Related papers: Guessing the upper bound free-energy difference be…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with…
By balancing the average energy gap with its typical change due to mutations for protein-like heteropolymers with M residues, we show that native states are unstable to mutations on a scale M* ~ (lambda/sigma_mu)^(1/zeta_s), where lambda is…
We study a bound system of N identical bosons interacting by model pair potentials of the form V(r) = A sgn(p)r^p + B/r^2, A > 0, B >= 0. By using a variational trial function and the `equivalent 2-body method', we find explicit upper and…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
A model which treats the denatured and native conformers of spontaneously-folding fixed two-state systems as being confined to harmonic Gibbs energy-wells has been developed.Within the assumptions of this model the Gibbs energy functions of…
The thermodynamics of ideal gas on the noncommutative geometry in the coherent state formalism is investigated. We first evaluate the statistical interparticle potential and see that there are residual "attraction (repulsion) potential"…
We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for $a^2 \rho \ll 1$ and $\beta \rho \gtrsim 1$ the free energy per unit volume differs from the one of the…
We introduce a natural nonhierarchical version of Derrida's generalized random energy model. We prove that, in the thermodynamical limit, the free energy is the same as that of a suitably constructed GREM.
Atomistic simulations are employed to demonstrate the existence of a well-defined thermodynamic phase transformation between grain boundary (GB) phases with different atomic structures. The free energy of different interface structures for…
Fluctuation theorems have become an important tool in single molecule biophysics to measure free energy differences from non-equilibrium experiments. When significant coarse-graining or noise affect the measurements, the determination of…
Sub-Gaussian and subexponential distributions are introduced and applied to study the fluctuation-response relation out of equilibrium. A bound on the difference in expected values of an arbitrary sub-Gaussian or subexponential physical…
The free energies of six-vertex models on general domain D with various boundary conditions are investigated with the use of the n-equivalence relation which classifies the thermodynamic limit properties. It is derived that the free energy…
The formal structure of geometrical thermodynamics is reviewed with particular emphasis on the geometry of equilibria submanifolds. On these submanifolds thermodynamic metrics are defined as the Hessian of thermodynamic potentials. Links…
At low temperatures the configurational phase space of a macroscopic complex system (e.g., a spin-glass) of $N\sim 10^{23}$ interacting particles may split into an exponential number $\Omega_s \sim \exp({\rm const} \times N)$ of ergodic…
By combining the upper and lower bounds to the free energy as given by the Gibbs inequality for two systems with the same intermolecular interactions but with external fields differing from each other only in a finite region of space Gamma,…
An open question in studying normal grain growth concerns the asymptotic state to which microstructures converge. In particular, the distribution of grain topologies is unknown. We introduce a thermodynamic-like theory to explain these…
In this paper we study computationally feasible bounds for relative free energies between two many-particle systems. Specifically, we consider systems out of equilibrium that do not necessarily satisfy a fluctuation-dissipation relation,…