相关论文: Investigation on non-ergodicity of protein dynamic…

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…

In this paper we discuss how the notion of subgeometric ergodicity in Markov chain theory can be exploited to study stationarity and ergodicity of nonlinear time series models. Subgeometric ergodicity means that the transition probability…

Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…

Quantum many-body systems can exhibit distinct regimes where dynamics is either ergodic, dynamically exploring an extensive region of available state-space, or non-ergodic, where the dynamics may be restricted. An example is the many-body…

We study a system of $N$ interacting particles on $\bf{Z}$. The stochastic dynamics consists of two components: a free motion of each particle (independent random walks) and a pair-wise interaction between particles. The interaction belongs…

Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…

We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…

Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…

The paper is devoted to a systematic account of the theory of conformational dynamics of protein molecules. As an example of application of this theory, we provide a complete analytical description of experiments on the kinetics of CO…

The purpose of the dynamics of moving systems is to search for the mathematical model that describes the link between the resultant applied force, that is the cause, and the speed of system that is the effect. This mathematical link…

An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…

A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…

In the simplest sequential decision problem for an ergodic stochastic process X, at each time n a decision u_n is made as a function of past observations X_0,...,X_{n-1}, and a loss l(u_n,X_n) is incurred. In this setting, it is known that…

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…

The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…

Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…

Algorithms and dynamics over networks often involve randomization, and randomization may result in oscillating dynamics which fail to converge in a deterministic sense. In this paper, we observe this undesired feature in three applications,…