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1. Implementing Reactivity in Molecular Dynamics Simulations with the Interface Force Field (IFF-R) and Other Harmonic Force Fields

   Jordan J. Winetrout, Krishan Kanhaiya ( July 2021 , ArXivorg)

   null (Ed.)

   The Interface force field (IFF) enables accurate simulations of bulk and interfacial properties of compounds and multiphase materials. However, the simulation of reactions and mechanical properties up to failure remains challenging and expensive. Here we introduce the Reactive Interface Force Field (IFF-R) to analyze bond breaking and failure of complex materials using molecular dynamics simulations. IFF-R uses a Morse potential instead of a harmonic potential as typically employed in molecular dynamics force fields to describe the bond energy, which can render any desired bond reactive by specification of the curve shape of the potential energy and the bond dissociation energy. This facile extension of IFF and other force fields that utilize a harmonic bond energy term allows the description of bond breaking without loss in functionality, accuracy, and speed. The method enables quantitative, on-the-fly computations of bond breaking and stress-strain curves up to failure in any material. We illustrate accurate predictions of mechanical behavior for a variety of material systems, including metals (iron), ceramics (carbon nanotubes), polymers (polyacrylonitrile and cellulose I\b{eta}), and include sample parameters for common bonds based on using experimental and high-level (MP2) quantum mechanical reference data. Computed structures, surface energies, elastic moduli, and tensile strengths are in excellent agreement with available experimental data. Non-reactive properties are shown to be essentially identical to IFF values. Computations are approximately 50 times faster than using ReaxFF and require only a single set of parameters. Compatibility of IFF and IFF-R with biomolecular force fields allows the quantitative analysis of the mechanics of proteins, DNA, and other biological molecules. 

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2. Recent Milestones in Unraveling the Full-Field Structure of Dynamic Shear Cracks and Fault Ruptures in Real-Time: From Photoelasticity to Ultrahigh-Speed Digital Image Correlation

   https://doi.org/10.1115/1.4045715  

   Rosakis, A. J. ; Rubino, V. ; Lapusta, N. ( March 2020 , Journal of Applied Mechanics)

   Abstract The last few decades have seen great achievements in dynamic fracture mechanics. Yet, it was not possible to experimentally quantify the full-field behavior of dynamic fractures, until very recently. Here, we review our recent work on the full-field quantification of the temporal evolution of dynamic shear ruptures. Our newly developed approach based on digital image correlation combined with ultrahigh-speed photography has revolutionized the capabilities of measuring highly transient phenomena and enabled addressing key questions of rupture dynamics. Recent milestones include the visualization of the complete displacement, particle velocity, strain, stress and strain rate fields near growing ruptures, capturing the evolution of dynamic friction during individual rupture growth, and the detailed study of rupture speed limits. For example, dynamic friction has been the biggest unknown controlling how frictional ruptures develop but it has been impossible, until now, to measure dynamic friction during spontaneous rupture propagation and to understand its dependence on other quantities. Our recent measurements allow, by simultaneously tracking tractions and sliding speeds on the rupturing interface, to disentangle its complex dependence on the slip, slip velocity, and on their history. In another application, we have uncovered new phenomena that could not be detected with previous methods, such as the formation of pressure shock fronts associated with “supersonic” propagation of shear ruptures in viscoelastic materials where the wave speeds are shown to depend strongly on the strain rate. 

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3. Probing stress-regulated ordering of the plant cortical microtubule array via a computational approach

   https://doi.org/10.1186/s12870-023-04252-5  

   Li, Jing ; Szymanski, Daniel B. ; Kim, Taeyoon ( December 2023 , BMC Plant Biology)

   Morphological properties of tissues and organs rely on cell growth. The growth of plant cells is determined by properties of a tough outer cell wall that deforms anisotropically in response to high turgor pressure. Cortical microtubules bias the mechanical anisotropy of a cell wall by affecting the trajectories of cellulose synthases in the wall that polymerize cellulose microfibrils. The microtubule cytoskeleton is often oriented in one direction at cellular length-scales to regulate growth direction, but the means by which cellular-scale microtubule patterns emerge has not been well understood. Correlations between the microtubule orientation and tensile forces in the cell wall have often been observed. However, the plausibility of stress as a determining factor for microtubule patterning has not been directly evaluated to date.

