Related papers: PolyHoop: Soft particle and tissue dynamics with t…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
We introduce the `nhppp' package for simulating events from one-dimensional non-homogeneous Poisson point processes (NHPPPs) in R fast and with a small memory footprint. We developed it to facilitate the sampling of event times in discrete…
Multiscale modeling, which integrates material properties from ab initio calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while ab initio methods…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
The accurate, reliable and efficient numerical approximation of multi-physics processes in heterogeneous porous media with varying media coefficients that include fluid flow and structure interactions is of fundamental importance in energy,…
The Cellular Automaton (CA) modeling and simulation of solid dynamics is a long-standing difficult problem. In this paper we present a new two-dimensional CA model for solid dynamics. In this model the solid body is represented by a set of…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…
The PointHop method was recently proposed by Zhang et al. for 3D point cloud classification with unsupervised feature extraction. It has an extremely low training complexity while achieving state-of-the-art classification performance. In…
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We…
Modal synthesis is an important area of physical modeling whose exploration in the past has been held back by a large number of control parameters, the scarcity of general-purpose design tools and the difficulty of obtaining the…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
A unified simulator that can model diverse physical phenomena without solver-specific redesign is a long-standing goal across simulation science. We present a learning-based particle simulator built on a single transformer architecture to…
Diffuse-interface theory provides a foundation for the modeling and simulation of microstructure evolution in a very wide range of materials, and for the tracking/capturing of dynamic interfaces between different materials on larger scales.…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
Differentiable physics simulation provides an avenue to tackle previously intractable challenges through gradient-based optimization, thereby greatly improving the efficiency of solving robotics-related problems. To apply differentiable…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense…