Related papers: Polyply: a python suite for facilitating simulatio…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
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…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
In resent years, the software ecosystem for numerical simulation still remains fragmented, with different algorithms and discretization methods often implemented in isolation, each with distinct data structures and programming conventions.…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
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…
This paper presents a lightweight, open-source and high-performance python package for solving peridynamics problems in solid mechanics. The development of this solver is motivated by the need for fast analysis tools to achieve the large…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
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…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Magnetron sputtering is an essential technique in combinatorial materials science, enabling the efficient synthesis of thin-film materials libraries with continuous compositional gradients. For exploring multidimensional search spaces,…