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Robert J. Silbey

Publications and source records attributed to Robert J. Silbey.

At least 19 recordsLinked to original sources
arXiv2012

Efficient Energy Transfer in Light-Harvesting Systems, II: Quantum-Classical Comparison, Flux Network, and Robustness Analysis

Following the calculation of optimal energy transfer in thermal environment in our first paper (Wu et al., New J. Phys., 2010, 12, 105012), full quantum dynamics and leading-order `classical' hopping kinetics are compared in the seven-site Fenna-Matthews-Olson (FMO) protein complex. The difference between these two dynamic descriptions is due to higher-order quantum corrections. Two thermal bath models, classical white noise (the Haken-Strobl-Reineker model) and quantum Debye model, are considered. In the seven-site FMO model, we observe that higher-order corrections lead to negligible changes in the trapping time or in energy transfer efficiency around the optimal and physiological conditions (2% in the HSR model and 0.1% in the quantum Debye model for the initial site at BChl 1). However, using the concept of integrated flux, we can identify significant differences in branching probabilities of the energy transfer network between hopping kinetics and quantum dynamics (26% in the HSR model and 32% in the quantum Debye model for the initial site at BChl 1). This observation indicates that the quantum coherence can significantly change the distribution of energy transfer pathways in the flux network with the efficiency nearly the same. The quantum-classical comparison of the average trapping time with the removal of the bottleneck site, BChl 4, demonstrates the robustness of the efficient energy transfer by the mechanism of multi-site quantum coherence. To reconcile with the latest eight-site FMO model, the quantum-classical comparison with the flux network analysis is summarized in the appendix. The eight-site FMO model yields similar trapping time and network structure as the seven-site FMO model but leads to a more disperse distribution of energy transfer pathways.

physics.chem-ph↗
arXiv2012

Generic Mechanism of Optimal Energy Transfer Efficiency: A Scaling Theory of the Mean First Passage Time in Exciton Systems

An asymptotic scaling theory is presented using the conceptual basis of trapping-free subspace (i.e., orthogonal subspace) to establish the generic mechanism of optimal efficiency of excitation energy transfer (EET) in light-harvesting systems. Analogous to Kramers' turnover in classical rate theory, the enhanced efficiency in the weak damping limit and the suppressed efficiency in the strong damping limit define two asymptotic scaling regimes, which are interpolated to predict the functional form of optimal efficiency of the trapping-free subspace. In the presence of static disorder, the scaling law of transfer time with respect to dephasing rate changes from linear to square root, suggesting a weaker dependence on the environment. Though formulated in the context of EET, the analysis and conclusions apply in general to open quantum processes, including electron transfer, fluorescence emission, and heat conduction.

quant-ph↗
arXiv2011

Correlated interaction fluctuations in photosynthetic complexes

The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies of and interactions between the chlorophyll molecules, and due to the fact that different fluctuations will partially be caused by the same environmental factors, correlations between the various fluctuations will occur. We argue that fluctuations of the interactions should in general not be neglected, as these have a considerable impact on population transfer rates, decoherence rates and the efficiency of photosynthetic complexes. Furthermore, while correlations between transition energy fluctuations have been studied, we provide the first quantitative study of the effect of correlations between interaction fluctuations and transition energy fluctuations, and of correlations between the various interaction fluctuations. It is shown that these additional correlations typically lead to changes in interchromophore transfer rates, population oscillations and can lead to a limited enhancement of the light harvesting efficiency.

physics.bio-ph↗
arXiv2010

Efficient energy transfer in light-harvesting systems, I: optimal temperature, reorganization energy, and spatial-temporal correlations

Understanding the mechanisms of efficient and robust energy transfer in light-harvesting systems provides new insights for the optimal design of artificial systems. In this paper, we use the Fenna-Matthews-Olson (FMO) protein complex and phycocyanin 645 (PC 645) to explore the general dependence on physical parameters that help maximize the efficiency and maintain its stability. With the Haken-Strobl model, the maximal energy transfer efficiency (ETE) is achieved under an intermediate optimal value of dephasing rate. To avoid the infinite temperature assumption in the Haken-Strobl model and the failure of the Redfield equation in predicting the Forster rate behavior, we use the generalized Bloch-Redfield (GBR) equation approach to correctly describe dissipative exciton dynamics and find that maximal ETE can be achieved under various physical conditions, including temperature, reorganization energy, and spatial-temporal correlations in noise. We also identify regimes of reorganization energy where the ETE changes monotonically with temperature or spatial correlation and therefore cannot be optimized with respect to these two variables.

physics.chem-ph↗
arXiv2009

The Work-Hamiltonian Connection and the Usefulness of the Jarzynski Equality for Free Energy Calculations

The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes. In this paper, we discuss the relationship between two possible definitions of free energy and show how some recent disagreements regarding the applicability of the Jarzynski equality are the result of different authors using different definitions of free energy. Finally, in light of the recently raised doubts, we explicitly demonstrate that it is indeed possible to obtain physically relevant free energy profiles from molecular pulling experiments by using the Jarzynski equality and the results of Hummer and Szabo.

