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arXiv2013

Vibronic speed-up of the excitation energy transfer in the Fenna-Matthews-Olson complex

We show that the efficient excitation energy transfer in the Fenna-Matthews-Olson molecular aggregate under realistic physiological conditions is fueled by underdamped vibrations of the embedding proteins. For this, we present numerically exact results for the quantum dynamics of the excitons in the presence of nonadiabatic vibrational states in the Fenna-Matthews-Olson aggregate employing a environmental fluctuation spectral function derived from experiments. Assuming the prominent 180 cm$^{-1}$ vibrational mode to be underdamped, we observe, on the one hand, besides vibrational coherent oscillations between different excitation levels of the vibration also prolonged electronic coherent oscillations between the initially excited site and its neighbours. On the other hand, however, the underdamped vibrations provide additional channels for the excitation energy transfer and by this increase the transfer speed by up to $30\%$ .

physics.chem-ph↗

arXiv2013

Dating a random walk: Statistics of the duration time of a random walk given its present position

We consider the distribution of the duration time, the time elapsed since it began, of a diffusion process given its present position, under the assumption that the process began at the origin. For unbiased diffusion, the distribution does not exist (it is identically zero) for one and two dimensional systems. We find the explicit expression for the distribution for three and higher dimensions and discuss the behavior of the duration time statistics: we find that the expected duration time exists only for dimensions five and higher, whereas the variance becomes finite for seven dimensions and above. We then turn to the case of biased diffusion. The drift velocity introduces a new time scale and the resulting statistics arise from the interplay of the diffusive time scale and the drift time scale. For these systems all the moments exist and explicit expressions are presented and discussed for the expected duration time and its variance for all dimensions.

cond-mat.stat-mech↗

arXiv2013

Point-to-set correlations and instantons

For a generic many-body system, we define a soft point-to-set correlation function. We then show that this function accepts a representation in terms of an effective overlap field theory. In particular, instantons in this effective field theory encode point-to-set correlations for supercooled liquids.

cond-mat.dis-nn↗

arXiv2013

Phase behavior under the averaging over disorder realizations

Effects of the averaging over disorder realizations (samples) on the phase behavior are analyzed in terms of the mean field approximation for the random field Ising model with infinite range interactions. It is found that the averaging is equivalent to a drastic modification in the statistics of the quenched variables. In its turn, this lowers the critical temperature of a second-order phase transition or, depending on the sampling, even suppresses the ordered phase. Possible first order transitions are shown to be softened by the sample averaging. Common issues and differences in the interpretation of these effects in the context of the simulation and experimental studies are discussed.

cond-mat.stat-mech↗

arXiv2013

Dispersions of ellipsoidal particles in a nematic liquid crystal

Colloidal particles dispersed in a partially ordered medium, such as a liquid crystal (LC) phase, disturb its alignment and are subject to elastic forces. These forces are long-ranged, anisotropic and tunable through temperature or external fields, making them a valuable asset to control colloidal assembly. The latter is very sensitive to the particle geometry since it alters the interactions between the colloids. We here present a detailed numerical analysis of the energetics of elongated objects, namely prolate ellipsoids, immersed in a nematic host. The results, complemented with qualitative experiments, reveal novel LC configurations with peculiar topological properties around the ellipsoids, depending on their aspect ratio and the boundary conditions imposed on the nematic order parameter. The latter also determine the preferred orientation of ellipsoids in the nematic field, because of elastic torques, as well as the morphology of particles aggregates.

cond-mat.soft↗

arXiv2013

Hysteresis behavior of the anisotropic quantum Heisenberg model driven by periodic magnetic field

Dynamic behavior of a quantum Heisenberg ferromagnet in the presence of a periodically oscillating magnetic field has been analyzed by means of the effective field theory with two spin cluster. The dynamic equation of motion has been constructed with the help of a Glauber type stochastic process and solved for a simple cubic lattice. After the phase diagrams given, the behavior of the hysteresis loop area, coercive field and remanent magnetization with the anisotropy in the exchange interaction has been investigated in detail. Especially, by comparing of the magnitudes of the hysteresis loop area in the high anisotropy limit (i.e. Ising model) and low anisotropy limit (i.e. isotropic Heisenberg model), detailed description of the hysteresis loop area with the anisotropy in the exchange interaction given. Some interesting features have been obtained about this behavior as well as in phase diagrams such as tricritical points.

