Characterization and quantification of the role of coherence in ultrafast quantum biological experiments using quantum master equations, atomistic simulations, and quantum process tomography
Patrick Rebentrost, Sangwoo Shim, Joel Y. Yuen-Zhou, Alán Aspuru‐Guzik
Long-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.
Long-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.
Ultrafast spectroscopy experiments show that photosynthetic systems can preserve quantum beats in the process of electronic energy transfer between pigments, even at room temperature. But what does this discovery imply for biology - and for quantum mechanics? This dissertation examines photosynthesis through the tools of quantum information science. We evaluate to what extent photosynthesis can be thought of as a type of quantum technology, and consider how we can apply experimental tools widely used for quantum technologies (state tomography and coherent control) to photosynthesis. Throughout, we use the Fenna-Matthews-Olson (FMO) complex of greens sulfur bacteria as a model photosynthetic pigment-protein complex.In Part I, we evaluate two mechanisms for the possible biological relevance of quantum coherent motion. First, we consider the extent to which dynamics in light-harvesting systems exhibit the quantum speedups characteristic of quantum algorithms and quantum walks. Second, we demonstrate a ratchet effect in electronic energy transfer enabled by partially coherent dynamics. To do so, we build a new model of energy transfer between weakly coupled light-harvesting complexes to understand how electronic coherence arises under natural conditions.In Part II, we present proposals for experimental probes of light harvesting dynamics with ultrafast spectroscopy. We show how the signal from pump-probe spectroscopy can be formally inverted to determine the excited state electronic density matrix. Finally, we examine the feasiblity of coherent control experiments on light-harvesting systems, and provide two realistic targets feasible with present-day technology.
Applications of the concepts of quantum information theory are usually related to the powerful and counter-intuitive quantum mechanical effects of superposition, interference and entanglement. In this thesis, I examine the role of coherence and entanglement in complex chemical systems. The research has focused mainly on two related projects: The first project is developing a theoretical model to explain the recent ultrafast experiments on excitonic migration in photosynthetic complexes that show long-lived coherence of the order of hundreds of femtoseconds and the second project developing the Grover algorithm for global optimization of complex systems. The first part can be divided into two sections. The first section is investigating the theoretical frame about the transfer of electronic excitation energy through the Fenna-Matthews-Olson (FMO) pigment-protein complex. The new developed modified scaled hierarchical equation of motion (HEOM) approach is employed for simulating the open quantum system. The second section is investigating the evolution of entanglement in the FMO complex based on the simulation result via scaled HEOM approach. We examine the role of multipartite entanglement in the FMO complex by direct computation of the convex roof optimization for a number of different measures, including pairwise, triplet, quadruple and quintuple sites entanglement. Our results support the hypothesis that multipartite entanglement is maximum primary along the two distinct electronic energy transfer pathways. The second part of this thesis can be separated into two sections. The first section demonstrated that a modified Grover's quantum algorithm can be applied to real problems of finding a global minimum using modest numbers of quantum bits. Calculations of the global minimum of simple test functions and Lennard-Jones clusters have been carried out on a quantum computer simulator using a modified Grover's algorithm. The second section is implementing the basic quantum logical gates upon arrays of trapped ultracold polar molecules as qubits for the quantum computer. Utilized herein is the Multi-Target Optimal Control Theory (MTOCT) as a means of manipulating the initial-to-target transition probability via external laser field. The detailed calculation is applied for the SrO molecule, an ideal candidate in proposed quantum computers using arrays of trapped ultra-cold polar molecules.
