Related papers: Effective dynamics using conditional expectations
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
A thermodynamic formalism describing the efficiency of information learning is proposed, which is applicable for stochastic thermodynamic systems with multiple internal degree of freedom. The learning rate, entropy production rate (EPR),…
The optimization of the conversion of thermal energy into work and the minimization of dissipation for nano- and mesoscopic systems is a complex challenge because of the important role fluctuations play on the dynamics of small systems. We…
We present a coarse-graining method applicable to dry scalar active matter with motility regulation. Our approach, based on a multiscale perturbative expansion of the backward Kolmogorov equation, does not rely on any specific microscopic…
A careful derivation of the generalized Langevin equation using "Zwanzig flavor" projection operator formalism is presented. We provide arguments why this formalism has better properties compared to alternative projection-operator…
Finding reduced models of spatially-distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy…
Fluctuating hydrodynamics provides a quantitative, large-scale description of many-body systems in terms of smooth variables, with microscopic details entering only through a small set of transport coefficients. Although this framework has…
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…
We study coarse-grained (group-level) alignment dynamics of individual-based animal group models for {\it heterogeneous} populations consisting of informed (on preferred directions) and uninformed individuals. The orientation of each…
The R\'enyi entanglement entropy is calculated exactly for mode-partitioned isolated systems such as the two-mode squeezed state and the multi-mode Silbey-Harris polaron ansatz state. Effective thermodynamic descriptions of the correlated…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
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…
When describing the effective dynamics of an observable in a many-body system, the repeated randomness assumption, which states that the system returns in a short time to a maximum entropy state, is a crucial hypothesis to guarantee that…
Modeling a high-dimensional Hamiltonian system in reduced dimensions with respect to coarse-grained (CG) variables can greatly reduce computational cost and enable efficient bottom-up prediction of main features of the system for many…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
We study the motion of an overdamped particle connected to a thermal heat bath in the presence of an external periodic potential in one dimension. When we coarse-grain, i.e., bin the particle positions using bin sizes that are larger than…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
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…
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
An analysis of the dynamics is performed, of exactly solvable models for fragile and strong glasses, exploiting the partitioning of the free energy landscape in inherent structures. The results are compared with the exact solution of the…