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This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Background and objective: Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell…
Particle tracking has several important applications for solute transport studies in aquifer systems. Travel time distribution at observation points, particle coordinates in time and streamlines are some practical results providing…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by the computational cost. To address this, a surge of deep…
Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density…
Summary: R and Matlab are two high-level scientific programming languages which are frequently applied in computational biology. To extend the wide variety of available and approved implementations, we present the Rcall interface which runs…
The RDF Mapping Language (RML) enables, among other formats, the mapping of tabular data as Comma-Separated Values (CSV) files to RDF graphs. Unfortunately, the widely used spreadsheet format is currently neglected by its specification and…
Monte Carlo Application Toolkit (MCATK) commonly uses surface tracking on a structured mesh to compute scalar fluxes. In this mode, higher fidelity requires more mesh cells and isotopes and thus more computational overhead -- since every…
The analysis of ordinary differential equation (ODE) dynamical systems, particularly in applied disciplines such as mathematical biology and neuroscience, often requires flexible computational workflows tailored to model-specific questions.…
Porting GCC to new architecture requires writing a Machine Description (MD) file that contains mapping from GCC's intermediate form to the target assembly code. Constructing an MD file is a difficult task because it requires the user to…
Modern embedded and cyber-physical systems require every day more performance, power efficiency and flexibility, to execute several profiles and functionalities targeting the ever growing adaptivity needs and preserving execution…
In moir\'e systems, the impact of lattice relaxation on electronic band structures is significant, yet the computational demands of first-principles relaxation are prohibitively high due to the large number of atoms involved. To address…