Related papers: Mapping of mutation-sensitive sites in protein-lik…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Diffusion is often accompanied by a reaction or sorption which can induce temperature inhomogeneities. Monte Carlo simulations of Lennard-Jones atoms in zeolite NaCaA are reported with a hot zone presumed to be created by a reaction. Our…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
We analyze diffusion of small particles in a solid polymeric medium taking into account a short range particle-polymer interaction. The system is modeled by a particle diffusion on a ternary lattice where the sites occupied by polymer…
We analyze diffusion of particles on a two dimensional square lattice. Each lattice site contains an arbitrary number of particles. Interactions affect particles only in the same site, and are macroscopically represented by the excess…
In this work we study the spreading dynamics of tiny liquid droplets on solid surfaces in the case where the ends of the molecules feel different interactions with respect to the surface. We consider a simple model of dimers and short…
Reaction-diffusion systems where transition rates exhibit quenched disorder are common in physical and chemical systems. We study pair reactions on a periodic two-dimensional lattice, including continuous deposition and spontaneous…
Using an example of physical interactions between proteins, we study how perturbations propagate in interconnected networks whose equilibrium state is governed by the law of mass action. We introduce a comprehensive matrix formalism which…
We consider a pair of identical fermions with a short-range attractive interaction on a finite lattice cluster in the presence of strong site disorder. This toy model imitates a low density regime of the strongly disordered Hubbard model.…
Reaction-diffusion systems may lead to the formation of steady state heterogeneous spatial patterns, known as Turing patterns. Their mathematical formulation is important for the study of pattern formation in general and play central roles…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…