cond-mat.stat-mech↗
arXiv2008

Diffusion of two particles with a finite interaction potential in one dimension

We investigate the dynamics of two interacting diffusing particles in an infinite effectively one dimensional system; the particles interact through a step-like potential of width b and height phi_0 and are allowed to pass one another. By solving the corresponding 2+1-variate Fokker-Planck equation an exact result for the two particle conditional probability density function (PDF) is obtained for arbitrary initial particle positions. From the two-particle PDF we obtain the overtake probability, i.e. the probability that the two particles has exchanged positions at time t compared to the initial configuration. In addition, we calculate the trapping probability, i.e. the probability that the two particles are trapped close to each other (within the barrier width b) at time t, which is mainly of interest for an attractive potential, phi_0<0. We also investigate the tagged particle PDF, relevant for describing the dynamics of one particle which is fluorescently labeled. Our analytic results are in excellent agreement with the results of stochastic simulations, which are performed using the Gillespie algorithm.

q-bio.BM↗
arXiv2008

Single-file dynamics with different diffusion constants

We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally efficient stochastic simulation technique based on the Gillespie algorithm. We find that the mean square displacement for a tagged particle scales as the square root of time (as for identical particles) for long times, with a prefactor which depends on the diffusion constants for the particles; these results are in excellent agreement with very recent analytic predictions in the mathematics literature.

cond-mat.stat-mech↗
arXiv2007

Unique mechanisms from finite two-state trajectories

Single molecule data made of on and off events are ubiquitous. Famous examples include enzyme turnover, probed via fluorescence, and opening and closing of ion-channel, probed via the flux of ions. The data reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process, but the determination of the underlying KS is difficult, and sometimes even impossible, due to the loss of information in the mapping of the mutli-dimensional KS onto two dimensions. A way to deal with this problem considers canonical (unique) forms. (Unique canonical form is constructed from an infinitely long trajectory, but many KSs.) Here we introduce canonical forms of reduced dimensions that can handle any KS (i.e. also KSs with symmetry and irreversible transitions). We give the mapping of KSs into reduced dimensions forms, which is based on topology of KSs, and the tools for extracting the reduced dimensions form from finite data. The canonical forms of reduced dimensions constitute a powerful tool in discriminating between KSs.

q-bio.QM↗
arXiv2007

Utilizing the information content in two-state trajectories

The signal from many single molecule experiments monitoring molecular processes, such as enzyme turnover via fluorescence and opening and closing of ion channel via the flux of ions, consists of a time series of stochastic on and off (or open and closed) periods, termed a two-state trajectory. This signal reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process. The determination of the underlying KS is difficult and sometimes even impossible due to the loss of information in the mapping of the mutli dimensional KS onto two dimensions. Here we introduce a new procedure that efficiently and optimally relates the signal to all equivalent underlying KSs. This procedure partitions the space of KSs into canonical (unique) forms that can handle any KS, and obtains the topology and other details of the canonical form from the data without the need for fitting. Also established are relationships between the data and the topology of the canonical form to the on-off connectivity of a KS. The suggested canonical forms constitute a powerful tool in discriminating between KSs. Based on our approach, the upper bound on the information content in two state trajectories is determined.

q-bio.QM↗
arXiv2007

Correctly validating results from single molecule data: the case of stretched exponential decay in the catalytic activity of single lipase B molecules

The question of how to validate and interpret correctly the waiting time probability density functions (WT-PDFs) from single molecule data is addressed. It is shown by simulation that when a stretched exponential WT-PDF, with a stretched exponent alfa and a time scale parameter tau, generates the off periods of a two-state trajectory, a reliable recovery of the input WT-PDF from the trajectory is obtained even when the bin size used to define the trajectory, dt, is much larger than the parameter tau. This holds true as long as the first moment of the WT-PDF is much larger than dt. Our results validate the results in an earlier study of the activity of single Lipase B molecules and disprove recent related critique.

q-bio.SC↗
arXiv2006

Fluorescence Intermittency of A Single Quantum System and Anderson Localization

The nature of fluorescence intermittency for semiconductor quantum dots (QD) and single molecules (SM) is proposed as a manifestation of Anderson localization. The power law like distribution for the \emph{on} time is explained as due to the interaction between QD/SM with a random environment. In particular, we find that the \emph{on}-time probability distribution behaves differently in localized and delocalized regimes. They, when properly scaled, are \emph{universal} for different QD/SM systems. The \emph{on}-time probability distribution function in the delocalized QD/SM regime can be approximated by power laws with exponents covering $-2\le m <0$. QD/SM switches to a dark (\emph{off}) state when a charge of QD/SM hops into the trap states, which becomes localized after stabilization by the surrounding matrix.

