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Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe". It remains a question what the minimally required description for the…
Entropy production is the crucial quantity characterizing irreversible phenomena and the second law of thermodynamics. Yet, a ubiquitous definition eludes consensus. Given that entropy production arises from incomplete access to…
The rate of entropy production by a stochastic process quantifies how far it is from thermodynamic equilibrium. Equivalently, entropy production captures the degree to which detailed balance and time-reversal symmetry are broken. Despite…
Herein (the first part of my work), I debunk the long-standing hypotheses that explain mitochondrial oxidative phosphorylation. Simple calculations point out that mitochondria are highly proton-deficient microcosms and therefore, elaborate…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
All cells must sustain ionic motive forces (IMFs) -- the electrochemical gradients of permeant ions, together with the membrane potential they produce -- to regulate intracellular pH, drive secondary transport, and power ATP synthesis.…
A demonic being, introduced by Maxwell, to miraculously create thermal non-equilibrium and violate the Second law of thermodynamics, has been among the most intriguing and elusive wishful concepts for over 150 years. Maxwell and his…
Chemical gradients provide the primordial energy for biological functions by driving the mechanical movement of microscopic engines. Their thermodynamic properties remain elusive, especially concerning the dynamic change in energy demand in…
In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by…
Delta degrees of freedom are introduced into antisymmetrized molecular dynamics (AMD). This is done by increasing the number of basic states in the AMD wave function, introducing a Skyrme-type delta-nucleon potential, and including…
We present a minimal Path-Dependent Energy Lagrangian (PDEL) that generates, from a single action, the balance equations of mechanics and the entropy/heat equation for irreversible thermomechanical systems. The reversible part is the…
This paper develops an analytical and rigorous formulation of the maximum entropy generation principle. The result is suggested as the Fourth Law of Thermodynamics.
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
It is known that the viscosity of a dilute gas can be derived by using kinetic theory. We present here a new derivation by using two entropy production principles: the steepest entropy ascent (SEA) principle and the maximum entropy…
A model is presented from which the observed morphology of the inner mitochondrial membrane can be inferred as minimizing the system's free energy. Besides the usual energetic terms for bending, surface area, and pressure difference, our…
We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
A theory to predict the steady state position of a dissipative, flow-controlled system, as defined by a control volume, is developed based on the Maximum Entropy (MaxEnt) principle of Jaynes, involving minimisation of a generalised free…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
We extend the approach of [Smith et al. 2019] to derive analytical expressions for the eigenvalues and eigenmatrices of an isotropic membrane energy density function $\psi : \mathbb{R}^{3x2} \to \mathbb{R}$. Clamping the eigenvalue…
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…