   Here, we simulated how different attributes of tensile forces in the cell wall can orient and pattern the microtubule array in the cortex. We implemented a discrete model with transient microtubule behaviors influenced by local mechanical stress in order to probe the mechanisms of stress-dependent patterning. Specifically, we varied the sensitivity of four types of dynamic behaviors observed on the plus end of microtubules – growth, shrinkage, catastrophe, and rescue – to local stress. Then, we evaluated the extent and rate of microtubule alignments in a two-dimensional computational domain that reflects the structural organization of the cortical array in plant cells.

   Our modeling approaches reproduced microtubule patterns observed in simple cell types and demonstrated that a spatial variation in the magnitude and anisotropy of stress can mediate mechanical feedback between the wall and of the cortical microtubule array.

    

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4. On the computational solution of vector-density based continuum dislocation dynamics models: a comparison of two plastic distortion and stress update algorithms

   https://doi.org/https://doi.org/10.1016/j.ijplas.2021.102943  

   P. Lin, V. Vivekanandan. ( January 2021 , International journal of plasticity)

   null (Ed.)

   Continuum dislocation dynamics models of mesoscale plasticity consist of dislocation transport-reaction equations coupled with crystal mechanics equations. The coupling between these two sets of equations is such that dislocation transport gives rise to the evolution of plastic distortion (strain), while the evolution of the latter fixes the stress from which the dislocation velocity field is found via a mobility law. Earlier solutions of these equations employed a staggered solution scheme for the two sets of equations in which the plastic distortion was updated via time integration of its rate, as found from Orowan’s law. In this work, we show that such a direct time integration scheme can suffer from accumulation of numerical errors. We introduce an alternative scheme based on field dislocation mechanics that ensures consistency between the plastic distortion and the dislocation content in the crystal. The new scheme is based on calculating the compatible and incompatible parts of the plastic distortion separately, and the incompatible part is calculated from the current dislocation density field. Stress field and dislocation transport calculations were implemented within a finite element based discretization of the governing equations, with the crystal mechanics part solved by a conventional Galerkin method and the dislocation transport equations by the least squares method. A simple test is first performed to show the accuracy of the two schemes for updating the plastic distortion, which shows that the solution method based on field dislocation mechanics is more accurate. This method then was used to simulate an austenitic steel crystal under uniaxial loading and multiple slip conditions. By considering dislocation interactions caused by junctions, a hardening rate similar to discrete dislocation dynamics simulation results was obtained. The simulations show that dislocations exhibit some self-organized structures as the strain is increased. 

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5. Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto‐Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme

   https://doi.org/10.1029/2022JB024548  

   Abdelmeguid, Mohamed ; Elbanna, Ahmed ( December 2022 , Journal of Geophysical Research: Solid Earth)

   We present a coupled finite element spectral boundary integral framework for modeling sequences of earthquakes and aseismic slip on a 2‐D planar rate‐and‐state fault with off‐fault visco‐plastic response in the plane strain approximation. The model resolves both slow aseismic deformation and inertia effects during rapid slip. As an application, we perform two sets of simulations with different choices of cohesion to explore the co‐evolution of fault slip, bulk plasticity and local stress fields. The first set implements a relatively large value of the cohesion parameter, which results in limiting inelastic strain accumulation to dynamic rupture phases. The second set implements a smaller cohesion, allowing for plastic strain to accumulate in both seismic and aseismic phases. For the first model, our results indicate that the extent and distribution of plastic strain depend on the angle of maximum compressive principal stress. At larger angles, inelastic strain accumulates on the extensional side of a dynamically propagating rupture. At smaller angles, the extent of plasticity is limited to the compressional side of the domain. At smaller cohesion values, off‐fault plasticity may occur during aseismic slip, which alters the nucleation characteristics and earthquake sequence pattern. Furthermore, our results at lower cohesion values indicate that plastic strain accumulation may occur in both the extensional and compressional sides of the off‐fault bulk even at higher angles of maximum compression. This produces damage patterns that deviate from the traditional off‐fault fan‐like distribution observed in dynamic rupture simulations and emphasizes the significance of long‐term deformation in interpreting observations.

    

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