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

We study an intermittent quasistatic dynamical system composed of nonuniformly hyperbolic Pomeau--Manneville maps with time-dependent parameters. We prove an ergodic theorem which shows almost sure convergence of time averages in a certain…

The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…

We study the breaking of ergodicity measured in terms of return probability in the evolution of a quantum state of a spin chain. In the non ergodic phase a quantum state evolves in a much smaller fraction of the Hilbert space than would be…

Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled…

The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…

Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…

Recently a number of approaches has been developed to connect the microscopic dynamics of particle systems to the macroscopic properties of systems in nonequilibrium stationary states, via the theory of dynamical systems. This way a direct…

A theoretical description of the weakly nonlinear and mode-dependent dynamics of a nanoscale beam that is under intrinsic tension is developed. A full analysis of the dynamic range of the beam over a wide range of conditions is presented.…

We consider the thermodynamic potential describing the macroscopic fluctuation of the current and local energy of a general class of Hamiltonian models including aerogels. We argue that this potential is neither analytic nor strictly…

We use large-scale computer simulations to explore the non-equilibrium aging dynamics in a microscopic model for colloidal gels. We find that gelation resulting from a kinetically-arrested phase separation is accompanied by `anomalous'…

Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…

Thermostats are dynamic equations used to model thermodynamic variables in molecular dynamics. The applicability of thermostats is based on the ergodic hypothesis. The most commonly used thermostats are designed according to the…

Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…

Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required.…

Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…

Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…

The fluid-mechanics community is currently divided in assessing the boundaries of applicability of the macroscopic approach to fluid mechanical problems. Can the dynamics of nano-droplets be described by the same macroscopic equations as…

Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…

It has been observed that an interesting class of non-Gaussian stationary processes is obtained when in the harmonics of a signal with random amplitudes and phases, frequencies can also vary randomly. In the resulting models, the…

This paper studies ergodic properties of certain measures arising in the dynamics of holomorphic correspondences. These measures, in general, are not invariant in the classical sense of ergodic theory. We define a notion of ergodicity, and…