Related papers: ESPResSo 4.0 -- An Extensible Software Package for…
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…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and…
We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software to design custom Coarse-Grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides and globular proteins in the Extensible…
Electronic structure simulation (ESS) has been used for decades to provide quantitative scientific insights on an atomistic scale, enabling advances in chemistry, biology, and materials science, among other disciplines. Following standard…
Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory,…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
We review the lattice-Boltzmann (LB) method coupled with the immersed boundary (IB) method for the description of combined flow of particulate suspensions with immersed elastic objects. We describe the implementation of the combined LB-IB…
TENSO is a versatile and powerful open-source software package for numerically exact simulations of the dynamics of quantum systems immersed in structured thermal environments. It is based on a tree tensor network decomposition of the…
We present an open-source software for the simulation of observables in magnetic resonance experiments, including nuclear magnetic/quadrupole resonance NMR/NQR and electron spin resonance (ESR), developed to assist experimental research in…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing…
Soft materials play an integral part in many aspects of modern life including autonomy, sustainability, and human health, and their accurate modeling is critical to understand their unique properties and functions. Today's finite element…
The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named Exploratory…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We…
An emerging theme across many domains of science and engineering is materials that change shape, often dramatically. Determining their structure involves solving a shape optimization problem where a given energy functional is minimized with…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…