Related papers: Hybrid Simulation between Molecular Dynamics and B…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal…
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for…
We describe an open source GPU implementation of a hybrid symplectic N-body integrator, GENGA (Gravitational ENcounters with Gpu Acceleration), designed to integrate planet and planetesimal dynamics in the late stage of planet formation and…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
The complexity of binary droplet collisions increases for the collision of immiscible liquids with the occurrence of triple lines and thin encapsulating films. The Volume of Fluid (VOF) method is extended with an efficient interface…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Dielectric barrier discharge (DBD) plasma is used for various applications. DBD is also one of the most efficient and low-cost methods for active fluid flow control. In this study, a detailed physical model of DBD in atmospheric pressure at…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We investigate the spectral properties of plasma turbulence from fluid to sub-ion scales by means of high-resolution three-dimensional (3D) numerical simulations performed with the hybrid particle-in-cell (HPIC) code CAMELIA. We produce…
A new three-dimensional, non-linear Magnetohydrodynamics (MHD) model has been extended in MIPS code, incorporating parallel heat diffusivity. The model has been benchmarked against the former MHD model used in MIPS code. A preliminary study…
We describe an implementation of a particle physics module available for the PLUTO code, appropriate for the dynamical evolution of a plasma consisting of a thermal fluid and a non-thermal component represented by relativistic charged…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…