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The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
We find the free-energy in the thermodynamic limit of a one dimensional XY model associated to a system of N qubits. The coupling among the sigma_i^z is a long range two bodies random interaction. The randomness in the couplings is the…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
The nature of the interplay between fluctuations and quenched random disorder is a long-standing open problem, particularly in systems with a continuous order parameter. This lack of a full theoretical treatment has been underscored by…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
Recent work on random field Ising model is described briefly emphasizing exact solutions of the model in simple cases and their relevance in understanding equilibrium and non-equilibrium properties of systems with quenched disorder.
We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Motivated by the observation of the storage of excess elastic free energy - (prestress) -- in cross linked semiflexible networks, we consider the problem of the conformational statistics of a single semiflexible polymer in a quenched random…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
For the generalized Ising models with all possible interactions within a face of the square lattice the formulas for finding partition function and free energy per lattice site in the thermodynamic limit were derived on a certain, in the…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
This work aims at providing a mathematical and numerical framework for the analysis on the effects of pulsed electric fields on biological media. Biological tissues and cell suspensions are described as having a heteregeneous permittivity…
We investigate a disordered multi-dimensional linear system in which the interaction parameters vary stochastically in time with defined temporal correlations. We refer to this type of disorder as "annealed", in contrast to quenched…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
Using a formalism based on the spectral decomposition of the replicated transfer matrix for disordered Ising models, we obtain several results that apply both to isolated one-dimensional systems and to locally tree-like graph and factor…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
We apply the Wako-Saito-Munoz-Eaton model to the study of Myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary…
The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be…