Coherent and incoherent dynamics in excitonic energy transfer: correlated fluctuations and off-resonance effects

We study the nature of the energy transfer process within a pair of coupled two-level systems (donor and acceptor) subject to interactions with the surrounding environment. Going beyond a standard weak-coupling approach, we derive a master equation within the polaron representation that allows for investigation of both weak and strong system-bath couplings, as well as reliable interpolation between these two limits. With this theory, we are then able to explore both coherent and incoherent regimes of energy transfer within the donor-acceptor pair. We elucidate how the degree of correlation in the donor and acceptor fluctuations, the donor-acceptor energy mismatch, and the range of the environment frequency distribution impact upon the energy transfer dynamics. In the resonant case (no energy mismatch) we describe in detail how a crossover from coherent to incoherent transfer dynamics occurs with increasing temperature [A. Nazir, Phys. Rev. Lett. 103, 146404 (2009)], and we also explore how fluctuation correlations are able to protect coherence in the energy transfer process. We show that a strict crossover criterion is harder to define when off-resonance, though we find qualitatively similar population dynamics to the resonant case with increasing temperature, while the amplitude of coherent population oscillations also becomes suppressed with growing site energy mismatch.Comment: 14 pages, 7 figures, builds upon PRL 103, 146404 (2009) (arXiv:0906.0592). Comments welcome. V2 - Section IV shortened to improve presentation, references updated, new Imperial College affiliation added for A. Nazir. Published versio

Accurate prediction of gene feedback circuit behavior from component properties

A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology

Finite-temperature time-dependent variation with multiple Davydov states

The Dirac-Frenkel time-dependent variational approach with Davydov Ans\"atze is a sophisticated, yet efficient technique to obtain an acuurate solution to many-body Schr\"odinger equations for energy and charge transfer dy- namics in molecular aggregates and light-harvesting complexes. We extend this variational approach to finite temperatures dynamics of the spin-boson model by adopting a Monte Carlo importance sampling method. In or- der to demonstrate the applicability of this approach, we compare real-time quantum dynamics of the spin-boson model calculated with that from numerically exact iterative quasiadiabatic propagator path integral (QUAPI) technique. The comparison shows that our variational approach with the single Davydov Ans\"atze is in excellent agreement with the QUAPI method at high temperatures, while the two differ at low temperatures. Accuracy in dynamics calculations employing a multitude of Davydov trial states is found to improve substantially over the single Davydov Ansatz, especially at low temperatures. At a moderate computational cost, our variational approach with the multiple Davydov Ansatz is shown to provide accurate spin-boson dynamics over a wide range of temperatures and bath spectral densities.Comment: 8 pages, 3 figure

Multiple-charge transfer and trapping in DNA dimers

We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated hopping and the bond-bond interaction, which were recently calculated by Starikov [E. B. Starikov, Phil. Mag. Lett. {\bf 83}, 699 (2003)] for different DNA dimers. The electronic degrees of freedom are coupled to an ohmic or a super-ohmic bath serving as dissipative environment. We employ the numerical renormalization group method in the nuclear tunneling regime and compare the results to Marcus theory for the thermal activation regime. For realistic parameters, the rate that at least one charge is transferred from the donor to the acceptor in the subspace of two excess electrons significantly exceeds the rate in the single charge sector. Moreover, the dynamics is strongly influenced by the Coulomb matrix elements. We find sequential and pair transfer as well as a regime where both charges remain self-trapped. The transfer rate reaches its maximum when the difference of the on-site and inter-site Coulomb matrix element is equal to the reorganization energy which is the case in a GC-GC dimer. Charge transfer is completely suppressed for two excess electrons in AT-AT in an ohmic bath and replaced by damped coherent electron-pair oscillations in a super-ohmic bath. A finite bond-bond interaction $W$ alters the transfer rate: it increases as function of $W$ when the effective Coulomb repulsion exceeds the reorganization energy (inverted regime) and decreases for smaller Coulomb repulsion

