Related papers: Discrete breathers in protein secondary structure
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
A study of the dynamics of a tunneling particle in a driven bistable potential which is moderately-to-strongly coupled to a bath is presented. Upon restricting the system dynamics to the Hilbert space spanned by the M lowest energy…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
Dynamics of array of coupled self-excited oscillators is considered. Model of Franklin bell is adopted as a mechanism for the self-excitation. The model allows derivation of exact analytic solutions for discrete breathers (DBs), and…
It is shown that, an entire class of off-diagonally disordered linear lattices composed of two basic building blocks and described within a tight binding model can be tailored to generate absolutely continuous energy bands. It can be…
For fully connected populations of diffusively coupled bistable elements, we identified three qualitatively distinct mechanisms of noise-induced escape as coupling strength varies [H. Ishii and H. Kori, arXiv:2512.01388 (2025)]. Here we…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
The role of discrete (or point-group) symmetries is discussed in the framework of the Cluster Shell Model which describes the splitting of single-particle levels in the deformed field of cluster potentials. We discuss the classification of…
The shapes of epithelial tissues result from a complex interplay of contractile forces in the cytoskeleta of the cells in the tissue, and adhesion forces between them. A host of discrete, cell-based models describe these forces by assigning…
Using the Fundamental-Measure Density Functional Theory, we have studied theoretically the phase behavior of extremely confined mixtures of parallel hard squares in slit geometry. The pore width is chosen such that configurations consisting…
We study the dynamics of a finite chain of diffusively coupled Lorenz oscillators with periodic boundary conditions. Such rings possess infinitely many fixed states, some of which are observed to be stable. It is shown that there exists a…
The existence and stability of discrete breathers (DBs) in one-dimensional and two-dimensional magnetic metamaterials (MMs), which consist of periodic arrangem ents (arrays) of split-ring resonators (SRRs), is investigated numerically. We…
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…
The paper develops the stiffness relationship between the movements and forces among a system of discrete interacting grains. The approach is similar to that used in structural analysis, but the stiffness matrix of granular material is…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
The Discrete NonLinear Schr\"odinger (DNLS) equation displays a parameter region characterized by the presence of localized excitations (breathers). While their formation is well understood and it is expected that the asymptotic…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…