Related papers: Cell List Algorithms for Nonequilibrium Molecular …
In this paper, a practicable simulation-free model order reduction method by nonlinear moment matching is developed. Based on the steady-state interpretation of linear moment matching, we comprehensively explain the extension of this…
The simulation of large nonlinear dynamical systems, including systems generated by discretization of hyperbolic partial differential equations, can be computationally demanding. Such systems are important in both fluid and kinetic…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box…
This paper presents a novel approach to the description and understanding of two-dimensional binary cellular automata with the Moore neighborhood that preserve the number of active cells. Such dynamical systems are known to successfully…
Kinetic instabilities are one of the most challenging aspects in computational plasma physics. Accurately capturing their onset and evolution requires fine resolution of the high-dimensional distribution functions of each relevant species,…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
Quantum computing holds great promise to accelerate scientific computations in fluid dynamics and other classical physical systems. While various quantum algorithms have been proposed for linear flows, developing quantum algorithms for…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
Model reduction for fluid flow simulation continues to be of great interest across a number of scientific and engineering fields. Here, we explore the use of Neural Ordinary Differential Equations, a recently introduced family of…
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…
Parallel multiphysics simulations often suffer from load imbalances originating from the applied coupling of algorithms with spatially and temporally varying workloads. It is thus desirable to minimize these imbalances to reduce the time to…
The quasi-neutral hybrid model with kinetic ions and fluid electrons is a promising approach for bridging the inherent multi-scale nature of many problems in space and laboratory plasmas. Here, a novel, implicit, particle-in-cell based…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient…
We demonstrate how three-dimensional fluid flow simulations can be carried out on the Cellular Automata Machine 8 (CAM-8), a special-purpose computer for cellular-automata computations. The principal algorithmic innovation is the use of a…
The Active Flux scheme is a finite volume scheme with additional point values distributed along the cell boundary. It is third order accurate and does not require a Riemann solver. Instead, given a reconstruction, the initial value problem…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…