相关论文: Discrete Nonlinear Schrodinger Equation, Solitons …

Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion, from a relatively small number of components. Here we propose to identify the…

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,…

Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

In this review we try to capture some of the recent excitement induced by experimental developments, but also by a large volume of theoretical and computational studies addressing multi-component nonlinear Schrodinger models and the…

We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…

In the present work, we study, by means of a one-dimensional lattice model, the collective excitations corresponding to intra molecular ones of a chain like proteins. It is shown that such excitations are described by the Nonlinear…

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…

We analyse the structure of the exact, dark and bright soliton solutions of the driven non-linear Schr\"odinger equation. It is found that, a wide class of solutions of the higher order non-linear Schr\"odinger equation with a source can…

We derive a class of discrete nonlinear Schr{\"o}dinger (DNLS) equations for general polynomial nonlinearity whose stationary solutions can be found from a reduced two-point algebraic problem. It is demonstrated that the derived class of…

We introduce a new nonlinear model for classification, in which we model the joint distribution of response variable, y, and covariates, x, non-parametrically using Dirichlet process mixtures. We keep the relationship between y and x linear…

We develop a general classification of the infinite number of families of solitons and soliton complexes in the one-dimensional Gross-Pitaevskii/nonlinear Schrodinger equation with a nonlinear lattice pseudopotential, i.e., periodically…

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…

A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…

We study the Derivative Nonlinear Schr\"odinger equation for generic initial data in a weighted Sobolev space that can support bright solitons (but exclude spectral singularities). Drawing on previous well-posedness results, we give a full…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

We characterize the soliton solutions of the nonlinear Schroedinger equation on the half line with linearizable boundary conditions. Using an extension of the solution to the whole line and the corresponding symmetries of the scattering…

We implement the dressing method for a novel integrable generalization of the nonlinear Schr\"odinger equation. As an application, explicit formulas for the $N$-soliton solutions are derived. As a by-product of the analysis, we find a…

We construct one soliton solutions for the nonlinear Schroedinger equation with variable quadratic Hamiltonians in a unified form by taking advantage of a complete (super) integrability of generalized harmonic oscillators. The soliton wave…

Irrotational ow of a spherical thin liquid layer surrounding a rigid core is described using the defocusing nonlinear Schrodinger equation. Accordingly, azimuthal moving nonlinear waves are modeled by periodic dark solitons expressed by…