Active particle diffusion in convection roll arrays.

Undesired advection effects are unavoidable in most nano-technological applications involving active matter. However, it is conceivable to govern the transport of active particles at the small scales by suitably tuning the relevant advection and self-propulsion parameters. To this purpose, we numerically investigated the Brownian motion of active Janus particles in a linear array of planar counter-rotating convection rolls at high Péclet numbers. Similarly to passive particles, active microswimmers exhibit advection enhanced diffusion, but only for self-propulsion speeds up to a critical value. The diffusion of faster Janus particles is governed by advection along the array's edges, whereby distinct diffusion regimes are observed and characterized. Contrary to passive particles, the relevant spatial distributions of active Janus particles are inhomogeneous. These peculiar properties of active matter are related to the combined action of noise and self-propulsion in a confined geometry and hold regardless of the actual flow boundary conditions.

Enhanced motility in a binary mixture of active nano/microswimmers.

It is often desirable to enhance the motility of active nano- or microscale swimmers such as, e.g., self-propelled Janus particles as agents of chemical reactions or weak sperm cells for better chances of successful fertilization. Here we tackle this problem based on the idea that motility can be transferred from a more active guest species to a less active host species. We performed numerical simulations of motility transfer in two typical cases, namely for interacting particles with a weak inertia effect, by analyzing their velocity distributions, and for interacting overdamped particles, by studying their effusion rate. In both cases, we detected motility transfer with a motility enhancement of the host species of up to a factor of four. This technique of motility enhancement can find applications in chemistry, biology and medicine.

Activated barrier crossing dynamics of a Janus particle carrying cargo.

We numerically study the escape kinetics of a self-propelled Janus particle, carrying a cargo, from a meta-stable state. We assume that the cargo is attached to the Janus particle by a flexible harmonic spring. We take into account the effect of the velocity field created in the fluid due to movements of the dimer's components, by considering a space-dependent diffusion tensor (Oseen tensor). Our simulation results show that the synchronization between barrier crossing events and the rotational relaxation process can enhance the escape rate to a large extent. Also, the load carrying capability of a Janus particle is largely controlled by its rotational dynamics and self-propulsion velocity. Moreover, the hydrodynamic interaction, conspicuously, enhances the escape rate of the Janus-cargo dimer. The most important features in escape kinetics have been justified based on analytic arguments.

Communication: Escape kinetics of self-propelled Janus particles from a cavity: numerical simulations.

We numerically investigate the escape kinetics of elliptic Janus particles from narrow two-dimensional cavities with reflecting walls. The self-propulsion velocity of the Janus particle is directed along either their major (prolate) or minor (oblate) axis. We show that the mean exit time is very sensitive to the cavity geometry, particle shape, and self-propulsion strength. The mean exit time is found to be a minimum when the self-propulsion length is equal to the cavity size. We also find the optimum mean escape time as a function of the self-propulsion velocity, translational diffusion, and particle shape. Thus, effective transport control mechanisms for Janus particles in a channel can be implemented.

Periodic force induced stabilization or destabilization of the denatured state of a protein.

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both stabilization or destabilization of the denatured state of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field.

Quantum effects in energy and charge transfer in an artificial photosynthetic complex.

We investigate the quantum dynamics of energy and charge transfer in a wheel-shaped artificial photosynthetic antenna-reaction center complex. This complex consists of six light-harvesting chromophores and an electron-acceptor fullerene. To describe quantum effects on a femtosecond time scale, we derive the set of exact non-Markovian equations for the Heisenberg operators of this photosynthetic complex in contact with a Gaussian heat bath. With these equations we can analyze the regime of strong system-bath interactions, where reorganization energies are of the order of the intersite exciton couplings. We show that the energy of the initially excited antenna chromophores is efficiently funneled to the porphyrin-fullerene reaction center, where a charge-separated state is set up in a few picoseconds, with a quantum yield of the order of 95%. In the single-exciton regime, with one antenna chromophore being initially excited, we observe quantum beatings of energy between two resonant antenna chromophores with a decoherence time of ∼100 fs. We also analyze the double-exciton regime, when two porphyrin molecules involved in the reaction center are initially excited. In this regime we obtain pronounced quantum oscillations of the charge on the fullerene molecule with a decoherence time of about 20 fs (at liquid nitrogen temperatures). These results show a way to directly detect quantum effects in artificial photosynthetic systems.

Artificial photosynthetic reaction centers coupled to light-harvesting antennas.

We analyze a theoretical model for energy and electron transfer in an artificial photosynthetic system. The photosystem consists of a molecular triad (i.e., with a donor, a photosensitive unit, and an acceptor) coupled to four accessory light-harvesting-antenna pigments. The resonant energy transfer from the antennas to the artificial reaction center (the molecular triad) is described here by the Förster mechanism. We consider two different kinds of arrangements of the accessory light-harvesting pigments around the reaction center. The first arrangement allows direct excitation transfer to the reaction center from all the surrounding pigments. The second configuration transmits energy via a cascade mechanism along a chain of light-harvesting chromophores, where only one chromophore is connected to the reaction center. We show that the artificial photosynthetic system using the cascade energy transfer absorbs photons in a broader wavelength range and converts their energy into electricity with a higher efficiency than the system based on direct couplings between all the antenna chromophores and the reaction center.

Geometric stochastic resonance.

A Brownian particle moving across a porous membrane subject to an oscillating force exhibits stochastic resonance with properties which strongly depend on the geometry of the confining cavities on the two sides of the membrane. Such a manifestation of stochastic resonance requires neither energetic nor entropic barriers, and can thus be regarded as a purely geometric effect. The magnitude of this effect is sensitive to the geometry of both the cavities and the pores, thus leading to distinctive optimal synchronization conditions.

