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Coarse-graining is central to reducing dimensionality in molecular dynamics, and is typically characterized by a mapping which projects the full state of the system to a smaller class of variables. While extensive literature has been…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…
We introduce a general framework for deriving effective dynamics from arbitrary time-dependent generators, based on a systematic operator cumulant expansion. Unlike traditional approaches, which typically assume periodic or adiabatic…
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Constrained quantum dynamics is used to propose a nonlinear dynamical equation for pure states of a generalized coarse-grained system. The relevant constraint is given either by the generalized purity or by the generalized invariant…
Hybrid multiscale modelling has emerged as a useful framework for modelling complex biological phenomena. However, when accounting for stochasticity in the internal dynamics of agents, these models frequently become computationally…
We present a coarse-graining (or model order reduction) procedure for stochastic matrices by clustering. The method is consistent with the natural structure of Markov theory, preserving positivity and mass, and does not rely on any tools…
Magnus expansion is used to identify effective Hamiltonians describing the coarse-grained dynamics of more complex problems. Here, we apply this method to a two-level system driven by an and AC field. We derive Stark and Bloch-Siegert shifs…
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 explain a method, inspired by control theory model reduction and interpolation theory, that rigorously establishes the types of coarse graining that are appropriate for systems with quadratic, generalized Hamiltonians. For such systems,…
Finite stochastic Markov models play a major role for modelling biochemical pathways. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a…
We develop coarse-graining schemes for stochastic many-particle microscopic models with competing short- and long-range interactions on a d-dimensional lattice. We focus on the coarse-graining of equilibrium Gibbs states and using cluster…
We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…
We investigate nonequilibrium steady-state dynamics in both continuous- and discrete-state stochastic processes. Our analysis focuses on planar diffusion dynamics and their coarse-grained approximations by discrete-state Markov chains.…
Transient bonds between fast linkers and slower particles are widespread in physical and biological systems. In spite of their diverse structure and function, a commonality is that the linkers diffuse on timescales much faster compared to…
We poorly understand the macroscopic properties of complex fluids and of amorphous bodies in general. This is mainly due to the interplay between phenomena at different levels and length-scales. In particular, it is not necessarily true…
We use the system-plus-reservoir approach to study the quantum dynamics of a bipartite continuous variable system (two generic particles). We present an extension of the traditional model of a bath of oscillators which is capable of…
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.…