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The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Correlation among the observations in high-dimensional regression modeling can be a major source of confounding. We present a new open-source package, plmmr, to implement penalized linear mixed models in R. This R package estimates…
We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as…
Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which…
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…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
We present LBsoft, an open-source software developed mainly to simulate the hydro-dynamics of colloidal systems based on the concurrent coupling between lattice Boltzmann methods for the fluid and discrete particle dynamics for the…
We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
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…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
We present POMDPPlanners, an open-source Python package for empirical evaluation of Partially Observable Markov Decision Process (POMDP) planning algorithms. The package integrates state-of-the-art planning algorithms, a suite of benchmark…
We introduce a Markov Chain Monte Carlo simulation and data analysis package that extends the CMBEASY software. We have taken special care in implementing an adaptive step algorithm for the Markov Chain Monte Carlo in order to improve…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…