Modeling light-driven proton pumps in artificial photosynthetic reaction centers.

We study a model of a light-induced proton pump in artificial reaction centers. The model contains a molecular triad with four electron states (i.e., one donor state, two photosensitive group states, and one acceptor state) as well as a molecular shuttle having one electron and one proton-binding sites. The shuttle diffuses between the sides of the membrane and translocates protons energetically uphill: from the negative side to the positive side of the membrane, harnessing for this purpose the energy of the electron-charge separation produced by light. Using the methods of quantum transport theory we calculate the range of light intensity and transmembrane potentials that maximize both the light-induced proton current and the energy transduction efficiency. We also study the effect of temperature on proton pumping. The light-induced proton pump in our model gives a quantum yield of proton translocation of about 55%. Thus, our results explain previous experiments on these artificial photosynthetic reaction centers.

Kramers-like turnover in load-dependent activated dynamics.

Recent advancement of experimental techniques at the single molecule level has demonstrated how an external load affects a chemical reaction which controls the transport of biological motor proteins. Majority of these studies are concerned with thermodynamically open systems. We have examined a prototype model reaction in terms of inertial Brownian motion of a particle in a force field subjected to an overdamped motion of a viscous load coupled harmonically to the particle. A general analytical expression for the rate constant has been derived to demonstrate that depending on the strength of harmonic coupling and drag coefficient of the load a Kramers-like turnover can be realized in the spatial diffusion-limited regime. The turnover reduces to a crossover between the two states characterized by zero-load and finite load conditions.

Noise-induced transport in a rough ratchet potential.

Several years ago Zwanzig considered the diffusion in a potential that is spatially rough due to hierarchical structure of protein. We extend this idea to the overdamped Brownian dynamics in a one-dimensional periodic and rough ratchet potential. A general expression is obtained for the effective current at the steady state. Variation in both current and efficiency has been studied with respect to the amplitude of the roughness and an external nonequilibrium, nonthermal driving force. It has been shown that roughness hinders current quite significantly. Our analysis is corroborated by detailed numerical simulations and may be useful in the context of laser switching of current through molecular wires.

Kinetics of self-induced aggregation of Brownian particles: non-Markovian and non-Gaussian features.

In this paper we have explored a model for self-induced aggregation of Brownian particles incorporating non-Markovian and non-Gaussian character of the associated random noise processes. The time evolution of each individual is guided by an overdamped Langevin equation of motion with a nonlocal drift arising out of the imbalance in the local distribution of the other individuals. Our simulation results show that colored noise enhances the tendency of cluster formation. Another observation is that the critical noise variance decreases at first with increase in noise correlation time followed by an increase after exhibiting a minimum. Furthermore, in the long time limit the cluster number in the aggregation process exhibits depletion with time following a power law with an exponent which increases remarkably with non-Markovian character of the noise processes.

Noise correlation-induced splitting of Kramers' escape rate from a metastable state.

A correlation between two noise processes driving the thermally activated particles in a symmetric triple-well potential may cause a symmetry breaking and a difference in relative stability of the two side wells with respect to the middle one. This leads to an asymmetric localization of population and splitting of Kramers' rate of escape from the middle well, ensuring a preferential distribution of the products in the course of a parallel reaction.

Interference of stochastic resonances: splitting of Kramers' rate.

We consider the escape of particles located in the middle well of a symmetric triple well potential driven sinusoidally by two forces such that the potential wells rock as in stochastic resonance and the height of the potential barrier oscillates symmetrically about a mean as in resonant activation. It has been shown that depending on their phase difference the application of these two synchronized signals may lead to a splitting of time averaged Kramers' escape rate and a preferential product distribution in a parallel chemical reaction in the steady state.

A parametric variant of resonant activation: two-state model approach.

Mean first passage time of a periodically driven particle for its escape over a fluctuating barrier with wells remaining unbiased exhibits a resonance when the frequency of the driving field is varied. This parametric variant of resonant activation and associated features of noise induced transition are realized in terms of a two-state model to estimate analytically several quantifiers of the escape event. Numerical simulation on a continuous double-well model collaborates our theoretical analysis.

Stochastic energetics of quantum transport.

We examine the stochastic energetics of directed quantum transport due to rectification of nonequilibrium thermal fluctuations. We calculate the quantum efficiency of a ratchet device both in presence and absence of an external load to characterize two quantifiers of efficiency. It has been shown that the quantum current as well as efficiency in absence of load (Stokes efficiency) is higher as compared to classical current and efficiency, respectively, at low temperature. The conventional efficiency of the device in presence of load on the other hand is higher for a classical system in contrast to its classical counterpart. The maximum conventional efficiency being independent of the nature of the bath and the potential remains the same for classical and quantum systems.

Quantum escape kinetics over a fluctuating barrier.

The escape rate of a particle over a fluctuating barrier in a double-well potential exhibits resonance at an optimum value of correlation time of fluctuation. This has been shown to be important in several variants of kinetic model of chemical reactions. We extend the analysis of this phenomenon of resonant activation to quantum domain to show how quantization significantly enhances resonant activation at low temperature due to tunneling.

Noise-induced quantum transport.

We analyze the problem of directed quantum transport induced by external exponentially correlated telegraphic noise. In addition to quantum nature of the heat bath, nonlinearity of the periodic system potential brings in quantum contribution. We observe that quantization, in general, enhances classical current at low temperature, while the differences become insignificant at higher temperature. Interplay of quantum diffusion and quantum correction to system potential is analyzed for various ranges of temperature, correlation time and strength of external noise and asymmetry parameters. A possible experimental realization of the observed quantum effects in a superionic conductor placed in a random asymmetric dichotomous electric field has been suggested.