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Open Access Publications from the University of California

Scholarly Works (119 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2022)
Controlling the macroscopic properties of materials, particularly quantum materials, via external inputs such as optical fields is a key goal of modern physical science. The Faraday Discussion presented a cross section of current experimental and theoretical progress with mostly ultrashort pulse excitations with frequencies ranging from the X-ray to the THz regions of the spectrum. This paper offers a perspective on the meaning of control in different scientific and engineering contexts. Despite the enormous challenge of implementing full feedback control on the types of material of interest in this discussion, I sketch such a system taken from a photosynthetic context to provide inspiration for future development in control of materials.
    Cover page: Concluding remarks: Directing and controlling materials and moleculesCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2018)
    Progress in measuring and understanding the mechanism of the elementary energy transfer steps in photosynthetic light harvesting from roughly 1949 to the present is sketched with a focus on the group of scientists born in 1949 ± 1. Improvements in structural knowledge, laser spectroscopic methods, and quantum dynamical theories have led to the ability to record and calculate with reasonable accuracy the timescales of elementary energy transfer steps. The significance of delocalized excited states and of near-field Coulombic coupling is noted. The microscopic understanding enables consistent coarse graining and should enable a much-improved understanding of the regulation of photosynthetic light harvesting.
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2014)
      Recent observations of the long-lasting nonlinear signals in a variety of light-harvesting complexes have initiated an active debate on the origin of long-lived coherence in the biological systems. In this work we show that disorder of site energy can induce a long-lived electronic coherence between two chromophores in a strongly coupled dimer system, in addition to the ensemble dephasing effect. This phenomenon is physically explained as the correlated fluctuation of excitons with the equal delocalization on two sites, when the site-energy distributions overlap to give resonance. Using the integrated two-color coherence photon echo signal as an example, we show that the coherence in such a system exhibits a biexponential decay with a slow component with a lifetime of hundreds of femtoseconds and a rapid component with a lifetime of tens of femtoseconds. The current result provides a possible microscopic basis for the electronic coherence to be the origin of the long-lived coherence signals to be considered along with other recently proposed mechanisms.
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2013)
          Cover page: Three-Pulse Photon Echo of Finite Numbers of Molecules: Single-Molecule Traces
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2020)
          Two-dimensional electronic-vibrational spectroscopy (2DEVS) is a useful technique for studying the structure and dynamics of photoexcited molecules via monitoring of the vibrational spectrum in real-time. However, quantitative modeling or prediction of experimental spectra has been hampered by the lack of a firm theoretical basis for this quantity. Here, we develop a useful theory of 2DEVS and show that the time-dependent line shape of the 2DEVS spectrum provides invaluable information on the cross-correlation function of the solvation dynamics and vibrational spectral diffusion. The center and nodal line slopes of each 2DEVS peak are determined by the associated cross-electronic-vibrational frequency-frequency correlation function, which is shown to be related to the intermolecular interactions and vibrational anharmonicities. The present theory of 2DEVS would thus be of use for a refined understanding of the 2DEVS spectra of reactive chemical and biological systems. We anticipate that further development of the expressions developed here will illuminate the application of 2DEVS studies of vibronically induced energy and electron transfer in functional materials.
            Cover page: Two-Dimensional Electronic–Vibrational Spectroscopy Reveals Cross-Correlation between Solvation Dynamics and Vibrational Spectral Diffusion
            • Thesis
            • Peer Reviewed
            UC Berkeley Electronic Theses and Dissertations (2009)

            Photosynthesis begins with absorbing the sun light by the light harvesting complexes. The solar energy is then funneled into the reaction center (RC) via the energy transfer between the light harvesting complexes at ultrafast rates (~1/100fs ) with extremely high quantum efficiency (~100 %). Most of the complexes are composed of pigments and protein matrices that tightly bind them. The pigments are responsible for absorbing and transferring the energy. The roles of the protein environment of photosynthetic pigment-protein complexes have been suggested, but the detailed mechanisms are still not fully understood.

            In this dissertation, non-linear spectroscopic methods using ultrashort pulses (~ 40-fs FWHM), three-pulse photon echo studies are presented to investigate the roles of protein environment of the photosynthetic bacterial RC. The technique characterizes the protein dynamics around the pigments (a bacteriochlorophyll a, B and a bacteriopheophytin a, H) in the RC. In particular, two-color three-pulse electronic coherence photon echo technique is used to observe the quantum coherence between the excited states of coupled H and B, whose life time is sensitive to the protein dynamics. I found a long-lasting quantum coherence suggesting that the protein actively preserves the quantum coherence. A scenario in which the long-lasting coherence can accelerate the rate of energy trap is described with a simple Bloch model simulation.

