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The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…
Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large,…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the according X-ray scattering response in one-dimensional sample structures.…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
The large quantity and high quality of modern radio and infrared line observations require efficient modeling techniques to infer physical and chemical parameters such as temperature, density, and molecular abundances. We present a computer…
The package "fhi96md" is an efficient code to perform density-functional theory total-energy calculations for materials ranging from insulators to transition metals. The package employs first-principles pseudopotentials, and a plane-wave…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Quantum computers hold promise to enable efficient simulations of the properties of molecules and materials; however, at present they only permit ab initio calculations of a few atoms, due to a limited number of qubits. In order to harness…
We present a simple empirical function for the average density profile of cosmic voids, identified via the watershed technique in $\Lambda$CDM N-body simulations. This function is universal across void size and redshift, accurately…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…