相关论文: Peierls-Nabarro Barrier and Protein Loop Propagati…

Movements of individual domain walls in a ferromagnetic garnet were studied with angstrom resolution. The measurements reveal that domain walls can be locked between adjacent crystallographic planes and propagate by distinct steps matching…

We discuss the process by which energy, initially evenly distributed in a nonlinear lattice, can localize itself into large amplitude excitations. We show that, the standard modulational instability mechanism, which can initiate the process…

The Hubbard model on a semi-infinite three-dimensional lattice is considered to investigate electron-correlation effects at single-crystal surfaces. The standard second-order perturbation theory in the interaction U is used to calculate the…

A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…

The characteristic features of the renormalization of the electrons in the bilayer cuprate superconductors are investigated within the kinetic-energy driven superconductivity. It is shown that the quasiparticle excitation spectrum is split…

The theory of the dislocation motion in the periodic potential relief of the crystal lattice (the Peierls-Nabarro barriers) is reviewed. On the basis of the kink mechanism the temperature dependence of the flow stress is described for a…

Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…

Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are…

It was recently proposed a novel discretization for nonlinear Klein-Gordon field theories in which the resulting lattice preserves the topological (Bogomol'nyi) lower bound on the kink energy and, as a consequence, has no Peierls-Nabarro…

The peridynamic model of a solid does not involve spatial gradients of the displacement field and is therefore well suited for studying defect propagation. Here, bond-based peridynamic theory is used to study the equilibrium and steady…

The frictional dynamics of interacting surfaces under forced translation are critically dependent on lattice commensurability. Performing experiments in a trapped-ion friction emulator, we observe two distinct structural and frictional…

We study the dynamical response of a diatomic periodic chain of rotors coupled by springs, whose unit cell breaks spatial inversion symmetry. In the continuum description, we derive a nonlinear field theory which admits topological kinks…

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…

In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…

We clarify elementary excitations in the $\Delta$-chain. They are found to be `kink'-`antikink' type domain wall excitations to the dimer singlet ground state. The characters of a kink and an antikink are quite different in this system: a…

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…

Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a…

We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…

In a viscoelastic environment, the diffusion of a particle becomes non-Markovian due to the memory effect. An open question is to quantitatively explain how self-propulsion particles with directional memory diffuse in such a medium. Based…

We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…