Related papers: Correction of coarse-graining errors by a two-leve…

We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…

Significant efforts have been devoted in the last decade towards improving the predictivity of coarse-grained models in molecular dynamics simulations and providing a rigorous justification of their use, through a combination of theoretical…

Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical…

In this paper we present a systematic, data-driven approach to discovering "bespoke" coarse variables based on manifold learning algorithms. We illustrate this methodology with the classic Kuramoto phase oscillator model, and demonstrate…

We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving…

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…

We extend our previously developed coarse-graining strategy for linear polymers with a tunable number n of effective atoms (blobs) per chain [D'Adamo et al., J. Chem. Phys. 137, 4901 (2012)] to polymer systems in thermal crossover between…

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…

The objective of this work is to assess computationally efficient coarse-grained plasticity models against high-fidelity crystal plasticity simulations for magnesium polycrystals over a wide range of textures and grain sizes. A basic…

We consider the problem of coarse-graining in the context of finite-volume fluid models. If a variable is defined on a high-resolution grid it may be coarse-grained so that it is defined on a grid of lower resolution. In general this will…

We develop a simple model, in the spirit of the Asakura-Oosawa theory, able to describe the effects of surface roughness on the depletion potential as a function of a small set of parameters. The resulting explicit expressions are easily…

The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-Polybutadiene melts where each…

Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations…

Starting from a coarse-grained map of a quantum many-body system, we construct the inverse map that assigns a microscopic state to a coarse-grained state based on the maximum entropy principle. Assuming unitary evolution in the microscopic…

We study the structure and phase behavior of a binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the Asakura-Oosawa model, for colloid-polymer mixtures,…

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…

We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the…

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…

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…

To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…