Related papers: Exact Sequence Analysis for Three-Dimensional HP L…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the…
We provide the exact solution of several variants of simple models of the zipping transition of two bound polymers, such as occurs in DNA/RNA, in two and three dimensions using pairs of directed lattice paths. In three dimensions the…
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters we…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Realistic 3D-conformations of protein structures can be embedded in a cubic lattice using exclusively integer numbers, additions, subtractions and boolean operations.
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
Structure predictions of helical membrane proteins have been designed to take advantage of the structural autonomy of secondary structure elements, as postulated by the two-stage model of Engelman and Popot. In this context, we investigate…
A subset of vertices in a graph is called resolving when the geodesic distances to those vertices uniquely distinguish every vertex in the graph. Here, we characterize the resolvability of Hamming graphs in terms of a constrained linear…
The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we…
We study the Non-Hermitian quantum mechanics for the discrete system. This paper gives an exact analytic single-particle solution for an $N$-site tight-binding chain with two conjugated imaginary potentials $\pm i\gamma $ at two end sites,…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show…
We find and analyse the exact solution of a model of three different polymers with asymmetric contact interactions in two dimensions, modelling a scenario where there are different types of polymers involved. In particular, we find the…
The thermodynamics of a quantum system of layers containing perpendicularly oriented dipolar molecules is studied within an oscillator approximation for both bosonic and fermionic species. The system is assumed to be built from chains with…
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…