Related papers: Some remarks on free energy and coarse-graining
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…
We present a loss function for neural networks that encompasses an idea of trivial versus non-trivial predictions, such that the network jointly determines its own prediction goals and learns to satisfy them. This permits the network to…
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.…
A new averaging method linking discrete to continuum variables of granular materials is developed and used to derive average balance equations. Its novelty lies in the choice of the decomposition between mean values and fluctuations of…
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…
With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…
We introduce a new class of Fokker-Planck equations associated with an effective generalized thermodynamical framework. These equations describe a gas of Langevin particles in interaction. The free energy can take various forms which can…
The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard…
Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
Spatial multiscale methods have established themselves as useful tools for extending the length scales accessible by conventional statics (i.e., zero temperature molecular dynamics). Recently, extensions of these methods, such as the…
In recent papers, we have argued that kinetically constrained coarse grained models can be applied to understand dynamic properties of glass forming materials, and we have used this approach in various applications that appear to validate…
Physical scenarios that require a relativistic treatment are ubiquitous in nature, ranging from cosmological objects to charge carriers in Dirac materials. Interestingly all of these situations have in common that the systems typically…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
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…
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…
For a 2-dimensional freely jointed chain with 3 particles and a related model, the average and variance of the kinetic energies of each particle in thermal equilibrium are exactly obtained. The same is done for a related model. The excess…
Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been…
The recently introduced concept of generalized thermodynamics is explored here in the context of 1d, 2d and 3d data analysis, performed on samples drawn from a 3d X-ray soil sample image. Different threshold levels are used to binarize the…
To investigate the impact of non-linear interactions on dynamic coarse graining, we study a simplified model system, featuring a tracer particle in a complex environment. Using a projection operator formalism and computer simulations, we…