Related papers: Guessing the upper bound free-energy difference be…
We investigate the behavior of energy fluctuations in several models of granular gases maintained in a non-equilibrium steady state. In the case of a gas heated from a boundary, the inhomogeneities of the system play a predominant role.…
The topography of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form is investigated numerically using a ``microcanonical'' Monte…
We develop a continuum theory to model low energy excitations of a generic four-band time reversal invariant electronic system with boundaries. We propose a variational energy functional for the wavefunctions which allows us derive natural…
Using a novel thermodynamic integration scheme, we compute the excess free energy, $\gamma$, of a glass-forming, binary Lennard-Jones liquid in contact with a frozen amorphous wall, formed by particles frozen into a similar structure as the…
A particularly simple relation of proportionality between internal energy and pressure holds for scale invariant thermodynamic systems, including classical and quantum Bose and Fermi ideal gases. One can quantify the deviation from such a…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
We consider a homogeneous Bose gas in the Gross--Pitaevskii limit at temperatures that are comparable to the critical temperature for Bose--Einstein condensation. Recently, an upper bound for the grand canonical free energy was proved in…
We generalise the two-sided Bogoliubov inequality for classical particles from [L. Delle Site et al., J.Stat.Mech.Th.Exp. 083201 (2017)] to systems of quantum particles. As in the classical set-up, the inequality leads to upper and lower…
Free energy, widely used as a measure of turbulence intensity in weakly collisional plasmas, has been recently found to be a suitable basis to describe both linear and nonlinear growth in a wide class gyrokinetic systems. The simplicity…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
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 carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Grain boundary (GB) properties greatly influence the mechanical, electrical, and thermal response of polycrystalline materials. Most computational studies of GB properties at finite temperatures use molecular dynamics (MD), which is…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We investigate the extent to which the commonly used standard pairwise contact potential can be used to identify the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…