Related papers: Guessing the upper bound free-energy difference be…
We compute the pressure of the random energy model (REM) and generalized random energy model(GREM) by establishing variational upper and lower bounds. For the upper bound, we generalize Guerra's ``broken replica symmetry bounds",and…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Using the proof of Willmore's conjecture by Marques and Neves, we conjecture that the free energy of tensionless fluid membranes of arbitrary genus has an upper bound. This implies that the average genus of such a membrane, in equilibrium,…
In this study, variations with respect to temperature of the increments of enthalpy and Gibbs energy, arising in the dissolution of proteins in water, have been investigated by the methods of statistical thermodynamics. In this formalism,…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
We show the robustness of the structure of Legendre transform in thermodynamics against the replacement of the standard linear average with the Kolmogorov-Nagumo nonlinear average to evaluate the expectation values of the macroscopic…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
The topological transitions that occur to the grain boundary network during grain growth in a material with uniform grain boundary energies are believed to be known. The same is not true for more realistic materials, since more general…
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
We present a detailed analysis of the universal relationship between grain boundary (GB) free energy and GB self-diffusion coefficient derived by Borisov et al. (1964). This relationship was expressed by a simple equation that was used in…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
The critical behavior of a 3D Ising-like system is studied at the microscopic level of consideration. The free energy of ordering is calculated analytically as an explicit function of temperature, an external field and the initial…