A mechanical model of normal and anomalous diffusion

The overdamped dynamics of a charged particle driven by an uniform electric field through a random sequence of scatterers in one dimension is investigated. Analytic expressions of the mean velocity and of the velocity power spectrum are presented. These show that above a threshold value of the field normal diffusion is superimposed to ballistic motion. The diffusion constant can be given explicitly. At the threshold field the transition between conduction and localization is accompanied by an anomalous diffusion. Our results exemplify that, even in the absence of time-dependent stochastic forces, a purely mechanical model equipped with a quenched disorder can exhibit normal as well as anomalous diffusion, the latter emerging as a critical property.Comment: 16 pages, no figure

Quantum entanglement in photosynthetic light harvesting complexes

Light harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long time scales despite the decohering effects of their environments. Within this context, we analyze entanglement in multi-chromophoric light harvesting complexes, and establish methods for quantification of entanglement by presenting necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson (FMO) protein to extract the initial state and temperature dependencies of entanglement. We show that while FMO in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amount of long-range and multipartite entanglement exists even at physiological temperatures. This constitutes the first rigorous quantification of entanglement in a biological system. Finally, we discuss the practical utilization of entanglement in densely packed molecular aggregates such as light harvesting complexes.Comment: 14 pages, 7 figures. Improved presentation, published versio

Hierarchical Equations of Motion Approach to Quantum Thermodynamics

We present a theoretical framework to investigate quantum thermodynamic processes under non-Markovian system-bath interactions on the basis of the hierarchical equations of motion (HEOM) approach, which is convenient to carry out numerically "exact" calculations. This formalism is valuable because it can be used to treat not only strong system-bath coupling but also system-bath correlation or entanglement, which will be essential to characterize the heat transport between the system and quantum heat baths. Using this formalism, we demonstrated an importance of the thermodynamic effect from the tri-partite correlations (TPC) for a two-level heat transfer model and a three-level autonomous heat engine model under the conditions that the conventional quantum master equation approaches are failed. Our numerical calculations show that TPC contributions, which distinguish the heat current from the energy current, have to be take into account to satisfy the thermodynamic laws.Comment: 9 pages, 4 figures. As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and G. Adesso (eds.), "Thermodynamics in the quantum regime - Recent Progress and Outlook", (Springer International Publishing

Non-Markovian stochastic description of quantum transport in photosynthetic systems

We analyze several aspects of the transport dynamics in the LH1-RC core of purple bacteria, which consists basically in a ring of antenna molecules that transport the energy into a target molecule, the reaction center, placed in the center of the ring. We show that the periodicity of the system plays an important role to explain the relevance of the initial state in the transport efficiency. This picture is modified, and the transport enhanced for any initial state, when considering that molecules have different energies, and when including their interaction with the environment. We study this last situation by using stochastic Schr{\"o}dinger equations, both for Markovian and non-Markovian type of interactions.Comment: 21 pages, 5 figure

A self-consistent quantum master equation approach to molecular transport

We propose a self-consistent generalized quantum master equation (GQME) to describe electron transport through molecular junctions. In a previous study [M.Esposito and M.Galperin. Phys. Rev. B 79, 205303 (2009)], we derived a time-nonlocal GQME to cure the lack of broadening effects in Redfield theory. To do so, the free evolution used in the Born-Markov approximation to close the Redfield equation was replaced by a standard Redfield evolution. In the present paper, we propose a backward Redfield evolution leading to a time-local GQME which allows for a self-consistent procedure of the GQME generator. This approach is approximate but properly reproduces the nonequilibrium steady state density matrix and the currents of an exactly solvable model. The approach is less accurate for higher moments such as the noise.Comment: 9 pages, 4 figure

Electronic Coherence Dephasing in Excitonic Molecular Complexes: Role of Markov and Secular Approximations

We compare four different types of equations of motion for reduced density matrix of a system of molecular excitons interacting with thermodynamic bath. All four equations are of second order in the linear system-bath interaction Hamiltonian, with different approximations applied in their derivation. In particular we compare time-nonlocal equations obtained from so-called Nakajima-Zwanzig identity and the time-local equations resulting from the partial ordering prescription of the cummulant expansion. In each of these equations we alternatively apply secular approximation to decouple population and coherence dynamics from each other. We focus on the dynamics of intraband electronic coherences of the excitonic system which can be traced by coherent two-dimensional spectroscopy. We discuss the applicability of the four relaxation theories to simulations of population and coherence dynamics, and identify features of the two-dimensional coherent spectrum that allow us to distinguish time-nonlocal effects.Comment: 14 pages, 8 figure

Suppression of quantum oscillations and the dependence on site energies in electronic excitation transfer in the Fenna-Matthews-Olson trimer

