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Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate. Recent advances in large language models (LLM) have demonstrated success in automating complex scientific tasks…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler…
The "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface to common molecular dynamics codes, enabling rapid and portable development of…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
In the past decade, deep learning (DL) has achieved unprecedented success in numerous fields including computer vision, natural language processing, and healthcare. In particular, DL is experiencing an increasing development in applications…
Force field-based molecular dynamics (MD) simulations are indispensable for probing the structure, dynamics, and functions of biomolecular systems, including proteins and protein-ligand complexes. Despite their broad utility in drug…
The globalization of markets and world-wide competition forces manufacturing enterprises to enter into alliances leading to the creation of distributed manufacturing enterprises. Before forming a partnership it is essential to evaluate…
GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries…
Remarkable progress has been made in automated problem solving through societies of agents based on large language models (LLMs). Computational fluid dynamics (CFD), as a complex problem, presents unique challenges in automated simulations…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
The Non-Markovian Stochastic Schrodinger Equation (NMSSE) offers a promising approach for open quantum simulations, especially in large systems, owing to its low scaling complexity and suitability for parallel computing. However, its…