Decoherence dynamics of coherent electronic excited states in the photosynthetic purple bacterium Rhodobacter sphaeroides.

In this paper, we present a theoretical description to the quantum coherence and decoherence phenomena of energy transfer in photosynthesis observed in a recent experiment [Science 316, 1462 (2007)]. As a successive two-color laser pulses with selected frequencies cast on a sample of the photosynthetic purple bacterium Rb. sphaeroides two resonant excitations of electrons in chromophores can be generated. However, this effective two-level subsystem will interact with its protein environment and decoherence is inevitable. We describe this subsystem coupled with its environment as a dynamical spin-boson model. The non-Markovian decoherence dynamics is described using a quasiadiabatic propagator path integral (QUAPI) approach. With the photon-induced effective time-dependent level splitting energy and level flip coupling coefficient between the two excited states and the environment-induced non-Markovian decoherence dynamics, our theoretical result is in good agreement with the experimental data.

A dynamical model on the network of p53-Mdm2 feedback loop regulated by p14/19ARF.

Base on new experimental results, we give a dynamical model to study the dynamical mechanism of the negative feedback loop composed of p53 and Mdm2 proteins regulated by p14/19ARF. The oscillatory behaviors for the activities of p53 and Mdm2 proteins regulated by p14/19ARF in individual of cells are described in our dynamical model. The results help us build a basal network about oscillatory behaviors among p53, Mdm2 and P14/19ARF. The dynamical model and its numerical results will help us understand the oscillatory behavior among other network of different proteins.

The use of an "effective potential" to describe the directed motion of a two-state molecular motor.

Force generation and directed motion of molecular motors using a simple two-state model are studied in the paper. Here we consider the asymmetric and periodic potential in the model. The symmetric and periodic potential is adopted to describe the interactions between motor proteins and filaments that are periodic and polar. The flux and the slope of the effective potential as functions of the temperature and transition rates are calculated in the two-state model. The ratio of the slope of the effective potential to the flux is also calculated. It is concluded that the directed motion of motor proteins is relevant to the effective potential. The slope of the effective potential corresponds to an average force. The non-vanishing force therefore implies that detailed balance is broken in the process of transition between different states. Moreover, we compare the theoretical relationship of load force and velocity with the experimental data. It is shown that they are consistent.

Intermediate dynamics between Newton and Langevin.

A dynamics between Newton and Langevin formalisms is elucidated within the framework of the generalized Langevin equation. For thermal noise yielding a vanishing zero-frequency friction the corresponding non-Markovian Brownian dynamics exhibits anomalous behavior which is characterized by ballistic diffusion and accelerated transport. We also investigate the role of a possible initial correlation between the system degrees of freedom and the heat-bath degrees of freedom for the asymptotic long-time behavior of the system dynamics. As two test beds we investigate (i) the anomalous energy relaxation of free non-Markovian Brownian motion that is driven by a harmonic velocity noise and (ii) the phenomenon of a net directed acceleration in noise-induced transport of an inertial rocking Brownian motor.

Cancellation phenomenon of barrier escape driven by a non-Gaussian noise.

The Lévy noise, with a long-tail distribution induced particle escape from a metastable potential, is shown to display a feature called a cancellation phenomenon, as compared to the Brownian motion case. As a consequence, the escape rate is found to be a nonmonotonous function of the Lévy index mu and the Arrhenius law is not obeyed. We have also derived a rate expression using the reactive flux method, which supports our numerical findings, namely, with the decrease of mu, a large positive flow is allowed to establish at the barrier, however, the probability passing over the saddle point decreases. This implies that the particles outside the barrier come back to the inside and cancel with themselves.

Harmonic velocity noise: non-Markovian features of noise-driven systems at long times.

We propose a harmonic velocity noise with a broadband feature, which is the time derivative of the harmonic noise. If this noise is regarded as a thermal one, the system has a vanishing effective friction and it should induce ballistic diffusion of a free particle at long times. The effective temperature of the system coupled to such a structured heat bath represented by the harmonic velocity noise is introduced. This means that any initial preparation will approach asymptotically a preparation-dependent variance and mean value for velocity variable. Thus the fluctuation-dissipation theorem does not hold as there is no unique stationary state being connected with a breakdown of ergodicity. This noise can show greenness when it is taken as an external noise source to drive a correlation ratchet.

Anomalous dissipation: strong non-Markovian effect and its dynamical origin.

We report the effects of anomalous dissipation with a vanishing effective friction, which can induce ballistic diffusion and dissipative acceleration, where the fluctuation-dissipation theorem is fulfilled. An influence factor is introduced in order to describe the role of non-Markovian friction and the force-folded effect on the long-time results. The velocity-dependent coupling and force might be a dynamical origin of this dissipation. The steady acceleration of a particle moving in periodic and magnetic-force potentials are calculated.

Non-Markovian Brownian dynamics and nonergodicity.

We report the breaking of ergodicity for a class of generalized, Brownian motion obeying a non-Markovian dynamics being driven by a generalized Langevin equation (GLE). This very feature originates from a vanishing of the effective friction. A novel quantity b (being uniquely determined from the corresponding memory friction kernel gamma(t)of the GLE) is introduced as a parameter that is capable of measuring the strength of ergodicity breaking. The ergodicity breaking is accompanied by a nonunique stationary probability density for the corresponding embedded Markovian dynamics. Differing physical situations for a Brownian, non-Markovian particle dynamics occurring either in free Brownian motion, in a periodic potential, or in a confining potential are elucidated.

Ballistic diffusion induced by a thermal broadband noise.

We present a thermal broadband noise from the difference between two Ornstein-Uhlenbeck noises, which can induce a ballistic diffusion, i.e., long-time mean square displacement of a free particle driven by this noise reads proportional to t(2). We apply this noise to a flashing ratchet and the mean velocity of the particle is calculated via Langevin simulation. The results show that a double peak of the mean velocity and flux reversal appears for the ratchet with large and small asymmetries, respectively; the inertia effect induces a large mean velocity and multireversal of flux. These rich and interesting phenomena are explained.