Related papers: A consistency study of coarse-grained dynamical ch…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Volume conserving surface (VCS) models without deposition and evaporation, as well as ideal molecular-beam epitaxy models, are prototypes to study the symmetries of conserved dynamics. In this work we study two similar VCS models with…
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a…
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,…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
An important class of fluid-structure problems involve the dynamics of ordered arrays of immersed, flexible fibers. While specialized numerical methods have been developed to study fluid-fiber systems, they become infeasible when there are…
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…
In this study, a coarse-graining framework for discrete models is formulated on the basis of multiscale homogenization. The discrete model considered in this paper is the Lattice Discrete Particle Model (LDPM), which simulates concrete at…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…