Related papers: Scalable and fast heterogeneous molecular simulati…
Numerical simulations for flow and transport in subsurface porous media often prove computationally prohibitive due to property data availability at multiple spatial scales that can vary by orders of magnitude. A number of model order…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Network models are used as efficient representation of materials with complex, interconnected locally one-dimensional structures. They typically accurately capture the mechanical properties of a material, while substantially reducing…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
The life of the modern world essentially depends on the work of the large artificial homogeneous networks, such as wired and wireless communication systems, networks of roads and pipelines. The support of their effective continuous…
The Classic Howard's algorithm, a technique of resolution for discrete Hamilton-Jacobi equations, is of large use in applications for its high efficiency and good performances. A special beneficial characteristic of the method is the…
We propose a domain decomposition method for the efficient simulation of nonlocal problems. Our approach is based on a multi-domain formulation of a nonlocal diffusion problem where the subdomains share "nonlocal" interfaces of the size of…
The increasing complexity and scale of photonic and electromagnetic devices demand efficient and accurate numerical solvers. In this work, we develop a parallel overlapping domain decomposition method (DDM) based on the finite-difference…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
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…
Multiscale techniques have been widely shown to potentially overcome the limitation of homogenization schemes in representing the microscopic failure mechanisms in heterogeneous media as well as their influence on their structural response…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
This paper presents an algorithm for sampling random variables that allows to separation of the sampling process into subproblems by dividing the sample space into overlapping parts. The subproblems can be solved independently of each other…
Agent-based modelling constitutes a versatile approach to representing and simulating complex systems. Studying large-scale systems is challenging because of the computational time required for the simulation runs: scaling is at least…
In this paper, a parallel overlapping domain decomposition preconditioner is proposed to solve the linear system of equations arising from the extended finite element discretization of elastic crack problems. The algorithm partitions the…
We present a fully adaptive multiresolution scheme for spatially two-dimensional, possibly degenerate reaction-diffusion systems, focusing on combustion models and models of pattern formation and chemotaxis in mathematical biology.…
A micromorphic computational homogenization framework has recently been developed to deal with materials showing long-range correlated interactions, i.e. displaying patterning modes. Typical examples of such materials are elastomeric…
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…