            In addition, one- and two-color three-pulse photon echo peak shift (1C- and 2C3PEPS) techniques are used to measure the coupling strength between H and B in the wild type RC. The coupling strength is facilitated from the geometry between the pigments governed by the protein environment. The simulation based on the standard response function formalism is used to obtain the coupling strength. 2C3PEPS signal from H and B of the oxidized RC is reproduced to extract the coupling constant between them by quantum-master equation which efficiently incorporates pulse overlap effect and bath memory effect. The values will enable the molecular level of studies on the photosynthetic energy and electron transfer.

              Cover page: Two-color Three-pulse Photon Echo Studies on the Photosynthetic Bacterial Reaction Center
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2019)
              This work presents theoretical calculations of the two-dimensional electronic-vibrational (2DEV) spectrum of a vibronically coupled molecular dimer using a near-analytical method. In strongly coupled dimers, where the IR mode is resonant with the electronic energy gap between the excitons, multiple infrared transitions become allowed that are forbidden in weakly coupled systems that have a nonresonant IR mode. This formalism enables the coherences and population contributions to be explored separately and allows efficient calculation of relaxation rates between the vibronic states. At short times, we find strong contributions of vibronic coherences to the 2DEV spectra. They decay fairly rapidly, giving rise to strong population signals. Although the interpretation of 2DEV spectra is considerably more complex than that for weakly coupled systems, the richness of the spectra and the necessity to consider both visible and infrared transition moments suggest that such analysis will be very valuable in characterizing the role of vibronic effects in ultrafast molecular dynamics.
                Cover page: Two-Dimensional Electronic–Vibrational Spectroscopy of Coupled Molecular Complexes: A Near-Analytical Approach
                • Thesis
                • Peer Reviewed
                UC Berkeley Electronic Theses and Dissertations (2012)

                The research presented in this dissertation focuses on understanding the regulation of excited states, both in natural photosynthesis and in artificial systems.

                Chapters 1, 2, and 3 contribute to the understanding of natural photosynthesis by describ- ing a mathematical model that quantifies a process by which plants protect themselves from damage due to excess absorbed energy. Chapter 1 contains a description of a mathematical model of photosynthetic processes that govern the rapid components of nonphotochemical quenching. Chapter 2 contains a manual describing a Graphical User Interface (GUI) for this model. Chapter 3 extends the model of nonphotochemical quenching and applies the model to understand the role of the specific pigments and proteins which are required for rapidly-reversible nonphotochemical quenching to take place.

                Chapters 4 and 5 are focused on experimental work done on artificial systems. Chapter 4 reports on the excited state dynamics of a pH-sensitive dye that has been used to regulated the excited state lifetime of an artificial antenna. Chapter 5 reports measurements of four molecular donor-bridge-acceptor triads where the bridge between the donor and acceptor is different in each triad, with the aim of understanding how the chemical bonding between donor and acceptor affects the timescales and yield of energy transfer and charge separation.

                  Cover page: Regulatory Dynamics of Natural and Artificial Photosynthesis
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2021)
                  Giant strides in ultrashort laser pulse technology have enabled real-time observation of dynamical processes in complex molecular systems. Specifically, the discovery of oscillatory transients in the two-dimensional electronic spectra of photosynthetic systems stimulated a number of theoretical investigations exploring the possible physical mechanisms of the remarkable quantum efficiency of light harvesting processes. In this work, we revisit the elementary aspects of environment-induced fluctuations in the involved electronic energies and present a simple way to understand energy flow with the intuitive picture of relaxation in a funnel-type free-energy landscape. The presented free-energy description of energy transfer reveals that typical photosynthetic systems operate in an almost barrierless regime. The approach also provides insights into the distinction between coherent and incoherent energy transfer and the criteria by which the necessity of the vibrational assistance is considered.
                    Cover page: Insights into Photosynthetic Energy Transfer Gained from Free-Energy Structure: Coherent Transport, Incoherent Hopping, and Vibrational Assistance Revisited
                    • Article
                    • Peer Reviewed
                    UC Berkeley Previously Published Works (2020)
                    In this paper, we explore the scope of vibrations as quantum ratchets that serve as nonthermal routes to achieving population transport in systems where excitation transport between molecules is otherwise energetically unfavorable. In addition to their role as channels of transport, we investigate the effect of resonance of the vibrations, which are described by Huang-Rhys mixing, with excitonic energy gaps, which leads to strongly mixed vibronic excitons. Finally, we explore the interplay of resonance and Huang-Rhys mixing with electronic coupling between the molecules, in the presence of a dissipative bath, in optimizing transport in such systems. We find that while resonance is desirable, a moderate electronic coupling has a stronger positive effect in contrast to a large electronic coupling, which results in delocalized excitations across molecules and hampers unidirectional transport. We also report a special resonance regime that is able to circumvent the transport problems arising from large electronic couplings.
                      Cover page: Quantum Ratcheted Photophysics in Energy Transport
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