Related papers: PLUMED: a portable plugin for free-energy calculat…
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…
Probabilistic Programming Languages (PPLs) are a powerful tool in machine learning, allowing highly expressive generative models to be expressed succinctly. They couple complex inference algorithms, implemented by the language, with an…
The article deals with a number of the existings variants of direct calculation of amplitudes of processes with polarized Dirac particles. It is shown, that all of them are special cases of one and the same mathematical scheme. The…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Fluid flow simulation is a highly active area with applications in a wide range of engineering problems and interactive systems. Meshless methods like the Moving Particle Semi-implicit (MPS) are a great alternative to deal efficiently with…
Perturbo is a software package for first-principles calculations of charge transport and ultrafast carrier dynamics in materials. The current version focuses on electron-phonon interactions and can compute phonon-limited transport…
Simulations of colloidal suspensions consisting of mesoscopic particles and smaller species such as ions or depletants are computationally challenging as different length and time scales are involved. Here, we introduce a machine learning…
A MATLAB program has been developed for simulation of polymer blend self-assembly with nano-scaled features. The Cahn-Hilliard equation is implemented to calculate the free energy profile of the polymer blends. The Flory-Huggins type of…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
We present a framework for efficiently performing Monte Carlo wave-function simulations in cavity QED with moving particles. It relies heavily on the object-oriented programming paradigm as realised in C++, and is extensible and applicable…
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…
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…
An improved implementation of an N-body code for simulating collisionless cosmological dynamics is presented. TPM (Tree-Particle-Mesh) combines the PM method on large scales with a tree code to handle particle-particle interactions at small…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Developing engineering systems that rely on flow-induced reconfiguration, the phenomenon where a structure deforms under flow to reduce its drag, requires design tools that can predict the behavior of these flexible structures. Current…
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
The paper develops a method for the numerical simulation of a free-surface flow of incompressible viscous fluid around a streamlined body. The body is a rigid stationary construction partially submerged in the fluid. The application we are…
The progression of scientific computing resources has enabled the numerical approximation of mathematical models describing complex physical phenomena. A significant portion of researcher time is typically dedicated to the development of…