相关论文: Parallel computing and molecular dynamics of biolo…
Approximate Bayes Computations (ABC) are used for parameter inference when the likelihood function of the model is expensive to evaluate but relatively cheap to sample from. In particle ABC, an ensemble of particles in the product space of…
The development of cost-effective highperformance parallel computing on multi-processor supercomputers makes it attractive to port excessively time consuming simulation software from personal computers (PC) to super computes. The power…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
The numerical simulation of cardiac electrophysiology is a highly challenging problem in scientific computing. The Bidomain system is the most complete mathematical model of cardiac bioelectrical activity. It consists of an elliptic and a…
Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has…
We present benchmark computations of dynamic poroelasticity modeling fluid flow in deformable porous media by a coupled hyperbolic-parabolic system of partial differential equations. A challenging benchmark setting and goal quantities of…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
Discrete particle simulations are widely used to study large-scale particulate flows in complex geometries where particle-particle and particle-fluid interactions require an adequate representation but the computational cost has to be kept…
A parallel direct solution approach based on domain decomposition method (DDM) and directed acyclic graph (DAG) scheduling is outlined. Computations are represented as a sequence of small tasks that operate on domains of DDM or dense matrix…
Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…