Related papers: Discrete breathers in protein secondary structure
In the present work, we develop a systematic examination of the existence, stability and dynamical properties of a discrete breather at the interface between a diatomic and a monoatomic granular chain. We remarkably find that such an…
We explore breather propagation in the damped oscillatory chain with essentially nonlinear (non-linearizable) nearest-neighbour coupling. Combination of the damping and the substantially nonlinear coupling leads to rather unusual two-stage…
A nonlinear chain with six-order polynomial on-site potential is used to analyze the evolution of the total to kinetic energy ratio during development of modulational instability of extended nonlinear vibrational modes. For the on-site…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
A systematic correlation between the initial profile of discrete breathers and their frequency is described. The context is that of a very weakly harmonically coupled chain of softly anharmonic oscillators. The results are structurally…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
The existence and stability of dissipative discrete breathers (DDBs) in rf superconducting quantum interference device (SQUID) arrays in both one and two dimensions is investigated numerically. In an rf SQUID array, the nonlinearity which…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
We investigate the existence and stability of discrete breathers in a chain of masses connected by linear springs and subjected to vibro-impact on-site potentials. The latter are comprised of harmonic springs and rigid constraints limiting…
We report Monte Carlo results for the fluid structure of a system of dimeric particles interacting via a core-softened potential. More specifically, dimers interact through a repulsive pair potential of inverse-power form, modified in such…
We study the scattering of a moving discrete breather (DB) on a junction in a Fermi-Pasta-Ulam (FPU) chain consisting of two segments with different masses of the particles. We consider four distinct cases: (i) a light-heavy (abrupt)…
In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
One-dimensional chain of pointwise particles harmonically coupled with nearest neighbors and placed in six-order polynomial on-site potentials is considered. Power of the energy source in the form of single ac driven particles is calculated…
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…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
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…