. The analysis provides the connection between the discrete dislocation model and the continuous cohesive zone model of single–asperity friction.

Nanoimprint lithography (NIL) is one of the promising technologies for the fabrication of nanostructures at low cost (Chou et al., 1995) (Chou et al., 1996). In NIL, understanding the deformation behaviour of polymer during imprinting processes is an essential issue for high-speed and uniformed fabrication. Since numerical simulations can be efficient approaches for this issue, several studies using continuum mechanics are performed (Hirai et al., 2001) (Hirai et al., 2004) (Song et al., 2008). Continuum mechanics successfully predict the material deformation in submicron scale. However, as the pattern size becomes smaller than several tens of nanometers, continuum mechanics fails to analyze the material behaviour. Single-nanometre resolution has experimentally been demonstrated in NIL (Hua et al., 2004) (Hua et al., 2006). For the exact analysis of the material deformation in nanoscale system, the behaviour of atoms or molecules should be considered. Molecular dynamics (MD) simulation is a useful tool to study the deformation mechanism of the materials in atomic scale. Several MD studies on NIL process are reported. Kang et al. propose a MD simulation model of a NIL process imprinting an α-quartz stamp into an amorphous poly-(methylmethacrylate) film (Kang et al., 2007). In their study, the distributions of density and stress in the polymer film are calculated for the detail analysis of deformation behaviour. The qualitative agreement between the MD simulation and the experimental data for the density variation of patterned polymer is reported (Woo et al., 2007). Mold geometry effect on springback phenomenon in NIL process is also studied with the MD simulation (Yang et al., 2009). For metal direct imprinting, more MD studies are performed. Process parameters such as stamp taper angle, imprint depth, temperature and punch velocity are investigated for copper imprinting (Hsu et al., 2004) (Hsu et al., 2005). The mechanism of the atomic-scale friction is studied for aluminium imprinting (Hsieh & Sung, 2007). The metal film thickness effect on pattern formation is also studied (Cheng et al., 2007). Agreement between MD simulation and experimental results is reported for temperature effects on gold imprinting (Hsiung et al., 2009). MD simulation of nanoimprint for alloys is demonstrated (Fang et al., 2007). In order to save computational time, a multi-scale simulation for nanoimprint process that mixes the atomistic and continuum approaches is proposed (Wu & Lin, 2008). Recently, MD simulation of roller nanoimprint process is performed (Wu et al., 2009).

Since the pattern collapse was reported for the first time it has been getting more critical issue in wet cleaning process along with semiconductor scaling. The model of the pattern collapse is that structures such as fins deform due to capillary force during drying step, then they contact and stick each other due to surface tension. One technique to prevent pattern collapse involves lowering the surface tension by modifying the surface’s silanol groups with functional groups[1]. The expected mechanism is that the adhesive force becomes smaller than the elastic force of the pattern due to the reduced surface tension. However, the details, including the dynamics, are still unclear. In particular, how functional groups affect fin contact from a molecular perspective remains unknown. Clarifying these issues is crucial because it will lead to a better understanding of the pattern collapse, subsequently enhancing semiconductor fabrication efficiency. Molecular dynamics (MD) simulation is a useful tool to elucidate these phenomena, as it can obtain physical properties and forces of the system from statistical thermodynamics and visualize nanoscale dynamics[2].In this study, we prepared models of fins modified with trimethyl silanol (TMS) and calculated the adhesive forces between them by using MD techniques. We utilized the MD solver Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and the visualizer Open Visualization Tool (OVITO) [3, 4].The fin model utilized in these calculations is depicted in Figure 1. The size of the simulation box was 15.360×2.304×42.000 nm. Periodic boundary conditions were applied in the x and y directions, while specular boundary condition was applied in the z direction. This model primarily consisted of Si atoms. The height of fins was 30 nm, with the top 10 nm terminated by OH groups (912 in total) and the remaining terminated by H atoms. Here we introduced TMS substitutions for randomly selected OH groups. The numbers of substitutions were 0, 91, 228, and 365, resulting in 0%, 10%, 25%, and 40% TMS models, respectively. To reduce bias arising from the random placement of TMS groups, five TMS models were created for each level of TMS substitution. The first step in the calculation process involved placing water between the fins to simulate a wet condition and induce pattern collapse, followed by conducting a 2.0 ns MD calculation. As a result, in every model, the fins came into contact each other (Figure 1b). Subsequently, all water molecules were removed to simulate a dried condition, followed by a 2.0 ns MD calculation. In all models, under the dry condition, the fin contact established during the wet condition was kept (Figure 1c, d). The average adhesive forces between 1.0 ns and 2.0 ns of the MD trajectory after water removal were analyzed, revealing that the forces in the 10%, 25%, and 40% TMS models were less than 1/3 of those in the 0% TMS models. We interpret that, despite the persistence of pattern collapse in the dry condition, restoring the initially separated fins appears more feasible in TMS-modified surface models. The details will be reported in an oral presentation.[1] T. Koide et al., "Effect of Surface Energy Reduction for Nano-Structure Stiction," ECS Transactions, vol. 69, no. 8, p. 131, 2015, doi: 10.1149/06908.0131ecst.[2] R. Seki et al., "Insights into FinFET Structure Collapse: A Reactive Force Field-Based Molecular Dynamics Investigation," Solid State Phenomena, vol. 346, p. 123, 2023, doi: 10.4028/p-mUO0Oa.[3] A. P. Thompson et al., "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales," Computer Physics Communications, vol. 271, p. 108171, 2022, doi: 10.1016/j.cpc.2021.108171.[4] A. Stukowski, "Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool," Modelling and Simulation in Materials Science and Engineering, vol. 18, no. 1, p. 015012, 2010, doi: 10.1088/0965-0393/18/1/015012.Figure 1: (a) The wet Fin model with inter-fin water molecules for MD simulations. The top 10 nm of the fins were terminated with OH groups, while the remaining were terminated with H atoms. Through the introduction of TMS substitutions for randomly selected OH groups, we prepared 10%, 25%, and 40% TMS models. (b) The snapshot of MD simulation after 2.0 ns from the initial configuration of (a). (c) The dry model prepared by removing water molecules from the configuration of (b). (d) The snapshot of MD simulation after 2.0 ns from the configuration of (c). Figure 1

