Related papers: Statistically enhanced self-attraction of random p…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
The bilayer Hubbard model with an intra-layer hopping $t$ and an inter-layer hopping $t_\perp$ provides an interesting testing ground for several aspects of what has been called unconventional superconductivity. One can study the type of…
Networks of disparate phenomena-- be it the global ecology, human social institutions, within the human brain, or in micro-scale protein interactions-- exhibit broadly consistent architectural features. To explain this, we propose a new…
As proteins typically have charges of around 10, they will interact strongly with charged surfaces. We calculate the electrostatic contribution to the interaction of crystals of protein with charged surfaces. The surfaces repel like-charged…
Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
Adaptive humoral immunity, from the physical perspective, can be regarded as the self-organization of the binding energy landscape of antibodies. In biological terms, the humoral immune system evolves and adapts its repertoire of antigen…
The planar-diagrammatic technique of large-$N$ random matrices is extended to evaluate averages over the circular ensemble of unitary matrices. It is then applied to study transport through a disordered metallic ``grain'', attached through…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
A model of interacting one--dimensional fermions confined to a harmonic trap is proposed. The model is treated analytically to all orders of the coupling constant by a method analogous to that used for the Luttinger model. As a first…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
Unveiling individuals' preferences for connecting with similar others (choice homophily) beyond the structural factors determining the pool of opportunities, is a challenging task. Here, we introduce a robust methodology for quantifying and…
We argue that an ensemble of backgrounds best understands hydrodynamic dispersion relations in a medium with few degrees of freedom and is therefore subject to strong thermal fluctuations. In the linearized regime, dispersion relations…
We investigate the model of "reversible ratchet" with interacting particles, introduced by us earlier [Europhys. Lett. 84, 50009 (2008)]. We further clarify the effect of efficiency enhancement due to interaction and show that it is of…
The thermoelectric response of molecular junctions exhibits large fluctuations, as observed in recent experiments [e.g. Malen J. A. {\sl et al.}, Nano Lett. {\bf 10}, 3406 (2009)]. These were attributed to fluctuations in the energy…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Heterogeneity is classified in five categories---topologic, geometric, kinematic, static, and constitutive---and the first four categories are investigated in a numerical DEM simulation of biaxial compression. The simulation experiments…
One of the most interesting phenomena in the soft-matter realm consists in the spontaneous formation of super-molecular structures (microphases) in condition of thermodynamic equilibrium. A simple mechanism responsible for this…
The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved…
We present new method for studying the equilibrium properties of interacting fluids in an arbitrary external filed. The method is valid in any dimension and it yields an exact results in one dimension. Using this approach, we derive a…