Related papers: Peierls-Nabarro Barrier and Protein Loop Propagati…
We investigate transient nonlinear localization, namely the self-excitation of energy bursts in an atomic lattice at finite temperature. As a basic model we consider the diatomic Lennard-Jones chain. Numerical simulations suggest that the…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
The mitotic spindle lies at the heart of the spatio-temporal control over cellular components during cell division. The spindle consists of microtubules, which are not only crosslinked by motor proteins but also by passive binding proteins.…
We review the energy spectrum and transport properties of several types of one- dimensional superlattices (SLs) on single-layer and bilayer graphene. In single-layer graphene, for certain SL parameters an electron beam incident on a SL is…
We theoretically investigate the dynamics of atomic domain walls (DWs) in antiferromagnets driven by a spin-orbit field. For a DW with the width of a few lattice constants, we identify a Peierls-like pinning effect, with the depinning field…
The effect that an additional energy barrier E_{kr} for step adatoms moving around kinks has on equilibrium step edge fluctuations is explored using scaling arguments and kinetic Monte Carlo simulations. When mass transport is through step…
We present a numerical study of the transport and localization properties of excitations in one-dimensional lattices with diagonal disordered mosaic modulations. The model is characterized by the modulation period $\kappa$ and the disorder…
We numerically study a one dimensional, nonlinear lattice model which in the linear limit is relevant to the study of bending (flexural) waves. In contrast with the classic one dimensional mass-spring system, the linear dispersion relation…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
We investigate numerically the time evolution of wave packets incident on one-dimensional semi-infinite lattices with mosaic modulated random on-site potentials, which are characterized by the integer-valued modulation period $\kappa$ and…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
We present GW based self-energy calculations for the state of coexisting spin-density wave and d-wave superconductivity in a series of cuprate superconductors. In these systems, the spin resonance spectrum exhibits the typical `hour-glass'…
A dislocation moving through a quasicrystal is leaving in its wake a fault denoted phason wall. For a two-dimensional model quasicrystal the disregistry energy of this phason wall is studied to determine possible Burgers vectors of the…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
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 study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
We focus on existence and rigidity problems of the vectorial Peierls-Nabarro (PN) model for dislocations. Under the assumption that the misfit potential on the slip plane only depends on the shear displacement along the Burgers vector, a…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…