Related papers: Parallel computing and molecular dynamics of biolo…
Computer models are used as replacements for physical experiments in a large variety of applications. Nevertheless, direct use of the computer model for the ultimate scientific objective is often limited by the complexity and cost of the…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
We present and compare distributed parallelization strategies for the particle-in-Fourier (PIF) schemes used in kinetic plasma simulations. The different strategies are i) domain decomposition, where both the particles and Fourier modes are…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The dynamics of membranes, shells and capsules in fluid flow has become an active research area in computational physics and computational biology. The small thickness of these elastic materials enables their efficient approximation as a…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
It is known that the maximum diameter for the rupture-risk assessment of the abdominal aortic aneurysm is a generally good method, but not sufficient. Alternative features obtained with computational modeling may provide additional useful…
The numerical solution of large-scale PDEs, such as those occurring in data-driven applications, unavoidably require powerful parallel computers and tailored parallel algorithms to make the best possible use of them. In fact, considerations…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
In this work, we derive particle schemes, based on micro-macro decomposition, for linear kinetic equations in the diffusion limit. Due to the particle approximation of the micro part, a splitting between the transport and the collision part…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
Several methods for density matrix propagation in distributed computing environments, such as clusters and graphics processing units, are proposed and evaluated. It is demonstrated that the large communication overhead associated with each…
We describe computational tools that have been developed to simulate dynamical mass transfer in semi-detached, polytropic binaries that are initially executing synchronous rotation upon circular orbits. Initial equilibrium models are…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…