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Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful…
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…
Large language models have emerged as transformative tools in molecular science, demonstrating remarkable potential in molecular property prediction and de novo molecular design. However, their application to spectroscopy remains notably…
Toward the goal of using Scientific Machine Learning (SciML) emulators to improve the numerical representation of aerosol processes in global atmospheric models, we explore the emulation of aerosol microphysics processes under cloud-free…
A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
The numerical simulation of granular systems of even moderate size is a challenging computational problem. In most investigations, either Molecular Dynamics or Event-driven Molecular Dynamics is applied. Here we show that in certain cases,…
The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline…
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
In this review, we highlight recent developments in the application of machine learning for molecular modeling and simulation. After giving a brief overview of the foundations, components, and workflow of a typical supervised learning…
Computations have helped elucidate the dynamics of Earth's mantle for several decades already. The numerical methods that underlie these simulations have greatly evolved within this time span, and today include dynamically changing and…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
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…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…