Person: Shim, Sangwoo
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Shim
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Sangwoo
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Shim, Sangwoo
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Publication Characterization and Quantification of the Role of Coherence in Ultrafast Quantum Biological Experiments Using Quantum Master Equations, Atomistic Simulations, and Quantum Process Tomography(Elsevier, 2011) Rebentrost, Frank Patrick; Shim, Sangwoo; Yuen-Zhou, Joel; Aspuru-Guzik, AlanLong-lived electronic coherences in various photosynthetic complexes at cryogenic and room temperature have generated vigorous efforts both in theory and experiment to understand their origins and explore their potential role to biological function. The ultrafast signals resulting from the experiments that show evidence for these coherences result from many contributions to the molecular polarization. Quantum process tomography (QPT) is a technique whose goal is that of obtaining the time-evolution of all the density matrix elements based on a designed set of experiments with different preparation and measurements. The QPT procedure was conceived in the context of quantum information processing to characterize and understand general quantum evolution of controllable quantum systems, for example while carrying out quantum computational tasks. We introduce our QPT method for ultrafast experiments, and as an illustrative example, apply it to a simulation of a two-chromophore subsystem of the Fenna-Matthews-Olson photosynthetic complex, which was recently shown to have long-lived quantum coherences. Our Fenna-Matthews-Olson model is constructed using an atomistic approach to extract relevant parameters for the simulation of photosynthetic complexes that consists of a quantum mechanics/molecular mechanics approach combined with molecular dynamics and the use of state-of-the-art quantum master equations. We provide a set of methods that allow for quantifying the role of quantum coherence, dephasing, relaxation and other elementary processes in energy transfer efficiency in photosynthetic complexes, based on the information obtained from the atomistic simulations, or, using QPT, directly from the experiment. The ultimate goal of the combination of this diverse set of methodologies is to provide a reliable way of quantifying the role of long-lived quantum coherences and obtain atomistic insight of their causes.Publication First-Principles Semiclassical Initial Value Representation Molecular Dynamics(Royal Society of Chemistry, 2009) Ceotto, Michele; Atahan, Sule; Shim, Sangwoo; Tantardini, Gian Franco; Aspuru-Guzik, AlanIn this work, we explore the use of the semiclassical initial value representation (SC-IVR) method with first-principles electronic structure approaches to carry out classical molecular dynamics. The proposed approach can extract the vibrational power spectrum of carbon dioxide from a single trajectory providing numerical results that agree with experiment and quantum calculations. The computational demands of the method are comparable to those of classical single-trajectory calculations, while describing uniquely quantum features such as the zero-point energy and Fermi resonances. The method can also be used to identify symmetry properties of given vibrational peaks and investigate vibrational couplings by selected classical trajectories. The accuracy of the method degrades for the reproduction of anharmonic shifts for high-energy vibrational levels.Publication Simplified Sum-Over-States Approach for Predicting Resonance Raman Spectra. Application to Nucleic Acid Bases(American Chemical Society, 2011) Rappoport, Dmitrij; Shim, Sangwoo; Aspuru-Guzik, AlanResonance Raman spectra provide a valuable probe into molecular excited-state structures and properties. Moreover, resonance enhancement is of importance for the chemical contribution to surface-enhanced Raman scattering. In this work, we introduce a simplified sum-over-states scheme for computing Raman spectra and Raman excitation profiles. The proposed sum-over-states approach uses derivatives of electronic excitation energies and transition dipole moments, which can be efficiently computed from time-dependent density functional theory. We analyze and interpret the resonance Raman spectra and Raman excitation profiles of nucleic acid bases using the present approach. Contributions of individual excited states under strictly resonant and non-resonant conditions are investigated, and smooth interpolation between both limiting cases is obtained.Publication Atomistic Study of the Long-Lived Quantum Coherences in the Fenna-Matthews-Olson Complex(Biophysical Society, 2011) Shim, Sangwoo; Rebentrost, Patrick; Valleau, Stephanie; Aspuru-Guzik, AlanA remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear, and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.