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Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
In this paper, we study random embeddings of polymer networks distributed according to any potential energy which can be expressed in terms of distances between pairs of monomers. This includes freely jointed chains, steric effects,…
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 study the long-time average of the reduced density matrix (RDM) of an $m$-level central system, which is locally coupled to a large environment, under an overall Schr\"{o}dinger evolution of the total system. We consider a class of…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between…
We present a simple discrete model for the non-linear spatial interaction of different kinds of ``subpopulations'' composed of identical moving entities like particles, bacteria, individuals, etc. The model allows to mimic a variety of…
The spread of infectious diseases, rumors, fashions, innovations are complex contagion processes, embedded both in networked and spatial contexts. Here we investigate the pattern dynamics of a complex contagion, where two agents, say $A$…
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…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
The mechanism of fermionic pairing is the key to understanding various phenomena such as high-temperature superconductivity and the pseudogap phase in cuprate materials. We study the pair correlations in the attractive Hubbard model using…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Adsorption of dimers is modelled using random sequential adsorption algorithm. The interaction between molecules is given by screened electrostatic potential. The paper focuses on the properties of adsorbed monolayers as well as the…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
We construct the complete structural phase diagram of polymer adsorption at substrates with attractive stripe-like patterns in the parameter space spanned by the adsorption affinity of the stripes and temperature. Results were obtained by…
Impact phenomena of small clusters subject to thermal fluctuations are numerically investigated. From the molecular dynamics simulation for colliding two identical clusters, it is found that the restitution coefficient for head-on…
We observe that the reflection and transmission coefficients of a particle within a double, PT symmetric heterojunction with spatially varying mass, show interesting features, depending on the degree of non Hermiticity, although there is no…