Related papers: Coarse-graining strategy for modeling effective, h…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational…
Granular systems are not always homogeneous and can be composed of grains with very different mechanical properties. To improve our understanding of the behavior of real granular systems, in this experimental study, we compress 2D…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
In recent papers, we have argued that kinetically constrained coarse grained models can be applied to understand dynamic properties of glass forming materials, and we have used this approach in various applications that appear to validate…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
We conduct molecular dynamics simulations of a bidisperse Kob-Andersen (KA) glass former, modified to add in additional polydispersity. The original KA system is known to exhibit dynamical heterogeneity. Prior work defined propensity, the…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general…
Coarse-graining is central to reducing dimensionality in molecular dynamics, and is typically characterized by a mapping which projects the full state of the system to a smaller class of variables. While extensive literature has been…
We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density…
We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…
We present a coarse-graining method applicable to dry scalar active matter with motility regulation. Our approach, based on a multiscale perturbative expansion of the backward Kolmogorov equation, does not rely on any specific microscopic…
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on…
In this paper, a statistical physical derivation of thermodynamically consistent fluid mechanical equations is presented for non-isothermal viscous molecular fluids. The coarse-graining process is based on (i) the adiabatic expansion of the…
We present several numerical results on granular mixtures. In particular, we examine the efficiency of diffusion as a mixing mechanism in these systems. The collisions are inelastic and to compensate the energy loss, we thermalize the…