相关论文: Conformational Temperature Characterizing the Fold…

The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…

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…

We extend on ideas from standard thermodynamics to show that temperature can be assigned to a general nonequilibrium quantum system. By choosing a physically motivated complete set of observables and expanding the system state thereupon,…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…

Formation of the nonequilibrium subsystem in dynamical processes during defect generation is simulated by means of molecular dynamics. A particular process of dissipation of the low-frequency acoustic emission into high-frequency…

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…

Recent theoretical advances show that the temperature of a system in equilibriumcan be measured from static snapshots of its constituents' instantaneous configurations, withoutregard to their dynamics. We report the first measurements of…

Ultrafast laser radiation or beams of fast charged particles primarily excite the electronic system of a solid driving the target transiently out of thermal equilibrium. Apart from the nonequilibrium between the electrons and atoms, each…

Simulations are performed of a small quantum system interacting with a quantum environment. The system consists of various initial states of two harmonic oscillators coupled to give normal modes. The environment is "designed" by its level…

The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…

We are used to measure temperature with a thermometer and we know from everyday life that different types of thermometers measure the same temperature. This experience can be based on equilibrium thermodynamics, which explains the…

Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…

It was recently shown that entanglement in quantum systems being in a non-equilibrium state can appear at much higher temperatures than in an equilibrium state. However, any system is subject to the natural relaxation process establishing…

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…

Starting from a Huxley-type model for an agitated vibrational mode, we propose an embedding of standard active particle models in terms of two-temperature processes. One temperature refers to an ambient thermal bath, and the other…

We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…

The concept of effective temperatures in nonequilibrium systems is studied within an exactly solvable model of non-Markovian diffusion. The system is coupled to two heat baths which are kept at different temperatures: one ('fast') bath…