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We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often…

This paper describes a 2D and 3D simulation engine that quantitatively models the statics, dynamics, and non-linear deformation of heterogeneous soft bodies in a computationally efficient manner. There is a large body of work simulating…

A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…

Quantum simulations of photoexcited low-dimensional systems are pivotal for understanding how to functionalize and integrate novel two-dimensional (2D) materials in next-generation optoelectronic devices. First principles predictions are…

Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…

We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…

Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…

We consider the physical setup of a three-dimensional fluid-structure interaction problem. A viscous compressible gas or liquid interacts with a nonlinear, visco-elastic, three-dimensional bulk solid. The latter is described by a hyperbolic…

We present a computational framework for simulating filaments interacting with rigid bodies through contact. Filaments are challenging to simulate due to their codimensionality, i.e., they are one-dimensional structures embedded in…

Using the molecular dynamics method, we examine a discrete deterministic model for the motion of spherical particles in three-dimensional space. The model takes into account multiparticle collisions in arbitrary forms. Using fractional…

The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…

An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…

We present a system that allows users to visualize complex human motion via 3D motion sculptures---a representation that conveys the 3D structure swept by a human body as it moves through space. Given an input video, our system computes the…

We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…

A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…

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.…

Ultracold dipolar atoms and molecules provide a flexible quantum simulation platform for studying strongly interacting many-body systems. Determining microscopic Hamiltonian parameters of the simulator is crucial for it to be useful. We…

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

This article proposes a novel computational modeling approach for short-ranged molecular interactions between curved slender fibers undergoing large 3D deformations, and gives a detailed overview how it fits into the framework of existing…

We propose a multi-particle self-consistent Hamiltonian (derived from an N-body description) that is applicable for periodic structures such as traveling-wave tubes (TWTs), gyrotrons, free-electron lasers, or particle accelerators. We build…