cond-mat.mes-hall↗
arXiv2005

Electrodynamics of Amorphous Media at Low Temperatures

Amorphous solids exhibit intrinsic, local structural transitions, that give rise to the well known quantum-mechanical two-level systems at low temperatures. We explain the microscopic origin of the electric dipole moment of these two-level systems: The dipole emerges as a result of polarization fluctuations between near degenerate local configurations, which have nearly frozen in at the glass transition. An estimate of the dipole's magnitude, based on the random first order transition theory, is obtained and is found to be consistent with experiment. The interaction between the dipoles is estimated and is shown to contribute significantly to the Grüneisen parameter anomaly in low $T$ glasses. In completely amorphous media, the dipole moments are expected to be modest in size despite their collective origin. In partially crystalline materials, however, very large dipoles may arise, possibly explaining the findings of Bauer and Kador, J. Chem. Phys. {\bf 118}, 9069 (2003).

cond-mat.dis-nn↗
arXiv2003

A Stochastic Theory of Single Molecule Spectroscopy

A theory is formulated for time dependent fluctuations of the spectrum of a single molecule in a dynamic environment. In particular, we investigate the photon counting statistics of a single molecule undergoing a spectral diffusion process. Based on the stochastic optical Bloch equation, fluctuations are characterized by Mandel's $Q$ parameter yielding the variance of number of emitted photons and the second order intensity correlation function, $g^{(2)}(t)$. Using a semi-classical approach and linear response theory, we show that the $Q$ parameter can be described by a three-time dipole correlation function. This approach gene ralizes the Wiener-Khintchine formula that gives the average number of fluorescent photons in terms of a one-time dipole correlation function. We classify the time ordering properties of the three-time dipole correlation function, and show that it can be represented by three different pulse shape functions similar to those used in the context of nonlinear spectroscopy. An exact solution is found for a single molecule whose absorption frequency undergoes a two state random telegraph process (i.e., the Kubo-Anderson sudden jump process.) Simple expressions are obtained from the exact solution in the slow and fast modulation regimes based on appropriate approximations for each case. In the slow modulation regime $Q$ can be large even in the long time limit, while in the fast modulation regime it becomes small.

cond-mat.stat-mech↗
arXiv2002

Lineshape Theory and Photon Counting Statistics for Spectral Fluctuations in Quantum Dots: a Lévy Walk Process

Recent experimental observations have found two different kinds of ``strange kinetic behaviors" in individual semiconductor nanocrystals (or quantum dots). Fluorescence intermittency observed in the quantum dots shows power--law statistics in both {\it on} and {\it off} times. Spectral diffusion of the quantum dots is also described by power--law statistics in the sojourn times. Motivated by these experimental observations we consider two different but related problems: (a) a stochastic lineshape theory for the Kubo-Anderson oscillator whose frequency modulation follows power-law statistics and (b) photon counting statistics of quantum dots whose intensity fluctuation is characterized by power-law kinetics. In the first problem, we derive an analytical expression for the lineshape formula and find rich type of behaviors when compared with the standard theory. For example, new type of resonances and narrowing behavior have been found. We show that the lineshape is extremely sensitive to the way the system is prepared at time $t=0$ and discuss the problem of stationarity. In the second problem, we use semiclassical photon counting statistics to characterize the fluctuation of the photon counts emitted from quantum dots. We show that the photon counting statistics problem can be mapped onto a Lévy walk process. We find unusually large fluctuations in the photon counts that have not been encountered previously. In particular, we show that $Q$ may increase in time even in the long time limit.

cond-mat.stat-mech↗
arXiv2002

Nonequilibrium generalization of Förster-Dexter theory for excitation energy transfer

Förster-Dexter theory for excitation energy transfer is generalized for the account of short time nonequilibrium kinetics due to the nonstationary bath relaxation. The final rate expression is presented as a spectral overlap between the time dependent stimulated emission and the stationary absorption profiles, which allows experimental determination of the time dependent rate. For a harmonic oscillator bath model, an explicit rate expression is derived and model calculations are performed in order to examine the dependence of the nonequilibrium kinetics on the excitation-bath coupling strength and the temperature. Relevance of the present theory with recent experimental findings and possible future theoretical directions are discussed.

cond-mat.stat-mech↗
arXiv2000

Dispersive Lineshape Theory

Motivated by recent experiments we consider a stochastic lineshape theory for the case when the underlying process obeys power-law statistics, based on a generalized Anderson-Kubo oscillator model. We derive an analytical expression for the lineshape and find rich type of behaviors when compared with the standard theory, for example, new type of resonances and narrowing phenomena. We show that the lineshape is extremely sensitive to the way the system is prepared at time $t=0$ and discuss the problem of stationarity.

cond-mat↗
arXiv1997

Nonequilibrium spectral diffusion due to laser heating in stimulated photon echo spectroscopy of low temperature glasses

A quantitative theory is developed, which accounts for heating artifacts in three-pulse photon echo (3PE) experiments. The heat diffusion equation is solved and the average value of the temperature in the focal volume of the laser is determined as a function of the 3PE waiting time. This temperature is used in the framework of nonequilibrium spectral diffusion theory to calculate the effective homogeneous linewidth of an ensemble of probe molecules embedded in an amorphous host. The theory fits recently observed plateaus and bumps without introducing a gap in the distribution function of flip rates of the two-level systems or any other major modification of the standard tunneling model.

cond-mat.stat-mech↗