Related papers: Mxdrfile: read and write Gromacs trajectories with…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the…
Multi-Criteria Decision Making (MCDM) is a branch of operations research used in a variety of domains from health care to engineering to facilitate decision-making among multiple options based on specific criteria. Several R packages have…
Recent advances in materials discovery have been driven by structure-based models, particularly those using crystal graphs. While effective for computational datasets, these models are impractical for real-world applications where atomic…
We present an easily accessible, object oriented code (written exclusively in Matlab) for adaptive finite element simulations in 2D. It features various refinement routines for triangular meshes as well as fully vectorized FEM ansatz spaces…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
To retrieve and compare scientific data of simulations and experiments in materials science, data needs to be easily accessible and machine readable to qualify and quantify various materials science phenomena. The recent progress in open…
Nowadays most of the malware applications are either packed or protected. This techniques are applied especially to evade signature based detectors and also to complicate the job of reverse engineers or security analysts. The time one must…
Background: Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan…
Mixed integer linear programming (MILP) is a powerful tool for planning and control problems because of its modeling capability and the availability of good solvers. However, for large models, MILP methods suffer computationally. In this…
Docking-based virtual screening (VS process) selects ligands with potential pharmacological activities from millions of molecules using computational docking methods, which greatly could reduce the number of compounds for experimental…
Machine learning has been gaining traction in recent years to meet the demand for tools that can efficiently analyze and make sense of the ever-growing databases of biomedical data in health care systems around the world. However,…
Machine Learning Interatomic Potentials (MLIP) are a novel in silico approach for molecular property prediction, creating an alternative to disrupt the accuracy/speed trade-off of empirical force fields and density functional theory (DFT).…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Estimating instruction-level throughput is critical for many applications: multimedia, low-latency networking, medical, automotive, avionic, and industrial control systems all rely on tightly calculable and accurate timing bounds of their…
Molecular dynamics (MD) simulations have become indispensable for exploring tribological deformation patterns at the atomic scale. However, transforming the resulting high-dimensional data into interpretable deformation pattern maps remains…
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high…