Related papers: Some remarks on free energy and coarse-graining
We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a 1D Rouse chain or as an approximate model of single file diffusion. We discuss mainly two levels of description of this system:…
Inspired by holographic Wilsonian renormalization, we consider coarse graining a quantum system divided between short distance and long distance degrees of freedom, coupled via the Hamiltonian. Observations using purely long distance…
We formulate an effective-description framework for the dynamics of open quantum systems by extending the time-coarse-graining formalism to open systems. Our coarse-graining procedure efficiently removes high-frequency processes which are…
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 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 develop a rigorous error analysis for coarse-graining of defect-formation free energy. For a one-dimensional constrained atomistic system, we establish the thermodynamic limit of the defect-formation free energy and obtain explicitly the…
The critical behaviour of a system of two coupled scalar fields in three dimensions is studied within the formalism of the effective average action. The fixed points of the system are identified and the crossover between them is described…
A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained conformational dynamics. Constrained by the fluctuation-dissipation theorem, the…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
We present the conceptual and technical background required to describe and understand the correlations and fluctuations of the empirical density and current of steady-state diffusion processes on all time scales -- observables central to…
We consider Adaptively Restrained Langevin dynamics, in which the kinetic energy function vanishes for small velocities. Properly parameterized, this dynamics makes it possible to reduce the computational complexity of updating…
A large class of quantum and statistical field theoretical models, encompassing relevant condensed matter and non-abelian gauge systems, are defined in terms of complex actions. As the ordinary Monte-Carlo methods are useless in dealing…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
Equations of motion for the microscopic number density $\hat{\rho}({\bf x},t)$ and the momentum density $\hat{\bf g}({\bf x},t)$ of a fluid have been obtained in the past from the corresponding Langevin equations representing the dynamics…
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise…
We consider two basic types of coarse-graining: the Ehrenfests' coarse-graining and its extension to a general principle of non-equilibrium thermodynamics, and the coarse-graining based on uncertainty of dynamical models and Epsilon-motions…
In many far-from-equilibrium biological systems, energy injected by irreversible processes at microscopic scales propagates to larger scales to fulfill important biological functions. But given dissipative dynamics at the microscale, how…
We apply the functional Renormalisation Group (fRG) to study relaxation in a stochastic process governed by an overdamped Langevin equation with one degree of freedom, exploiting the connection with supersymmetric quantum mechanics in…
This article provides non-trivial technical ingredients for the article "The quantitative hydrodynamic limit of the Kawasaki dynamics" by the same authors. In that work a quantitative version of the hydrodynamic limit is deduced using a…
In the field of machine learning coarse-grained potentials in molecular dynamics, many propagators require that the effective Hamiltonian is quadratic in momentum, thus limiting the family of coarse-graining functions. In this paper, we…