Related papers: A symplectic integrator for molecular dynamics on …
We develop a modeling and simulation framework capable of massively parallel simulation of multicellular systems with spatially resolved stochastic kinetics in individual cells. By the use of operator-splitting we decouple the simulation of…
We present a novel hierarchical formulation of the fourth-order forward symplectic integrator and its numerical implementation in the GPU-accelerated direct-summation N-body code FROST. The new integrator is especially suitable for…
In this paper we study the performance of a symplectic numerical integrator based on the splitting method. This method is applied to a subtle problem i.e. higher order resonance of the elastic pendulum. In order to numerically study the…
We present the IAMReX, an adaptive and parallel solver for particle-resolved simulations on the multi-level grid. The fluid equations are solved using a finite-volume scheme on the block-structured semi-staggered grids with both subcycling…
High-intensity laser plasma interactions create complex computational problems because they involve both fluid and kinetic regimes, which need models that maintain physical precision while keeping computational speed. The research…
We investigate the performance of various methods of symplectic integration, which are based on two part splitting of the integration operator, for the numerical integration of multidimensional Hamiltonian systems. We implement these…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
The plasma edge flow, situated at the intricate boundary between plasma and neutral particles, plays a pivotal role in the design of nuclear fusion devices such as divertors and pumps. Traditional numerical simulation methods, such as the…
We develop a numerical method for simulating the dynamics of a droplet immersed in a generic time-dependent velocity gradient field. This approach is grounded on the hybrid coupling between the lattice Boltzmann (LB) method, employed for…
We present a new formulation of non-dissipative relativistic spin hydrodynamics that incorporates spin degrees of freedom into the divergence-type theory framework. Due to the divergence-type structure, it is straightforward to enforce…
This study aims to exploit the analogy of vortex dynamics in a 2D ideal fluid and 2D non-neutral plasma. Numerical simulations using contour dynamics with adaptive refinement are conducted to study the dynamics of one or more vortices…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
Geometric aspects play an important role in the construction and analysis of structure-preserving numerical methods for a wide variety of ordinary and partial differential equations. Here we review the development and theory of symplectic…
In this paper, we develop a multiscale hierarchy framework for objective molecular dynamics (OMD), a reduced order molecular dynamics with a certain symmetry, that connects it to the statistical kinetic equation, and the macroscopic…
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…
We formulate and test a hybrid fluid-Monte Carlo scheme for the treatment of elastic collisions in gases and plasmas. While our primary focus and demonstrations of applicability are for moderately collisional plasmas, as described by the…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…