Related papers: Discrete breathers in protein secondary structure
Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
Magnetic metamaterials composed of split-ring resonators or $U-$type elements may exhibit discreteness effects in THz and optical frequencies due to weak coupling. We consider a model one-dimensional metamaterial formed by a discrete array…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
In the present work we revisit the existence, stability and dynamical properties of moving discrete breathers in $\beta$-FPU lattices. On the existence side, we propose a numerical procedure, based on a continuation along a sequence of…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
We present analytical and numerical study of discrete breathers identified as localized deformations of valence angles accompanied by change of valence bonds in crystalline polyethylene (PE). It is shown that such breathers can exist inside…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
Discrete breathers are time-periodic, spatially localized solutions of the equations of motion for a system of classical degrees of freedom interacting on a lattice. We study the existence of energy thresholds for discrete breathers, i.e.,…
We investigate the properties of discrete breathers in a Bose-Einstein condensate with two- and three-body interactions in optical lattice. In the tight-binding approximation the Gross-Pitaevskii equation with periodic potential for the…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
The dynamics of static and travelling breathers in two-species Bose-Einstein condensates in a one-dimensional optical lattice is modelled within the tight-binding approximation. Two coupled discrete nonlinear Schr\"odinger equations…
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on…
We consider an infinite chain of particles linearly coupled to their nearest neighbours and subject to an anharmonic local potential. The chain is assumed weakly inhomogeneous. We look for small amplitude discrete breathers. The problem is…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…