Related papers: Dynamic of a non homogeneously coarse grained syst…
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…
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…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
In this brief article I show how the notion of coarse graining and the Renormalization Group enter naturally in the dynamics of genetic systems, in particular in the presence of recombination. I show how the latter induces a dynamics…
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…
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…
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…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Finding accurate reduced descriptions for large, complex, dynamically evolving networks is a crucial enabler to their simulation, analysis, and, ultimately, design. Here we propose and illustrate a systematic and powerful approach to…
A dynamical atomistic chain to simulate mechanical properties of a one-dimensional material with zero temperature may be modelled by the molecular dynamics (MD) model. Because the number of particles (atoms) is huge for a MD model, in…
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that…
Granular systems confined in a shallow box and driven by vertical vibration provide a simple geometry to study fluidized granular media. Grains gain kinetic energy vertically through collisions with the walls and redistribute it…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard…
Two coarse-grained models which capture some universal characteristics of stripe forming systems are stud- ied. At high temperatures, the structure factors of both models attain their maxima on a circle in reciprocal space, as a consequence…
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…
The Marginally Rigid State is a candidate paradigm for what makes granular material a state of matter distinct from both liquid and solid. Coordination number is identified as a discriminating characteristic, and for rough-surfaced…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
I briefly review a recent series of papers putting forward a coarse-grained theoretical approach to the physics of supercooled liquids approaching their glass transition. After a suitable coarse-graining, the dynamics of the liquid is…