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Thermally-activated 1/2〈111〉 screw dislocation motion is the controlling plastic mechanism at low temperatures in body-centered cubic (bcc) crystals. Dislocation motion proceeds by nucleation and propagation of atomic-sized kink pairs in close-packed planes. The atomistic character of kink pairs can be studied using techniques such as molecular dynamics (MD). However, MD's natural inability to properly sample thermally-activated processes as well as to capture {110} screw dislocation glide calls for the development of other methods capable of overcoming these limitations. Here we develop a kinetic Monte Carlo (kMC) approach to study single screw dislocation dynamics from room temperature to 0.5Tm and at stresses 0

Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM2. To demonstrate SEM2, we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM2. Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2. [ABSTRACT FROM AUTHOR]

Author(s): Luis A. Zepeda-Ruiz [1]; Alexander Stukowski [2]; Tomas Oppelstrup [1]; Vasily V. Bulatov (corresponding author) [1] Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line [...]

The dynamic evolution and interaction of defects under the conditions of shock loading in single crystal and nanocrystalline Cu are investigated using a series of large-scale molecular dynamics simulations for an impact velocity of 1 km/s. Four stages of defect evolution are identified during shock simulations that result in deformation and failure. These stages correspond to: the initial shock compression (I); the propagation of the compression wave (II); the propagation and interaction of the reflected tensile wave (III); and the nucleation, growth, and coalescence of voids (IV). The effect of the microstructure on the evolution of defect densities during these four stages is characterized and quantified for single crystal Cu as well as nanocrystalline Cu with an average grain size of 6 nm, 10 nm, 13 nm, 16 nm, 20 nm, and 30 nm. The evolution of twin densities during the shock propagation is observed to vary with the grain size of the system and affects the spall strength of the metal. The grain sizes of 6 nm and 16 nm are observed to have peak values for the twin densities and a spall strength that is comparable with the single crystal Cu. [ABSTRACT FROM AUTHOR]

Hybrid molecular dynamics and Monte-Carlo simulations on the deformation behavior of nanocrystalline Pd-Au are presented. A semi-grandcanonical Monte-Carlo scheme is employed during straining to allow for local relaxation by chemical equilibration and to effectively shortcut diffusional processes. Altering the balance between an imposed straining and local relaxation reveals a strong correlation of the irreversible plastic deformation and the frequency of local relaxation. Using a novel method to quantify the amount of crystal slip strain from atomistic data, it is demonstrated how plastic deformation carried by dislocations changes as a function of the local relaxation. The results indicate that conventional molecular dynamics simulations overestimate the contributions of dislocation slip to the overall plastic deformation of nanocrystalline samples. [ABSTRACT FROM AUTHOR]

In the present work, the dislocation structure evolution around and underneath the spherical indentations in (001) oriented single crystalline strontium titanate (STO) was revealed by using an etch-pit technique and molecular dynamics (MD) simulations. The 3D defect structure at various length scales and subsurface depths was resolved with the help of a sequential polishing, etching, and imaging technique. This analysis, combined with load-displacement data, shows that the incipient plasticity (manifested as sudden indenter displacement bursts) is strongly influenced by preexisting dislocations. In the early stage of plastic deformation, the dislocation pile-ups are all aligned in 〈100〉 directions, lying on {110}45 planes, inclined at 45° to the (001) surface. At higher mean contact pressure and larger indentation depth, however, dislocation pile-ups along 〈110〉 directions appear, lying on {110}90 planes, perpendicular to the (100) surface. MD simulations confirm the glide plane nature and provide further insights into the dislocation formation mechanisms by tracing the evolution of the complete dislocation line network as function of indentation depth. [ABSTRACT FROM AUTHOR]

Nanoindentation into single-crystalline Si is modeled by molecular dynamics simulation using a modified Tersoff potential. We observe that the high stress produced during indentation leads to three processes occurring consecutively in the substrate: (i) phase transformation of the original cubic diamond (cd) to the bct5 phase; (ii) generation of dislocations; and (iii) amorphization. The bct5 phase develops along {1 1 1} planes of the cd phase; when these meet, the enclosed volume of cd phase transforms to bct5. The particular role played by a stable tetrahedral structure formed by bct5 {1 1 1} planes and {1 1 1} intrinsic stacking faults in the cd structure is highlighted. The phase transformation to bct5 is partially reversed when dislocations nucleate in the cd phase and locally relieve stresses. The generation and reactions of the uncommon dislocations 1 4 〈 1 1 1 〉 and 1 3 〈 1 1 2 〉 are discussed. [ABSTRACT FROM AUTHOR]

