Related papers: Discrete breathers in protein secondary structure
Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DB) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an…
The existence, stability and movability of breathers in a model for alpha-helix proteins is studied. This model basically consists a chain of dipole moments parallel to it. The existence of localized linear modes brings about that the…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
Exact solutions for symmetric discrete breathers (DBs) are obtained in forced-damped linear chain with on-site vibro-impact constraints. The damping is related to inelastic impacts; the forcing may be chosen from broad class of periodic…
We explore dynamics of discrete breathers and multi-breathers in finite one-dimensional chain. The model involves parabolic on-site potential with rigid constraints and linear nearest-neighbor coupling. The rigid non-ideal impact…
The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are…
In strained monoatomic chains with Lennard-Jones interactions, we revealed a stable static non-homogeneous structure appearing as a result of a certain phase transition. Positions of individual particles in this structure form an exact…
The occurrence of single- or multisite localized vibrational modes, also called Discrete Breathers (DBs), in 2D hexagonal dusty plasma (DP) lattices is investigated. The system is described by a Klein-Gordon hexagonal lattice characterized…
We present a systematic study of the existence and stability of discrete breathers that are spatially localized in the bulk of a one-dimensional chain of compressed elastic beads that interact via Hertzian contact. The chain is diatomic,…
We report on the existence of discrete breathers in a one-dimensional, mass-in-mass chain with linear intersite coupling and nonlinear Hertzian local resonators, which is motivated by recent studies of the dynamics of microspheres adhered…
We examine the dynamics of strongly localized periodic solutions (discrete breathers) in two-dimensional array of coupled finite one-dimensional chains of oscillators. Localization patterns with both single and multiple localization sites…
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as…
We report the experimental observation of discrete breathers in a one-dimensional diatomic granular crystal composed of compressed elastic beads that interact via Hertzian contact. We first characterize their effective linear spectrum both…
We consider a previously experimentally realized discrete model that describes a mechanical metamaterial consisting of a chain of pairs of rigid units connected by flexible hinges. Upon analyzing the linear band structure of the model, we…
Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
The existence of discrete breathers (DBs), or intrinsic localized modes (localized periodic oscillations of transzigzag) is shown. In the localization region periodic contraction-extension of valence C-C bonds occurs which is accompanied by…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…