Related papers: Performance Analysis on Molecular Dynamics Simulat…

Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…

PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…

Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…

Most recently, the path integral molecular dynamics has been successfully used to consider the thermodynamics of single-component identical bosons and fermions. In this work, the path integral molecular dynamics is developed to simulate the…

We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…

Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…

The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…

The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the…

Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…

This computational experiment demonstrates that chain melting in lipids is a molecular process. BOMD is certainly the best method to reproduce such dynamics properties, since the electronic contributions to the various molecular structures…

Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…

Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…

We consider the problem of estimating the error when solving a system of differential algebraic equations. Richardson extrapolation is a classical technique that can be used to judge when computational errors are irrelevant and estimate the…

MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for…

One way to access the aggregated power of a collection of heterogeneous machines is to use a grid middleware, such as DIET, GridSolve or NINF. It addresses the problem of monitoring the resources, of handling the submissions of jobs and as…

Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…

High-performance graphical processing units (GPU) are used for the repeated parallelised propagation of non-linear partial differential equations on large spatio-temporal grids. The main challenge results as a combination of the requirement…

Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…

Magnetic skyrmions are magnetic quasi-particles with enhanced stability and different manipulation mechanisms using external fields and currents making them promising candidates for future applications for instance in neuromorphic…