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Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
The structure of the physical and strange attractors is inherently associated with the boundedness of fluctuations. The idea behind the boundedness is that a stable long-term evolution of any natural and engineered system is possible if and…
The theory is presented for resonance interaction between two atoms in an excited configuration: one atom, the "receptor" of information (i.e. energy), adsorbed on a phospholipid surface and the other atom, the "emitter" of information…
In physics we often use very simple models to describe systems with many degrees of freedom, but it is not clear why or how this success can be transferred to the more complex biological context. We consider models for the joint…
We examine fluctuation-induced (pseudo-Casimir) interactions in nematic liquid-crystalline films confined between two surfaces, where one of the surfaces imposes a strong homeotropic anchoring (ensuring a uniform mean director profile),…
The matching hypothesis in social psychology claims that people are more likely to form a committed relationship with someone equally attractive. Previous works on stochastic models of human mate choice process indicate that patterns…
Many biological systems fold thin sheets of lipid membrane into complex three-dimensional structures. This microscopic origami is often mediated by the adsorption and self-assembly of proteins on a membrane. As a model system to study…
Strongly interacting Fermi gases are of great current interest. Not only are fermions the most common particles in the universe, but they are also thought to have a universal thermodynamic behavior for strong interactions…
Numerous experiments demonstrate a high level of promiscuity and structural disorder in organismal proteomes. Here we ask the question what makes a protein promiscuous, i.e., prone to non-specific interactions, and structurally disordered.…
We connect the theories of the deformation of elastic surfaces and phase surfaces arising in the description of almost periodic patterns. In particular, we show parallels between asymptotic expansions for the energy of elastic surfaces in…
Low-energy scattering is well described by the effective-range expansion. In quantum mechanics, a tower of contact interactions can generate terms in this expansion after renormalization. Scattering parameters are also encoded in the…
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…
We develop a statistical theory of the mean field. It is based on the proposition that the mean field can be obtained as an energy average. Moreover, it is assumed that the matrix elements of the residual interaction are random with the…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Oscillations of mainly surface character (S=0 modes) give rise, in atomic nuclei, to an attractive (induced) pairing interaction, while spin (S=1) modes of mainly volume character generate a repulsive interaction, the net effect being an…
Proteins are regularly described with some general indices (mass fractal dimension, surface fractal dimension, entropy, enthalpy, free energies, hydrophobicity, denaturation temperature etc..), which are inherently statistical in nature.…
We study a process of pattern formation for a generic model of species anchored to the nodes of a network where local reactions take place, and that experience non-reciprocal long-range interactions, encoded by the network directed links.…
Spectral properties of Hermitian Toeplitz, Hankel, and Toeplitz-plus-Hankel random matrices with independent identically distributed entries are investigated. Combining numerical and analytic arguments it is demonstrated that spectral…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…