相关论文: Relationship Between Structural Fractal and Possib…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

Fractal structures appear in a vast range of physical systems. A literature survey including all experimental papers on fractals which appeared in the six Physical Review journals (A-E and Letters) during the 1990's shows that experimental…

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…

The structural evolution of a nano-powder by repeated dispersion and settling can lead to characteristic fractal substructures. This is shown by numerical simulations of a two-dimensional model agglomerate of adhesive rigid particles. The…

A dynamic scaling of a diffusion process involving the Langmuir type adsorption is studied. We find dynamic scaling functions in one and two dimensions and compare them with direct numerical simulations, and we further study the dynamic…

Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact…

Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

Using the concept of self similarity in the structure of the proton at small $x$, we comment on possibility of a single positive fractal dimension of proton in analogy with classical monofractals. Plausible dynamics and physical…

In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…

Optimal structure of proteins is described by linear stochastic differential equation with mean decrease of free energy and volatility. Structure determining strategy is given by a twin of stochastic variables for which empirical conditions…

Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…

With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…

We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…

Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…

Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…

Cohesive particles form agglomerates that are usually very porous. Their geometry, particularly their fractal dimension, depends on the agglomeration process (diffusion-limited or ballistic growth by adding single particles or…

There is a general agreement that galaxy structures exhibit fractal properties, at least up to some small scale. However the presence of an eventual crossover towards homogenization, as well as the exact value of the fractal dimension, are…

We study fractal measures on Euclidean space through the dynamics of "zooming in" on typical points. The resulting family of measures (the "scenery"), can be interpreted as an orbit in an appropriate dynamical system which often…