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A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical and thermodynamical properties in…
In this paper we focus on the development of new methods suitable for efficient and reliable coarse-graining of {\it non-equilibrium} molecular systems. In this context, we propose error estimation and controlled-fidelity model reduction…
A kinetic model for granular mixtures is considered to study three different non-equilibrium situations. The model is based on the equivalence between a gas of elastic hard spheres subjected to a drag force proportional to the particle…
Stochastic reduced-order models are widely used to represent the effective dynamics of complex systems, but estimating their drift and diffusion coefficients from data remains challenging. Standard approaches often rely on short-time…
A valuable step in the modeling of multiscale dynamical systems in fields such as computational chemistry, biology, materials science and more, is the representative sampling of the phase space over long timescales of interest; this task is…
Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat…
Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating and responsive media, e.g., polymeric materials such…
By reducing the number of global synchronization bottlenecks per iteration and hiding communication behind useful computational work, pipelined Krylov subspace methods achieve significantly improved parallel scalability on present-day HPC…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
Granular systems confined in a shallow box and driven by vertical vibration provide a simple geometry to study fluidized granular media. Grains gain kinetic energy vertically through collisions with the walls and redistribute it…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
State estimation techniques for continuum robots (CRs) typically involve using computationally complex dynamic models, simplistic shape approximations, or are limited to quasi-static methods. These limitations can be sensitive to unmodelled…
The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation (GLE) describes coarse-grained dynamics in reduced…
We identify the mechanism of slow heterogeneous relaxation in quantum kinetically constrained models (KCMs) in which the potential energy strength is controlled by a coupling parameter. The regime of slow relaxation includes the…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
A new framework is introduced for constructing interpretable and truly reliable reduced models for multiscale problems in situations without scale separation. Hydrodynamic approximation to the kinetic equation is used as an example to…
Molecular simulations as well as single molecule experiments have been widely analyzed in terms order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive,…