相关论文: Peierls-Nabarro Barrier and Protein Loop Propagati…
Lattice spin models featuring kinetic constraints constitute a paradigmatic setting for the investigation of glassiness and localization phenomena. The intricate dynamical behavior of these systems is a result of the dramatically reduced…
We examine the dynamic spreading of a dense overdamped suspension of particles under power law repulsive potentials, often called Riesz gases. That is, potentials that decay with distance as 1/r^k where k\in (-2,\infty]. Depending on the…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We report a new result concerning the dynamics of an initially localized wave packet in quantum nonlinear Schr\"odinger lattices with a disordered potential. A class of nonlinear lattices with subquadratic power nonlinearity is considered.…
We study the excitation spectrum of the $S=1/2$ Heisenberg model on the randomly diluted square lattice by analytic continuation of QMC data. At dilution fractions $p=1/16$ and $p=1/8$, the dynamic structure factor $S({\bf q},\omega)$…
We investigate the dynamical properties of a strongly disordered micropolar lattice made up of cubic block units. This phononic lattice model supports both transverse and rotational degrees of freedom hence its disordered variant posses an…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…
We study the bulk and surface nonlinear modes of the modified one-dimensional discrete nonlinear Schroedinger (mDNLS) equation. A linear and a modulational stability analysis of the lowest-order modes is carried out. While for the…
The free propagation of acoustic plane waves through cellular periodic materials is generally accompanied by a flow of mechanical energy across the adjacent cells. The paper focuses on the energy transport related to dispersive waves…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers physical intuition is that of a diffusion process. However, the…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The topological properties of fermions arise from their low-energy Dirac-like band dispersion and associated chiralities. Initially confined to points, extensions of the Dirac dispersion to lines and even loops have now been uncovered and…
Fractionalization remains one of the most fascinating manifestations of strong interactions in quantum many-body systems. In quantum magnetism, the existence of spinons -- collective magnetic excitations that behave as quasiparticles with…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…