Related papers: Configurational space discretization and free ener…
First-order energy dissipative schemes in time are available in literature for the Poisson-Nernst-Planck (PNP) equations, but second-order ones are still in lack. This work proposes novel second-order discretization in time and finite…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
Information-theoretic quantities play a crucial role in understanding non-linear relationships between random variables and are widely used across scientific disciplines. However, estimating these quantities remains an open problem,…
We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…
The presence of defects in solids formed by active particles breaks their discrete translational symmetry. As a consequence, many of their properties become space-dependent and different from those characterizing perfectly ordered…
The metriplectic formalism is useful for describing complete dynamical systems which conserve energy and produce entropy. This creates challenges for model reduction, as the elimination of high-frequency information will generally not…
We present a physics-based neural network framework for the discovery of constitutive models in fully coupled thermomechanics. In contrast to classical formulations based on the Helmholtz energy, we adopt the internal energy and a…
We propose utilizing entropy as a diagnostic tool to distinguish between constant and dynamical dark energy models. Entropy, a measure of the system's disorder or information content, captures the complexity and evolution of the universe.…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
Free energy is arguably the most importance function(al) for understanding of molecular systems. A number of rigorous and approximate free energy calculation/estimation methods have been developed over many decades. One important issue, the…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Whether a system is to be considered complex or not depends on how one searches for correlations. We propose a general scheme for calculation of entropies in lattice systems that has high flexibility in how correlations are successively…
Systems with many interacting stochastic constituents are fully characterized by their free energy. Computing this quantity is therefore the objective of various approaches, notably perturbative expansions, which are applied in problems…
Mixed-monotone systems are separable via a decomposition function into increasing and decreasing components, and this decomposition function allows for embedding the system dynamics in a higher-order monotone embedding system. Embedding the…
Automated synthesis of correct-by-construction controllers for autonomous systems is crucial for their deployment in safety-critical scenarios. Such autonomous systems are naturally modeled as stochastic dynamical models. The general…
It is often stated that if one is presented with a snapshot of the positions of the molecules of a glass and one of a liquid, one is unable to tell the difference. Here we argue instead that given several such snapshots taken over a…
This paper formulates variational integrators for finite element discretizations of deformable bodies with heat conduction in the form of finite speed thermal waves. The cornerstone of the construction consists in taking advantage of the…
The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…
Predictive simulations of complex systems are essential for applications ranging from weather forecasting to drug design. The veracity of these predictions hinges on their capacity to capture the effective system dynamics. Massively…