3C-SiC (the only polytype of SiC that resides in a diamond cubic lattice structure) is a relatively new material that exhibits most of the desirable engineering properties required for advanced electronic applications. The anisotropy exhibited by 3C-SiC during its nanometric cutting is significant, and the potential for its exploitation has yet to be fully investigated. This paper aims to understand the influence of crystal anisotropy of 3C-SiC on its cutting behaviour. A molecular dynamics simulation model was developed to simulate the nanometric cutting of single-crystal 3C-SiC in nine (9) distinct combinations of crystal orientations and cutting directions, i.e. (1 1 1) <-1 1 0>, (1 1 1) <-2 1 1>, (1 1 0) <-1 1 0>, (1 1 0) <0 0 1>, (1 1 0) <1 1-2>, (0 0 1) <-1 1 0>, (0 0 1) <1 0 0>, (1 1-2) <1-1 0> and (1-2 0) <2 1 0>. In order to ensure the reliability of the simulation results, two separate simulation trials were carried out with different machining parameters. In the first trial, a cutting tool rake angle of -25°, d/r (uncut chip thickness/cutting edge radius) ratio of 0.57 and cutting velocity of 10m s-1 were used whereas a second trial was done using a cutting tool rake angle of -30°, d/r ratio of 1 and cutting velocity of 4m s-1 . Both the trials showed similar anisotropic variation. variation of up to 45%, while the resultant cutting forces showed a variation of 37%. This suggests that 3C-SiC is highly anisotropic in its ease of deformation. These results corroborate with the experimentally observed anisotropic variation of 43.6% in Young's modulus of 3C-SiC. The recently developed dislocation extraction algorithm (DXA) [1, 2] was employed to detect the nucleation of dislocations in the MD simulations of varying cutting orientations and cutting directions. Based on the overall analysis, it was found that 3C-SiC offers ease of deformation on either (1 1 1) <-1 1 0>, (1 1 0) <0 0 1>,or (1 0 0) <1 0 0> setups. [ABSTRACT FROM AUTHOR]

The article presents information on the requirement of the Monte Carlo algorithm for the purpose of studying the atomistic simulations of the precipitation in the alloys. The transmutation of the simulations of the multicomponent systems is allowed by the semi-grand-canonical ensemble. Information on the study of the precipitation of copper in the nanocrystalline iron through the algorithm is also presented.

Nanoglasses consist of glassy grains connected by an amorphous interface. While internal interfaces in nanoglasses help to prevent brittle failure, they are usually not beneficial to the glasses overall strength. In this molecular dynamics study, we manipulate the glass–glass interfaces of a Cu–Zr nanoglass, such that they are replaced by stronger crystalline interphases. Analogous to grain boundary strengthening in crystalline materials, we show that it is possible to reinforce the nanoglass without compromising its ductility. [ABSTRACT FROM AUTHOR]

Highlights: [•] Molecular dynamics simulation of thermal spray of copper was performed. [•] A parameter “flattening aspect ratio” is proposed to characterize the process. [•] Reynolds number increases only up to a certain critical impact velocity. [•] Impact velocity dominates impact temperature to influence recrystallization. [ABSTRACT FROM AUTHOR]

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

Modeling multiscale mechanics in shape-shifting engineered tissues, such as organoids and organs-on-chip, is both important and challenging. In fact, it is difficult to model relevant tissue-level large non-linear deformations mediated by discrete cell-level behaviors, such as migration and proliferation. One approach to solve this problem is subcellular element modeling (SEM), where ensembles of coarse-grained particles interacting via empirically defined potentials are used to model individual cells while preserving cell rheology. However, an explicit treatment of multiscale mechanics in SEM was missing. Here, we incorporated analyses and visualizations of particle level stress and strain in the open-source software SEM++ to create a new framework that we call subcellular element modeling and mechanics or SEM 2 . To demonstrate SEM 2 , we provide a detailed mechanics treatment of classical SEM simulations including single-cell creep, migration, and proliferation. We also introduce an additional force to control nuclear positioning during migration and proliferation. Finally, we show how SEM 2 can be used to model proliferation in engineered cell culture platforms such as organoids and organs-on-chip. For every scenario, we present the analysis of cell emergent behaviors as offered by SEM++ and examples of stress or strain distributions that are possible with SEM 2 . Throughout the study, we only used first-principles literature values or parametric studies, so we left to the Discussion a qualitative comparison of our insights with recently published results. The code for SEM 2 is available on GitHub at https://github.com/Synthetic-Physiology-Lab/sem2., Competing Interests: Alexander Stukowski and Constanze Kalcher are employed by OVITO GmbH which sells the software we used in the preparation of some of the figures., (© 2023 Author(s).)

Recent molecular dynamics simulation results have increased conceptual understanding of the grazing and the ploughing friction at elevated temperatures, particularly near the substrate's melting point. In this commentary we address a major constraint concerning its experimental verification.