Xylooligosaccharides (XOS) such as xylobiose and xylotriose are prebiotics with important functions and relevance and the study of interaction mechanism between these substrate and their respective enzymes has scope and applications. Thus, the present study aimed to decipher the interaction mechanisms of xylose isomerase (XylA) and xylokinase (XylB) towards their xylo-substrates namely xylobiose and xylotriose by computational modeling and molecular dynamic simulation studies. The three-dimensional structures of XylA and XylB, not available in their native forms, were predicted, energy minimized and validated by various computational biology tools and software. The binding mechanisms of xylobiose and xylotriose towards XylA and XylB were modeled by molecular docking and the stability of the docked complexes was confirmed by molecular dynamic (MD) simulation. The current study suggested that the theoretical models of XylA and XylB possessed good stereo-chemical validity, structural stabilities and minimum energy conformers. The molecular docking studied showed that xylotriose showed better binding interactions to XylA than xylobiose and xylobiose showed better binding interaction to XylB than xylotriose with ideal root mean square deviation (RMS), minimum binding energy (kcal/mol), hydrogen bonding and weak interactions. The MD simulation confirmed the stabilities of the docked complexes predicted by docking studies. The study suggested that interactions between the probiotics and prebiotics and provides the novel insights in exploring synbiotics as functional foods towards their futuristic applications. Highlights This study deciphers the interactions of xylosubstrates to XylA and XylB. The XylA and XylB possessed ideal structural stability and stereochemistry Xylotriose and Xylobiose showed significant interactions The interactions of Xylotriose-XylA and Xylobiose-XylB were found stable in MD studies. Communicated by Ramaswamy H. Sarma

An atomistic survey of shear coupling in asymmetric tilt grain boundaries and interpretation using the disconnections framework

In this study, we systematically investigate the influence of stress states, relative locations, and orientations of crack—γ/γ′ phase interfaces on the deformation and crack propagation behaviors of the Ni-based superalloy through molecular dynamics simulations. The stress state with high stress triaxiality will impede the plastic deformation process of the system, thereby promoting brittle crack propagation within the system. But the stress state of low stress triaxiality results in obvious plastic deformation and plastic crack propagation behaviors of the system. The deformation system with cracks located in both the γ and γ′ phase exhibits the slowest growth rate, regardless of applied stress states. Additionally, the deformation process demonstrates prominent plastic behavior. For the deformation system with cracks perpendicular to the γ/γ′ phase interface, the γ/γ′ phase interface will hinder the crack propagation. Our research provides interesting observations on deformation and crack propagation behaviors at an atomic level and at a nano-scale which are important for understanding deformation and fracture behaviors at a macroscopic scale for the Ni-based superalloy.