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Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…

This paper proposes a unified approach for dynamic modeling and simulations of general tensegrity structures with rigid bars and rigid bodies of arbitrary shapes. The natural coordinates are adopted as a non-minimal description in terms of…

We develop estimation for potentially high-dimensional additive structural equation models. A key component of our approach is to decouple order search among the variables from feature or edge selection in a directed acyclic graph encoding…

Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the…

We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…

Computational multi-scale methods capitalize on a large time-scale separation to efficiently simulate slow dynamics over long time intervals. For stochastic systems, one often aims at resolving the statistics of the slowest dynamics. This…

In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…

Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…

Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…

Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…

Model-based design of experiments (MBDOE) is essential for efficient parameter estimation in nonlinear dynamical systems. However, conventional adaptive MBDOE requires costly posterior inference and design optimization between each…

Computational modeling is usually applied to aid experimental exploration of advanced materials to better understand the fundamental plasticity mechanisms during mechanical testing. In this work, we perform Molecular dynamics (MD)…

Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…

We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…

The numerical simulation of structural mechanics applications via finite elements usually requires the solution of large-size and ill-conditioned linear systems, especially when accurate results are sought for derived variables interpolated…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…

Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…

Numerical simulation serves as a cornerstone in scientific modeling, yet the process of fine-tuning simulation parameters poses significant challenges. Conventionally, parameter adjustment relies on extensive numerical simulations, data…