1,720,986 research outputs found
Molecular basis of the exciton-phonon interactions in the PE545 light-harvesting complex
No full textLong-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low and at room temperatures have generated a heated debate over the impact that the coupling of electronic excitations to molecular vibrations of the relevant actors (pigments, proteins and solvents) has on the excitation energy transfer process. In this work, we use a combined MD and QM/MMPol strategy to investigate the exciton-phonon interactions in the PE545 light-harvesting complex by computing the spectral densities for each pigment and analyzing their consequences in the exciton dynamics. Insights into the origin of relevant peaks, as well as their differences among individual pigments, are provided by correlating them with normal modes obtained from a quasi-harmonic analysis of the motions sampled by the pigments in the complex. Our results indicate that both the protein and the solvent significantly modulate the intramolecular vibrations of the pigments thus playing an important role in promoting or suppressing certain exciton-phonon interactions. We also find that these low-frequency features are largely smoothed out when the spectral density is averaged over the complex, something difficult to avoid in experiments that underscores the need to combine theory and experiment to understand the origin of quantum coherence in photosynthetic light-harvesting. This journal is © the Partner Organisations 2014
Isolating the chiral contribution in optical two-dimensional chiral spectroscopy using linearly polarized light
Get PDFThe full development of mono- or multi-dimensional time-resolved spectroscopy techniques incorporating optical activity signals has been strongly hampered by the challenge of identifying the small chiral signals over the large achiral background. Here we propose a new methodology to isolate chiral signals removing the achiral background from two commonly used configurations for performing two-dimensional optical spectroscopy, known as BOXCARS and gradient assisted photon echo spectroscopy (GRAPES). It is found that in both cases an achiral signal from an isotropic system can be completely eliminated by small manipulations of the relative angles between the linear polarizations of the four input laser pulses. Starting from the formulation of a perturbative expansion of the signal in the angle between the beams and the propagation axis, we derive analytic expressions that can be used to estimate how to change the polarization angles of the four pulses to minimize achiral contributions in the studied configurations. The generalization to any other possible experimental configurations has also been discussed
Coherence specific signal detection via chiral pump-probe spectroscopy
Get PDFWe examine transient circular dichroism (TRCD) spectroscopy as a technique to investigate signatures of exciton coherence dynamics under the influence of structured vibrational environments. We consider a pump-probe configuration with a linearly polarized pump and a circularly polarized probe, with a variable angle θ between the two directions of propagation. In our theoretical formalism the signal is decomposed in chiral and achiral doorway and window functions. Using this formalism, we show that the chiral doorway component, which beats during the population time, can be isolated by comparing signals with different values of θ. As in the majority of time-resolved pump-probe spectroscopy, the overall TRCD response shows signatures of both excited and ground state dynamics. However, we demonstrate that the chiral doorway function has only a weak ground state contribution, which can generally be neglected if an impulsive pump pulse is used. These findings suggest that the pump-probe configuration of optical TRCD in the impulsive limit has the potential to unambiguously probe quantum coherence beating in the excited state. We present numerical results for theoretical signals in an example dimer system
Non-perturbative energy transfer rates and filtered photon correlations for excitonic systems
No full textPhotosynthetic bacteria use light-harvesting antenna complexes to absorb and funnel excitation energy that then drives metabolic processes. Ensemble experiments have established that the photoexcitation dynamics exhibit signatures
of coherences maintained for timescales comparable to their energy transfer process. Theoretical studies indicate that non-perturbative approaches are
obligatory for a detailed understanding of the energy transfer process, and to rationalise experimental observations. Several questions remain open such as: how can we characterise the energy transfer kinetics for dynamics involving coherences and non-Markovian processes; what experiments can probe quantum processes during energy transfer in single complexes that avoids the ambiguity of ensemble averaging? This thesis addresses these two important questions by deploying the non-perturbative hierarchical equations of motion (HEOM)
approach to investigate both generalised transfer rates in natural excitonic systems, and a theoretical investigation of quantum optical signatures of non-
trivial quantum effects under conditions of biological relevance. A detailed derivation of the HEOM and explanation of our efficient implementation is given, which enables us to analyse large bacteriochlorophyll complexes. We then consider the influence of vibronic mechanisms in the energy transfer process for the Fenna-Matthews-Olson complex and the light-harvesting complex 2, applying projection operator techniques to perform a
non-perturbative investigation of the excitonic kinetics. It is found that perturbative techniques are not appropriate, as a qualitative and quantitative disagreement with HEOM is observed. Next, we determine signatures of coherent energy transfer, exciton delocalisation, and steady-state coherence within the second-order cross correlation function for an acceptor-donor system. Then we present our dynamical expansion of frequency-resolved correlation functions that enables a simple and efficient numerical implementation, such that we may consider them for antenna complexes evolving in a non-perturbative manner. Finally, we give our approach towards simulating exact dynamics of disordered ensemble observables and demonstrate its effectiveness by considering examples of disordered qubits and dimers
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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