Related papers: ESPResSo 4.0 -- An Extensible Software Package for…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Mathematical modeling is a powerful tool in rheology, and we present pyRheo, an open-source package for Python designed to streamline the analysis of creep, stress relaxation, oscillation, and rotation tests. pyRheo contains a comprehensive…
We present and discuss a framework for computer-aided multiscale analysis, which enables models at a "fine" (microscopic/stochastic) level of description to perform modeling tasks at a "coarse" (macroscopic, systems) level. These…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
The accurate sampling of protein dynamics is an ongoing challenge despite the utilization of High-Performance Computers (HPC) systems. Utilizing only "brute force" MD simulations requires an unacceptably long time to solution. Adaptive…
A number of recent studies have focused on developing surgical simulation platforms to train machine learning (ML) agents or models with synthetic data for surgical assistance. While existing platforms excel at tasks such as rigid body…
We introduce SoliDualSPHysics, a novel open-source and GPU-accelerated software that extends DualSPHysics to enable the numerical simulation of hyperelastic, finite-strain plastic, and brittle fracture behavior in deformable solids within a…
We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations…
The landscape of high- and ultra-high-energy astrophysics has changed in the last decade, largely due to the inflow of data collected by large-scale cosmic-ray, gamma-ray, and neutrino observatories. At the dawn of the multimessenger era,…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Magnetic gels are soft elastic materials consisting of magnetic particles embedded in a polymer network. Their shape and elasticity can be controlled by an external magnetic field, which gives rise to both, engineering and biomedical…
OpenFMO framework, an open-source software (OSS) platform for Fragment Molecular Orbital (FMO) method, is extended to multi-physics simulations (MPS). After reviewing the several FMO implementations on distributed computer environments, the…
We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…
Aimed at the simulation, design, and interpretation of advanced pulse experiments crossing the boundaries between nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR), including the rapidly emerging, hybrid discipline…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
Modern computing systems are capable of exascale calculations, which are revolutionizing the development and application of high-fidelity numerical models in computational science and engineering. While these systems continue to grow in…
Safe reinforcement learning (RL) is crucial for deploying RL agents in real-world applications, as it aims to maximize long-term rewards while satisfying safety constraints. However, safe RL often suffers from sample inefficiency, requiring…
The structure and dynamics of a molecular system is governed by its potential energy surface (PES), representing the total energy as a function of the nuclear coordinates. Obtaining accurate potential energy surfaces is limited by the…