Energy transfer in the photosynthetic complex of the Green Sulfur Bacteria known as the Fenna-Matthews-Olson (FMO) complex is studied theoretically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll (BChl) molecule into account. We find that in all considered cases there is very little transfer between the monomers. Since it is believed that the eighth BChl is located near the main light harvesting antenna we look at the differences in transfer between the situation when BChl 8 is initially excited and the usually considered case when BChl 1 or 6 is initially excited. We find strong differences in the transfer dynamics, both qualitatively and quantitatively. When the excited state dynamics is initialized at site eight of the FMO complex, we see a slow exponential-like decay of the excitation. This is in contrast to the oscillations and a relatively fast transfer that occurs when only seven sites or initialization at sites 1 and 6 is considered. Additionally we show that differences in the values of the electronic transition energies found in the literature lead to a large difference in the transfer dynamics

Exciton Dynamics in Photosynthetic Complexes: Excitation by Coherent and Incoherent Light

In this paper we consider dynamics of a molecular system subjected to external pumping by a light source. Within a completely quantum mechanical treatment, we derive a general formula, which enables to asses effects of different light properties on the photo-induced dynamics of a molecular system. We show that once the properties of light are known in terms of certain two-point correlation function, the only information needed to reconstruct the system dynamics is the reduced evolution superoperator. The later quantity is in principle accessible through ultrafast non-linear spectroscopy. Considering a direct excitation of a small molecular antenna by incoherent light we find that excitation of coherences is possible due to overlap of homogeneous line shapes associated with different excitonic states. In Markov and secular approximations, the amount of coherence is significant only under fast relaxation, and both the populations and coherences between exciton states become static at long time. We also study the case when the excitation of a photosynthetic complex is mediated by a mesoscopic system. We find that such case can be treated by the same formalism with a special correlation function characterizing ultrafast fluctuations of the mesoscopic system. We discuss bacterial chlorosom as an example of such a mesoscopic mediator and propose that the properties of energy transferring chromophore-protein complexes might be specially tuned for the fluctuation properties of their associated antennae.Comment: 12 page

L\'{e}vy scaling: the Diffusion Entropy Analysis applied to DNA sequences

We address the problem of the statistical analysis of a time series generated by complex dynamics with a new method: the Diffusion Entropy Analysis (DEA) (Fractals, {\bf 9}, 193 (2001)). This method is based on the evaluation of the Shannon entropy of the diffusion process generated by the time series imagined as a physical source of fluctuations, rather than on the measurement of the variance of this diffusion process, as done with the traditional methods. We compare the DEA to the traditional methods of scaling detection and we prove that the DEA is the only method that always yields the correct scaling value, if the scaling condition applies. Furthermore, DEA detects the real scaling of a time series without requiring any form of de-trending. We show that the joint use of DEA and variance method allows to assess whether a time series is characterized by L\'{e}vy or Gauss statistics. We apply the DEA to the study of DNA sequences, and we prove that their large-time scales are characterized by L\'{e}vy statistics, regardless of whether they are coding or non-coding sequences. We show that the DEA is a reliable technique and, at the same time, we use it to confirm the validity of the dynamic approach to the DNA sequences, proposed in earlier work.Comment: 24 pages, 9 figure

Eco-friendly one-pot synthesis of Prussian blue-embedded magnetic hydrogel beads for the removal of cesium from water

A simple one-step approach to fabricating Prussian blue-embedded magnetic hydrogel beads (PBMHBs) was fabricated for the effective magnetic removal of radioactive cesium (Cs-137) from water. Through the simple dropwise addition of a mixed aqueous solution of iron salts, commercial PB and polyvinyl alcohol (PVA) to an ammonium hydroxide (NH4OH) solution, the formation of hydrogel beads and the encapsulation of PB in beads were achieved in one pot through the gelation of PVA with in situ-formed iron oxide nanoparticles as the cross-linker. The obtained PB-MHBs, with 43.77 weight %of PB, were stable without releasing PB for up to 2 weeks and could be effectively separated from aqueous solutions by an external magnetic field, which is convenient for the large-scale treatment of Cs-contaminated water. Detailed Cs adsorption studies revealed that the adsorption isotherms and kinetics could be effectively described by the Langmuir isotherm model and the pseudo-second-order model, respectively. Most importantly, the PB-MHBs exhibited excellent selectivity for Cs-137 in (137)Cscontaminated simulated groundwater (55 Bq/g) with a high removal efficiency (>99.5%), and the effective removal of Cs-137 from real seawater by these PB-MHBs demonstrated the excellent potential of this material for practical application in the decontamination of Cs-137-contaminated seawate