Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

DEM simulations of polydisperse media: efficient contact detection applied to investigate the quasi-static limit

Discrete element modeling (DEM) of polydisperse granular materials is significantly more computationally expensive than modeling of monodisperse materials as a larger number of particles are required to obtain a representative elementary volume, and standard contact detection algorithms become progressively less efficient with polydispersity. This paper presents modified contact detection and inter-processor communication schemes implemented in LAMMPS which account for particles of different sizes separately, greatly improving efficiency. This new scheme is applied to the inertial number (I), which quantifies the ratio of inertial to confining forces. This has been used to identify the quasi-static limit for shearing of granular materials, which is often taken to be I=10−3. However, the expression for the inertial number contains a particle diameter term and therefore it is unclear how to apply this for polydisperse media. Results of DEM shearing tests on polydisperse granular media are presented in order to determine whether I provides a unique quasi-static limit regardless of polydispersity and which particle diameter term should be used to calculate I. The results show that the commonly used value of I=10−3 can successfully locate the quasi-static limit for monodisperse media but not for polydisperse media, for which significant variations of macroscopic stress ratio and microscopic force and contact networks are apparent down to at least I=10−6. The quasi-static limit could not be conclusively determined for the polydisperse samples. Based on these results, the quasi-staticity of polydisperse samples should not be inferred from a low inertial number as currently formulated, irrespective of the particle diameter used in its calculation

Multiscale developments of cellular Potts models

Multiscale problems are ubiquitous and fundamental in all biological phenomena that emerge naturally from the complex interaction of processes which occur at various levels. A number of both discrete and continuous mathematical models and methods have been developed to address such an intricate network of organization. One of the most suitable individual cell-based model for this purpose is the well-known cellular Potts model (CPM). The CPM is a discrete, lattice-based, flexible technique that is able to accurately identify and describe the phenomenological mechanisms which are responsible for innumerable biological (and nonbiological) phenomena. In this work, we first give a brief overview of its biophysical basis and discuss its main limitations. We then propose some innovative extensions, focusing on ways of integrating the basic mesoscopic CPM with accurate continuous models of microscopic dynamics of individuals. The aim is to create a multiscale hybrid framework that is able to deal with the typical multilevel organization of biological development, where the behavior of the simulated individuals is realistically driven by their internal state. Our CPM extensions are then tested with sample applications that show a qualitative and quantitative agreement with experimental data. Finally, we conclude by discussing further possible developments of the metho

Modeling and Simulation of cracks and fractures with peridynamics in brittle materials

Today, ceramic materials are an essential component of batteries for electric cars. One key feature of this kind of battery is the safety of the ceramic core. Here, the precise approximation of the evolution of damage after the impact and the wave propagation is important to analyze the safety of the battery. The initiation of cracks is especially essential, because the core is normally not damaged. This thesis studies bond-based peridynamics (PD), a non-local generalization of continuum mechanics, with a focus on discontinuous displacements as they arise in fracture mechanics. With respect to the modeling, the initiation and growth of cracks, two bond-based peridynamic material models for linear isotropic elastic materials are considered. One important feature here is to relate the PD energy to the classical theory energy. The PD is a model, discretized here with the EMU nodal discretization. The neighbor search in node clouds is an essential part of the computational costs. Therefore, an efficient sorting-based library for the neighbor search in generic node clouds is presented. To achieve the full utilization of modern super computers, a combination of processors and acceleration cards is essential. The asynchronous integration of CUDA into the High Performance ParallelX framework is presented. For the comparison with experimental data, two post processing techniques for the extraction of fragments and stress waves are shown. Finally, three numerical results for the initiation and evolution of cracks are considered. First, the evolution of damage and wave propagation according to the Edge-On impact experiment. Second, the critical traction prescribed value for the critical traction for Mode I crack opening by Linear Fracture Mechanics (LEFM) is compared with the ones obtained in the simulation for a wide range of materials. Third, the Poisson ratio and the Young modulus obtained by a tensile test for PMMA are compared with the computed values