cond-mat.stat-mech↗

arXiv2013

Ultrametricity and long-range correlations in the Edwards-Anderson spin glass

In recent times, the theoretical study of the three-dimensional Edwards-Anderson model has produced several rigorous results on the nature of the spin-glass phase. In particular, it has been shown that, as soon as the overlap distribution is non-trivial, ultrametricity holds. However, these theorems are valid only in the thermodynamical limit and are therefore of uncertain applicability for (perennially off-equilibrium) experimental spin glasses. In addition, their basic assumption of non-triviality is still hotly debated. This paper intends to show that the predictions stemming from ultrametricity are already well satisfied for the lattice sizes where numerical simulations are possible (i.e., up to $V = 32^3$ spins) and are, therefore, relevant at experimental scales. To this end we introduce a three-replica correlation function, which evinces the ultrametric properties of the system and is shown to scale in the same way as the overlap correlation function.

cond-mat.dis-nn↗

arXiv2013

New conserved structural fields for supercooled liquids

By considering Voronoi tessellations of the configurations of a fluid, we propose two new conserved fields, which provide structural information not fully accounted for by the usual 2-point density field fluctuations (structure factor). One of these fields is scalar and associated to the Voronoi cell volumes, whereas the other one, termed the "geometrical polarisation", is vectorial, related to the very local anisotropy of the configurations. We study the static and dynamical properties of these fields in the supercooled regime of a model glass-forming liquid. We show in particular that the geometrical polarisation is both statically correlated to the force field and contrary to it develops a plateau regime when the temperature is lowered. We attribute this behaviour to the microsopic disorder of the underlying inherent structures (IS) which dictate the dynamics on time scales larger than the true microscopic time, in the strong supercooled regime. In this respect, this work raises the issue of to what extent the inter IS dynamics, intrinsically anisotropic and collective (cf. T.B. Schrøder et al. {\it J. of Chem. Phys.}, {\bf 112}, 9834 (2000)), could be related to their polarisation field.

cond-mat.stat-mech↗

arXiv2013

Conception of main local-strong-nonequilibriun state

A new conception of main local-strong-nonequilibrium state is proposed on the basis of development of the conception local equilibrium state. At list the conception is intended for description of evolution of internal defect structure in solids subjected severe external influences, for example, severe plastic deformation, radiation and so on, but can be developed on other closely related phenomena.

cond-mat.stat-mech↗

arXiv2013

Unfolding kinetics of periodic DNA hairpins

DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyse for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterising the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.

physics.bio-ph↗

arXiv2013

Direct observation of any two-point quantum correlation function

The existence of noncompatible observables in quantum theory makes a direct operational interpretation of two-point correlation functions problematic. Here we challenge such a view by explicitly constructing a measuring scheme that, independently of the input state $ρ$ and observables $A$ and $B$, performs an unbiased optimal estimation of the two-point correlation function $\operatorname{Tr}[A \ ρ\ B]$. This shows that, also in quantum theory, two-point correlation functions are as operational as any other expectation value. A very simple probabilistic implementation of our proposal is presented.

quant-ph↗

arXiv2013

Steepest entropy ascent paths towards the Max-Ent distribution

With reference to two general probabilistic description frameworks, Information Theory and Classical Statistical Mechanics, we discuss the geometrical reasoning and mathematical formalism leading to the differential equation that defines in probability space the smooth path of Steepest Entropy Ascent (SEA) connecting an arbitrary initial probability distribution to the unique Maximum Entropy (MaxEnt) distribution with the same mean values of a set of constraints. The SEA path is relative to a metric chosen to measure distances in square-root probability distribution space. Along the resulting SAE path, the metric turns out to be proportional to the concept of Onsager resistivity generalized to the far non-equilibrium domain. The length of the SEA path to MaxEnt provides a novel global measure of degree of disequilibrium (DoD) of the initial probability distribution, whereas a local measure of DoD is given by the norm of a novel generalized concept of non-equilibrium affinity.

