Related papers: Guessing the upper bound free-energy difference be…
Organisms are nonequilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy principle describes an…
Starting at the mesoscopic level with a general formulation of stochastic thermodynamics in terms of Markov jump processes, we identify the scaling conditions that ensure the emergence of a (typically nonlinear) deterministic dynamics and…
We consider (2+1)-QFT at finite temperature on a product of time with a static spatial geometry. The suitably defined difference of thermal vacuum free energy for the QFT on a deformation of flat space from its value on flat space is a UV…
We calculate the density of stationary points and minima of a $N\gg 1$ dimensional Gaussian energy landscape. We use it to show that the point of zero-temperature replica symmetry breaking in the equilibrium statistical mechanics of a…
Grain boundaries are thermodynamically unstable. Hence, their properties should be path-dependent: grain boundaries in nanocrystals prepared using different methods might exhibit different properties. Using molecular dynamics simulations,…
This work extends a recently developed mathematical theory of thermodynamics for Markov processes with, and more importantly, without detailed balance. We show that the Legendre transform in connection to ensemble changes in Gibbs'…
We develop a simple, mean-field-like theory for the normal phase of a unitary Fermi gas by deriving a self-consistent equation for its self-energy via a momentum-dependent coupling constant for both attractive and repulsive universal…
We discuss that the thermodynamical Legendre transform structure can be retained not only for the arbitrary entropic form but also for the arbitrary form of the energy constraints by following the discussion of Plastino and Plastino. The…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
The free energy of globular protein chain is considered to be a functional defined on smooth curves in three dimensional Euclidean space. From the requirement of geometrical invariance, together with basic facts on conformation of helical…
We present, for the Ising model on the Cayley tree, some explicit formulae of the free energies (and entropies) according to boundary conditions (b.c.). They include translation-invariant, periodic, Dobrushin-like b.c., as well as those…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The variation of the energy for a gravitational system is directly defined from the Hamiltonian field equations of General Relativity. When the variation of the energy is written in a covariant form it splits into two (covariant)…
Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We develop a theory of the effective disorder temperature in glass-forming materials driven away from thermodynamic equilibrium by external forces. Our basic premise is that the slow configurational degrees of freedom of such materials are…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
We consider the relationship between thermodynamics, fitness, and Darwinian selection in autocatalytic molecular replicators. We uncover a thermodynamic bound that relates fitness, replication rate, and thermodynamic affinity of…