Related papers: The Mesoscopic Partition Function:A Combined Spati…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
We present a solution to the problem of AC current partition in a multi-probe mesoscopic conductor within the nonequilibrium Green's function formalism. This allows the derivation of dynamic conductance which is appropriate for…
Non-Gaussian likelihoods, ubiquitous throughout cosmology, are a direct consequence of nonlinearities in the physical model. Their treatment requires Monte-Carlo Markov-chain or more advanced sampling methods for the determination of…
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.…
Motivated by the understanding of holography as realized in tensor networks, we develop a bulk procedure that can be interpreted as generating a sequence of coarse-grained holographic states. The coarse-graining procedure involves…
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…
Complex physical dynamics can often be modeled as a Markov jump process between mesoscopic configurations. When jumps between mesoscopic states are mediated by thermodynamic reservoirs, the time-irreversibility of the jump process is a…
A formalism for quantum many-body systems is proposed through a semiclassical treatment in phase space, allowing us to establish a stochastic thermodynamics incorporating quantum statistics. Specifically, we utilize a stochastic…
The rich and diverse dynamics of particle-based systems ultimately originates from the coupling of their degrees of freedom via internal interactions. To arrive at a tractable approximation of such many-body problems, coarse-graining is…
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…
Mesoscopic density functional theory for inhomogeneous mixtures of sperical particles is developed in terms of mesoscopic volume fractions by a systematic coarse-graining procedure starting form microscopic theory. Approximate expressions…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
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…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
The Mesoscopic Mechanics (MeM), which has been introduced in a previous paper, is relevant to the electron gas confined to two spatial dimensions. It predicts a special way of collective response of correlated electrons to the external…
We calculate the phase space volume $\Omega$ occupied by a nonextensive system of $N$ classical particles described by an equilibrium (or steady-state, or long-term stationary state of a nonequilibrium system) distribution function, which…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
We present general results on fluctuations and spatial correlations of the coarse-grained empirical density and current of Markovian diffusion in equilibrium or non-equilibrium steady states on all time scales. We unravel a deep connection…
We derive a class of mesoscopic virial equations governing energy partition between conjugate position and momentum variables of individual degrees of freedom. They are shown to apply to a wide range of nonequilibrium steady states with…