Related papers: Thermodynamically Consistent Coarse-graining: from…
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…
Recent theories predict phase separation among orientationally disordered active particles whose propulsion speed decreases rapidly enough with density. Coarse-grained models of this process show time-reversal symmetry (detailed balance) to…
We extend the analysis of the thermodynamics of the climate system by investigating the role played by processes taking place at various spatial and temporal scales through a procedure of coarse graining. The coarser is the graining of the…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
While linear response theory, manifested by the fluctuation dissipation theorem, can be applied at any level of coarse graining, nonlinear response theory is fundamentally of microscopic nature. For perturbations of equilibrium systems, we…
We investigate fundamental connections between thermodynamics and quantum information theory. First, we show that the operational framework of thermal operations is nonequivalent to the framework of Gibbs-preserving maps, and we comment on…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
In this paper, we focus on the data-driven discovery of a general second-order particle-based model that contains many state-of-the-art models for modeling the aggregation and collective behavior of interacting agents of similar size and…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…
The goal of this thesis is to obtain new exact results for models of active particles in one dimension, focusing on two different aspects: their behavior in the presence of long-range interactions and their first-passage properties. In the…
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…
We formulate a generalized self-consistent stochastic quantum kinetic theory for finite-temperature ultracold Bose gases interacting via a generic long-range interaction, applicable to a broad range of systems, by means of Keldysh…
Within a continuous-time, stochastic model of single-cell size homeostasis, we study how the structure of feedback from size to growth rates and cell-cycle progression shapes overall size dynamics, both within and across cell cycles. We…
In this work, we derive a coarse-grained finite-temperature theory for a Bose condensate in a one-dimensional optical lattice, in addition to a confining harmonic trap potential. We start from a two-particle irreducible (2PI) effective…
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…
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…
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…
We propose a probabilistic model for refining coarse-grained spatial data by utilizing auxiliary spatial data sets. Existing methods require that the spatial granularities of the auxiliary data sets are the same as the desired granularity…
Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master Equation that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…