Related papers: Thermodynamically Consistent Coarse Graining of Bi…
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…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
We study the coarse-graining approach to derive a generator for the evolution of an open quantum system over a finite time interval. The approach does not require a secular approximation but nevertheless generally leads to a…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
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…
Starting from the stochastic thermodynamics description of two coupled underdamped Brownian particles, we showcase and compare three different coarse-graining schemes leading to an effective thermodynamic description for the first of the…
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…
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…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
In this paper, we examine how to build coarse-grain transport models consistently from the kinetic to fluid regimes. The internal energy of the gas particles is described through a state-to-state approach. A kinetic equation allows us to…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
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…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
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…
Optically confined colloidal particles, when placed in close proximity, form a dissipatively coupled system through hydrodynamic interactions. The role of such interactions influencing irreversibility and energy dissipation in…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We extend classical coarse-grained entropy, commonly used in many branches of physics, to the quantum realm. We find two coarse-grainings, one using measurements of local particle numbers and then total energy, and the second using local…