Effects of tunnelling and asymmetry for system-bath models of electron transfer

We apply the newly derived nonadiabatic golden-rule instanton theory to asymmetric models describing electron-transfer in solution. The models go beyond the usual spin-boson description and have anharmonic free-energy surfaces with different values for the reactant and product reorganization energies. The instanton method gives an excellent description of the behaviour of the rate constant with respect to asymmetry for the whole range studied. We derive a general formula for an asymmetric version of Marcus theory based on the classical limit of the instanton and find that this gives significant corrections to the standard Marcus theory. A scheme is given to compute this rate based only on equilibrium simulations. We also compare the rate constants obtained by the instanton method with its classical limit to study the effect of tunnelling and other quantum nuclear effects. These quantum effects can increase the rate constant by orders of magnitude.Comment: 10 pages, 3 figure

Generalization of escape rate from a metastable state driven by external cross-correlated noise processes

We propose generalization of escape rate from a metastable state for externally driven correlated noise processes in one dimension. In addition to the internal non-Markovian thermal fluctuations, the external correlated noise processes we consider are Gaussian, stationary in nature and are of Ornstein-Uhlenbeck type. Based on a Fokker-Planck description of the effective noise processes with finite memory we derive the generalized escape rate from a metastable state in the moderate to large damping limit and investigate the effect of degree of correlation on the resulting rate. Comparison of the theoretical expression with numerical simulation gives a satisfactory agreement and shows that by increasing the degree of external noise correlation one can enhance the escape rate through the dressed effective noise strength.Comment: 9 pages, 1 figur

Transport and optical response of molecular junctions driven by surface plasmon-polaritons

We consider a biased molecular junction subjected to external time-dependent electromagnetic field. The field for two typical junction geometries (bowtie antennas and metal nanospheres) is calculated within finite-difference time-domain technique. Time-dependent transport and optical response of the junctions is calculated within non-equilibrium Green's function approach expressed in a form convenient for description of multi-level systems. We present numerical results for a two-level (HOMO-LUMO) model, and discuss influence of localized surface plasmon polariton modes on transport.Comment: 9 pages, 6 figure

Quantum Transition State Theory for proton transfer reactions in enzymes

We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of kinetic isotope effects for two classes of enzymes which have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction due to the environment is weak and only slightly modifies the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental degrees of freedom with frequencies much less than 1000 cm$^{-1}$ do not have a significant effect on quantum corrections to the reaction rate.Comment: Aspects of the article are discussed at condensedconcepts.blogspot.co

Assigning the right credit to the wrong action: compulsivity in the general population is associated with augmented outcome-irrelevant value-based learning.

Funder: NIHR Senior InvestigatorCompulsive behavior is enacted under a belief that a specific act controls the likelihood of an undesired future event. Compulsive behaviors are widespread in the general population despite having no causal relationship with events they aspire to influence. In the current study, we tested whether there is an increased tendency to assign value to aspects of a task that do not predict an outcome (i.e., outcome-irrelevant learning) among individuals with compulsive tendencies. We studied 514 healthy individuals who completed self-report compulsivity, anxiety, depression, and schizotypal measurements, and a well-established reinforcement-learning task (i.e., the two-step task). As expected, we found a positive relationship between compulsivity and outcome-irrelevant learning. Specifically, individuals who reported having stronger compulsive tendencies (e.g., washing, checking, grooming) also tended to assign value to response keys and stimuli locations that did not predict an outcome. Controlling for overall goal-directed abilities and the co-occurrence of anxious, depressive, or schizotypal tendencies did not impact these associations. These findings indicate that outcome-irrelevant learning processes may contribute to the expression of compulsivity in a general population setting. We highlight the need for future research on the formation of non-veridical action-outcome associations as a factor related to the occurrence and maintenance of compulsive behavior

Credit assignment to state-independent task representations and its relationship with model-based decision making.

Model-free learning enables an agent to make better decisions based on prior experience while representing only minimal knowledge about an environment's structure. It is generally assumed that model-free state representations are based on outcome-relevant features of the environment. Here, we challenge this assumption by providing evidence that a putative model-free system assigns credit to task representations that are irrelevant to an outcome. We examined data from 769 individuals performing a well-described 2-step reward decision task where stimulus identity but not spatial-motor aspects of the task predicted reward. We show that participants assigned value to spatial-motor representations despite it being outcome irrelevant. Strikingly, spatial-motor value associations affected behavior across all outcome-relevant features and stages of the task, consistent with credit assignment to low-level state-independent task representations. Individual difference analyses suggested that the impact of spatial-motor value formation was attenuated for individuals who showed greater deployment of goal-directed (model-based) strategies. Our findings highlight a need for a reconsideration of how model-free representations are formed and regulated according to the structure of the environment