math-ph↗

arXiv2013

Self-assembly of Brownian motor by reduction of its effective temperature

Emergence, optimization and stability of a motor-like motion in a fluctuating environment are analyzed. The emergence of motion is shown to be a general phenomenon. A motor converges to the state with the minimum of effective temperature and with the corresponding minimum in the rate of conformation changes similarly as some stochastic processes converge to the states with minimum diffusion activity. This mechanism is important to bacterial foraging (chemotaxis). This work, therefore, raises an analogy between chemotaxis and the emergence of living-like systems. The implications include the deviation of stable natural or artificial machines from the minimum entropy production principle, with a novel self-assembly mechanism for the emergence of the first molecular motors and for mass fabrication of the future nanodevices.

cond-mat.stat-mech↗

arXiv2013

Undulations in a weakly interacting mechanically generated molecular braid under tension

We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid, steric interactions between the molecules, and external mechanical forces. In this model, both sets of ends, of the two molecules, are considered to be separated by a fixed distance apart much larger than the radius of the braid. One set of ends are rotated to generate a braid of a certain number of pitches (or turns), while the other set remains fixed. This model may describe the situation in which the ends of each molecule are attached to a substrate and a magnetic bead; to the latter a pulling force and rotational torque can be applied. We discuss various aspects of our model. Most importantly, an expression for the free energy is given, from which equations, determining the various geometric parameters of the braid, can be obtained. By numerically solving these equations, we give predictions from the model for the external torque needed to produce a braid with a certain number of turns per bending persistence length, as well as the end to end extension of the two molecules for a given pulling force. Other geometric parameters, as well as the lateral force required to keep the ends of the two molecules apart, are also calculated.

cond-mat.soft↗

arXiv2013

Quantum Jarzynski equalities for the energy costs of the information processes

We present quantum versions of the Jarzynski equality for the energy costs of information processes, namely the measurement and the information erasure. We also obtain inequalities for the energy costs of the information processes, using the Jensen inequality. The inequalities include Sagawa and Ueda's inequalities [Phys. Rev. Lett. 102, 250602 (2009)] as a special case.

cond-mat.stat-mech↗

arXiv2013

Proof and extension of the resistance formula for an m x n cobweb network conjectured by Tan, Zhou and Yang

An m x n cobweb network consists of n radial lines emanating from a center and connected by $m$ concentric n-sided polygons. A conjecture of Tan, Zhou and Yang for the resistance from center to perimeter of the cobweb is proved by extending the method used by the above authors to derive formulae for m = 1, 2 and 3 and general n. The resistance of an m x (s+t+1) fan network from the apex to a point on the boundary distant s from the corner is also found.

cond-mat.stat-mech↗

arXiv2013

An effective-field theory study of hexagonal Ising nanowire: Thermal and magnetic properties

By means of the effective-field theory (EFT) with correlations, the thermodynamic and magnetic quantities such as magnetization, susceptibility, internal energy, free energy, hysteresis curves and compensation behaviors of the spin-1/2 hexagonal Ising nanowire (HIN) system with core/shell structure have been presented. The hysteresis curves are obtained for different values of the system parameters on both ferromagnetic and antiferromagnetic case. It has been shown that the system only undergoes a second-order phase transition. Moreover, from the thermal variations of the total magnetization, the five compensation types can be found under certain conditions, namely the Q-, R-, S-, P-, and N-types.

cond-mat.stat-mech↗

arXiv2013

Quantum H-theorem and irreversibility in quantum mechanics

We investigate temporal evolution of von Neumann's entropy in exemplary quantum mechanical systems and show that it grows in systems evolving with incrementally increasing decoherence during scattering processes. We demonstrate that the origin of irreversibility lies in complexity of preparing time-reversed quantum states due to entanglement and in partitioning of the wave function of the evolving system.

quant-ph↗