Related papers: Reverse Coarse-graining for Equation-free Modeling…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in…
Motivated by the understanding of holography as realized in tensor networks, we develop a bulk procedure that can be interpreted as generating a sequence of coarse-grained holographic states. The coarse-graining procedure involves…
We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
The combination of high-dimensionality and disparity of time scales encountered in many problems in computational physics has motivated the development of coarse-grained (CG) models. In this paper, we advocate the paradigm of data-driven…
Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely…
Quantum geometrical molecular dynamics provides a quantum geometric picture for understanding reactive dynamics, especially excited-state conical intersection dynamics, and also a numerically exact method for strongly correlated…
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…
We show how the Equation-Free approach for mutliscale computations can be exploited to extract, in a computational strict and systematic way the emergent dynamical attributes, from detailed large-scale microscopic stochastic models, of…
In molecular dynamics and sampling of high dimensional Gibbs measures coarse-graining is an important technique to reduce the dimensionality of the problem. We will study and quantify the coarse-graining error between the coarse-grained…
We present an application of equation-free computation to the coarse-grained feedback linearization problem of nonlinear systems described by microscopic/stochastic simulators. Feedback linearization with pole placement requires 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…
Identifying the relevant coarse-grained degrees of freedom in a complex physical system is a key stage in developing powerful effective theories in and out of equilibrium. The celebrated renormalization group provides a framework for this…
In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed,…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
In this report we introduce the basic techniques (of the Closed Time Path - Coarse Grained Effective Action CTP-CGEA) and ideas (scaling, coarse-graining and backreaction) behind the treatment of quantum processes in dynamical background…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…