Related papers: curvedSpaceSim: A framework for simulating particl…
We define an evolution of multiple particles on a discrete manifold $G$. Each particle alone moves on geodesics and particles can interact if they are on the same facet. They move deterministically and reversibly on the frame bundle $P$ of…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
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…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Quantum simulation is making a significant impact on scientific research. The prevailing tendency of the field is to build quantum simulators that get closer to real-world systems of interest, in particular electronic materials. However,…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Spacetime geometry is supposed to be measured by identifying the trajectories of free test particles with geodesics. In practice, this cannot be done because, being described by Quantum Mechanics, particles do not follow trajectories. As a…
Dense suspensions of particles dispersed in liquids are central to industrial and geophysical processes and serve as model systems for out-of-equilibrium soft matter. At high particle concentrations, they exhibit stress-dependent rheology,…
In this work, we present a high-fidelity and efficient point-particle direct numerical simulation framework based on a multi-block overset curvilinear grid system, enabling large-scale Lagrangian particle tracking in complex geometries with…
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…
Quantum particle simulations have largely been based on time-independent, split-operator schemes in which kinetic and potential operators are interwoven to provide accurate approximations to system dynamics. These simulations can be very…
Kinetic plasma processes, such as magnetic reconnection, collisionless shocks, and turbulence, are fundamental to the dynamics of astrophysical and laboratory plasmas. Simulating these processes often requires particle-in-cell (PIC)…
Curvature plays a central organizational role in active polymer dynamics. Using large-scale Langevin-dynamics simulations, we study active semiflexible filaments confined to smooth curved surfaces and map how curvature, bending rigidity,…
This study presents an innovative direct numerical simulation approach for complex particle systems with irregular shapes and large numbers. Using partially saturated methods, it accurately models arbitrary shapes, albeit at considerable…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…