Simulated Annealing

The book contains 15 chapters presenting recent contributions of top researchers working with Simulated Annealing (SA). Although it represents a small sample of the research activity on SA, the book will certainly serve as a valuable tool for researchers interested in getting involved in this multidisciplinary field. In fact, one of the salient features is that the book is highly multidisciplinary in terms of application areas since it assembles experts from the fields of Biology, Telecommunications, Geology, Electronics and Medicine

Dislocation Slip and Deformation Twinning in Face Centered Cubic Low Stacking Fault Energy High Entropy Alloys

There is an ongoing need for the design and development of metal alloys with improved properties for extreme environment applications. High entropy alloys (HEAs) are a group of metal alloys that in contrary to conventional metal alloys can have multiple principal elements in high concentrations. HEAs show promising properties better than or comparable to conventional metal alloys for a range of temperature down to cryogenic temperature. HEAs are good candidates to be used as structural materials for extreme environments applications such as in aerospace, automotive, transportation, and energy industries, among others. Mechanical behavior and the underlying plastic deformation mechanisms and the factors affecting HEAs need to be fully understood to be able to use these alloys for the mentioned applications and to design and develop further improved metal alloys.Low stacking fault energy face centered cubic (fcc) HEAs show simultaneous high strength and ductility and specially by the decrease in temperature down to cryogenic temperatures, whereas there is usually a tradeoff between strength and ductility in conventional metal alloys. Plastic deformation in low stacking fault energy fcc HEAs starts with dislocation slip and with the increase in stress, deformation twins nucleate and grow as an additional mode of deformation. There have been studies that experimentally and computationally looked at slip and deformation twins and the effect of different parameters on their nucleation and growth in HEAs. However, the critical resolved shear stress for slip which indicates the beginning of the plastic deformation region in some of these HEAs has not been found. Also, different factors in deformation twin nucleation and growth have been studied but the effect of grain boundary (GB) types and elemental segregation at GBs have not been fully investigated. In this research experimental and computational approaches are used to further identify the underlying plastic deformation mechanisms in HEAs giving rise to their improved properties. High resolution digital image correlation and electron backscatter diffraction have been used to find the dislocation slip critical resolved shear stress (CRSS) in Al0.3CoCrFeNi polycrystalline under tension. Molecular dynamics (MD) simulations and Monte Carlo molecular dynamics (MCMD) simulations have been used to identify the effect of different symmetric twist GB types and elemental segregation on deformation twins in CoCrFeNi bicrystals at three different temperatures 77 K, 100 K, and 300 K. Experimentally Al0.3CoCrFeNi polycrystalline was tested under tension at room temperature slip CRSS was found to be 63±2 MPa based on the activated slip system of (-1 1 1)[-1 -1 0] which also had the highest Schmid factor of 0.42. The MD simulations and the MCMD simulations studies on the CoCrFeNi HEA bicrystals confirmed GBs as deformation twin nucleation sites. The mechanical properties and deformation twin nucleation changed with different symmetric twist GBs having different sigma values and misorientation angles. MCMD simulations revealed GBs becoming Cr-rich and Ni-deficient which matches the results from experimental observations and MCMD simulations of HEAs of similar compositions. Temperature also was shown to influence the material properties in this alloy. With the decrease in temperature from 600 K, to 300 K, to 77 K, the yield strength and stress, and the overall plastic flow stress increased, and the modulus of elasticity decreased. The mentioned scientific contributions guide HEA design and development with improved properties through GB engineering by populating the polycrystals with symmetric twist grain boundaries of high angle misorientation angles and segregation engineering and designing chromium-rich GBs. As a next step to this research, experimentally, tensile tests at cryogenic temperatures with further post-mortem microscopy can be performed to find the CRSS at cryogenic temperatures and characterize the slip and deformation twins. Computationally, MCMD chemical equilibrium can be continued and reinforcement learning algorithms can be implemented to optimize the process. Furthermore, other types of GBs can be considered and the effect of GB geometry on the elemental segregation itself can be another route branching from this research