Related papers: Scalable and fast heterogeneous molecular simulati…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
We develop numerical multiscale methods for viscous boundary layer flow. The goal is to derive effective boundary conditions, or wall laws, through high resolution simulations localized to the boundary coupled to a coarser simulation in the…
A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), Brownian Dynamics (BD), Green's Function…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
Multi-scale problems, where variables of interest evolve in different time-scales and live in different state-spaces, can be found in many fields of science. Here, we introduce a new recursive methodology for Bayesian inference that aims at…
We present scalable hybrid-parallel algorithms for training large-scale 3D convolutional neural networks. Deep learning-based emerging scientific workflows often require model training with large, high-dimensional samples, which can make…
We propose a decomposition framework for the parallel optimization of the sum of a differentiable function and a (block) separable nonsmooth, convex one. The latter term is typically used to enforce structure in the solution as, for…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for…
In this contribution, a finite element scheme to impose mixed boundary conditions without introducing Lagrange multipliers is presented for hyperbolic systems described as port-Hamiltonian systems. The strategy relies on finite element…
By a high-order numerical homogenization method, a heterogeneous multiscale scheme was developed in Jin & Li (2022) for evolving differential equations containing two time scales. In this paper, we further explore the technique to propose…
A multiscale scheme combining molecular dynamics (MD) and microscopic phase-field theory is proposed to study the structural phase transformations in solids with inhomogeneous strain field. The approach calculates strain response based on…
A new method for the simulation of evolving multi-domains problems has been introduced in a previous work (RealIMotion), Florez et al. (2020). In this article further developments of the model will be presented. The main focus here is a…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
This paper presents a three-scale computational strategy for the study of composite modeled at the mesoscale so that delamination can be reliably simulated. The solver is based on a LaTIn approach so that nonlinearities can be tackled at…
In this work, we derive particle schemes, based on micro-macro decomposition, for linear kinetic equations in the diffusion limit. Due to the particle approximation of the micro part, a splitting between the transport and the collision part…
Spatial decomposition is a popular basis for parallelising code. Cast in the frame of task parallelism, calculations on a spatial domain can be treated as a task. If neighbouring domains interact and share results, access to the specific…
We present a simple, parallel and distributed algorithm for setting up and partitioning a sparse representation of a regular discretized simulation domain. This method is scalable for a large number of processes even for complex geometries…
We seek to accelerate and increase the size of simulations for fluid-structure interactions (FSI) by using multiple resolutions in the spatial discretization of the equations governing the time evolution of systems displaying two-way…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…