Related papers: Systematic Coarse-graining of Epoxy Resins with Ma…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
We present a new framework for coarse-graining molecular dynamics models for crystalline solids. The reduction method is based on a Galerkin projection to a subspace, whose dimension is much smaller than that of the full atomistic model.…
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…
Epoxy polymers are used in wide range of applications. The properties and performance of epoxy polymers depend upon various factors like the type of constituents and their proportions used and other process parameters. The conventional way…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
In computational materials science, coarse-graining approaches often lack a priori uncertainty quantification (UQ) tools that estimate the accuracy of a reduced-order model before it is calibrated or deployed. This is especially the case in…
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 present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
Generative diffusion models can provide powerful prior probability models for inverse problems in imaging, but existing implementations suffer from two key limitations: $(i)$ the prior density is represented implicitly, and $(ii)$ they rely…
Applying an excess entropy scaling formalism to the coarse-grained (CG) dynamics of liquids, we discovered that missing rotational motions during the CG process are responsible for artificially accelerated CG dynamics. In the context of the…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Statistical (machine learning) tools for equation discovery require large amounts of data that are typically computer generated rather than experimentally observed. Multiscale modeling and stochastic simulations are two areas where learning…
Accurate prediction of polymer material properties through data-driven approaches greatly accelerates novel material development by reducing redundant experiments and trial-and-error processes. However, inevitable outliers in empirical…
Although the process variables of epoxy resins alter their mechanical properties, the visual identification of the characteristic features of X-ray images of samples of these materials is challenging. To facilitate the identification, we…
An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond…
Continuum models of dislocation plasticity require constitutive closure assumptions, e.g., by relating details of the dislocation microstructure to energy densities. Currently, there is no systematic way for deriving or extracting such…
Accurate electronic structure calculations are essential in modern materials science, but strongly correlated systems pose a significant challenge due to their computational cost. Traditional methods, such as complete active space…