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A recently proposed class of machine-learning interatomic potentials --- Moment tensor potentials (MTPs) --- is investigated in this work. MTPs are able to actively select configurations and parametrize the potential on-the-fly. It is shown…
The maximum entropy production (MEP) principle is a hypothetical law of physics which dictates that complex systems, far from equilibrium, evolve into an ordered dissipative structure (DS) which generates as much entropy per second as…
We study the high-frequency micro-mechanical response of suspensions composed by cardiac and skeletal muscle myosin by optical trapping interferometry. We observe that in low ionic strength solutions upon the addition of magnesium adenosine…
This thesis focuses on three fundamental aspects of biological systems; namely, entropy production, Bayesian mechanics, and the free-energy principle. The contributions are threefold: 1) We compute the entropy production for a greater class…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
Recent fluorescence spectroscopy measurements of single-enzyme kinetics have shown that enzymatic turnovers form a renewal stochastic process in which the inverse of the mean waiting time between turnovers follows the Michaelis-Menten…
In this paper we study multi-matrix models whose potentials are perturbations of the quadratic potential associated with independent GUE random matrices. More precisely, we compute the free energy and the expectation of the trace of…
The objective of this manuscript consists in a critical consideration of the Maximum Entropy Production Principle (MEPP) and an analysis of its corollaries for some (primarily morphological) nonequilibrium phase transitions.
It is well known that collisionless systems are dissipation free from the perspective of particle collision and thus conserve entropy. On the other hand, processes such as magnetic reconnection and turbulence appear to convert large-scale…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
The question of characterization of the degree of non-equilibrium activity in active matter systems is studied in the context of a stochastic microswimmer model driven by a chemical cycle. The resulting dynamical properties and entropy…
It is argued that a typical many body energy eigenstate has a well defined thermodynamic entropy and that individual eigenstates possess thermodynamic characteristics analogous to those of generic isolated systems. We examine large systems…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport,…
An expression is derived for the free energy of nonideal atomic plasma, which corresponds to exact asymptotic expansions. The analytical dependence of correction for the interaction of free charges on the partition function of atom is…
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy…
Entropy, its production, and its change in a dynamical system can be understood from either a fully stochastic dynamic description or from a deterministic dynamics exhibiting chaotic behavior. By taking the former approach based on the…
Stochastic dynamics with random resetting leads to a non-equilibrium steady state. Here, we consider the thermodynamics of resetting by deriving the first and second law for reset processes far from equilibrium. We identify the…
Recent studies have shown that the entropy production rate for the master equation consists of two nonnegative terms: the adiabatic and non-adiabatic parts, where the non-adiabatic part is also known as the dissipation rate of a…
We introduce a family of Maxwellian Demons for which correlations among information bearing degrees of freedom can be calculated exactly and in compact analytical form. This allows one to precisely determine Demon functional thermodynamic…