Related papers: Computational Complexity of Flattening Fixed-Angle…
Real filaments are not perfectly homogeneous. Most of them have various materials composition and shapes making their stiffnesses not constant along the arclength. We investigate the existence of circular and helical equilibrium solutions…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
Ordered matchings, defined as graphs with linearly ordered vertices, where each vertex is connected to exactly one edge, play a crucial role in the area of ordered graphs and their homomorphisms. Therefore, we consider related problems from…
We investigate the tight packing of nematic polymers inside a confining hard sphere. We model the polymer {\sl via} the continuum Frank elastic free energy augmented by a simple density dependent part as well as by taking proper care of the…
Oblique decision trees combine the transparency of trees with the power of multivariate decision boundaries, but learning high-quality oblique splits is NP-hard, and practical methods still rely on slow search or theory-free heuristics. We…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
In typical flat-band models, defined as nearest-neighbor tight-binding models, flat bands are usually pinned to the special energies, such as top or bottom of dispersive bands, or band-crossing points. In this paper, we propose a simple…
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…
Hierarchical embedding constraints define a set of allowed cyclic orders for the edges incident to the vertices of a graph. These constraints are expressed in terms of FPQ-trees. FPQ-trees are a variant of PQ-trees that includes F-nodes in…
Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
In this study, we propose an analytic statistical mechanics approach to solve a fundamental problem in biological physics called protein design. Protein design is an inverse problem of protein structure prediction, and its solution is the…
A recurring motif in the organization of biological tissues are networks of long, fibrillar protein strands effectively confined to cylindrical surfaces. Often, the fibers in such curved, quasi-2D geometries adopt a characteristic order:…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
By using the properties of orthogonal polynomials, we present an exact unitary transformation that maps the Hamiltonian of a quantum system coupled linearly to a continuum of bosonic or fermionic modes to a Hamiltonian that describes a…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…