Assessing the role of interference in natural and artificial quantum dynamical processes is a crucial task in quantum information theory. To this aim, an appropriate formalism is provided by the decoherent histories framework. While this approach has been deeply explored from different theoretical perspectives, it still lacks of a comprehensive set of tools able to concisely quantify the amount of coherence developed by a given dynamics. In this paper, we introduce and test different measures of the (average) coherence present in dissipative (Markovian) quantum evolutions, at various time scales and for different levels of environmentally induced decoherence. In order to show the effectiveness of the introduced tools, we apply them to a paradigmatic quantum process where the role of coherence is being hotly debated: exciton transport in photosynthetic complexes. To spot out the essential features that may determine the performance of the transport, we focus on a relevant trimeric subunit of the Fenna-Matthews-Olson complex and we use a simplified (Haken-Strobl) model for the system-bath interaction. Our analysis illustrates how the high efficiency of environmentally assisted transport can be traced back to a quantum recoil avoiding effect on the exciton dynamics, that preserves and sustains the benefits of the initial fast quantum delocalization of the exciton over the network. Indeed, for intermediate levels of decoherence, the bath is seen to selectively kill the negative interference between different exciton pathways, while retaining the initial positive one. The concepts and tools here developed show how the decoherent histories approach can be used to quantify the relation between coherence and efficiency in quantum dynamical processes.
In the first part of the dissertation, we develop a theoretical approach to analyze nonlinear spectroscopy experiments based on the formalism of quantum state (QST) and process tomography (QPT). In it, a quantum system is regarded as a black box which can be systematically tested in its performance, very much like an electric circuit is tested by sending a series of inputs and measuring the corresponding outputs, but in the quantum sense. We show how to collect a series of pump-probe or photon-echo experiments, and by varying polarizations and frequency components of the perturbations, reconstruct the quantum state (density matrix) of the probed system for a set of different initial conditions, hence simultaneously achieving QST and QPT. Furthermore, we establish the conditions under which a set of two-dimensional optical spectra also yield the desired results. Simulations of noisy experiments with inhomogeneous broadening show the feasibility of the protocol. A spin-off of this work is our suggestion of a witness that distinguishes between spectroscopic time-oscillations corresponding to vibronic only coherences against their electronic counterparts. We conclude by noting that the QST/QPT approach to nonlinear spectroscopy sheds light on the amount of quantum information contained in the output of an experiment, and hence, is a convenient theoretical and experimental paradigm even when the goal is not to perform a full QPT. In the second part of the thesis, we discuss a methodology to study the electronic dynamics of complex molecular systems, such as photosynthetic units, in the framework of time-dependent density functional theory (TD-DFT). By treating the electronic degrees of freedom as the system and the nuclear ones as the bath, we develop an open quantum systems (OQS) approach to TD-DFT. We formally extend the theoretical backbone of TD-DFT to OQS, and suggest a Markovian bath functional which can be readily included in electronic structure codes.
The description of excited state dynamics in energy transfer systems constitutes a theoretical and experimental challenge in modern chemical physics. A spectroscopic protocol that systematically characterizes both coherent and dissipative processes of the probed chromophores is desired. Here, we show that a set of two-color photon-echo experiments performs quantum state tomography (QST) of the one-exciton manifold of a dimer by reconstructing its density matrix in real time. This possibility in turn allows for a complete description of excited state dynamics via quantum process tomography (QPT). Simulations of a noisy QPT experiment for an inhomogeneously broadened ensemble of model excitonic dimers show that the protocol distills rich information about dissipative excitonic dynamics, which appears nontrivially hidden in the signal monitored in single realizations of four-wave mixing experiments.
Ultrafast pulses allow observation of molecular dynamics with femtosecond time resolution through pump probe experiments. However, averaging over an ensemble of molecules tends to wash out phase sensitive information, necessary to probe quantum effects, due to the intrinsic inhomogeneity in molecular conformations, orientations and interactions that lead to unique potential energy landscapes for each molecule. It is therefore important to go beyond the ensemble average when looking at quantum dynamics of organic systems at room temperature, and resolve the behaviour of specific molecules on an individual basis. In this thesis, we show the creation, manipulation and observation of ultrafast coherent effects in single molecules at room temperature, and resolve a certain measure of environmental influence on the specific dynamics of each molecule. Moreover, we apply this insight to investigate a functional light harvesting biosystem, and lay the basis for a technique that has the time and space resolution required to observe these systems in vivo. In chapter 1, we introduce the concepts and techniques the research in this thesis is built on. In chapter 2, we treat the possibility of controlling ultrafast pulses at the high-NA diffraction limit, and come to conclusions about the procedure to follow there that hold for all pulse-shaping experiments. We show in proof of principle experiments that we can control the ultrafast characteristics of optical pulses in nanometric excitation volumes. In chapters 3 and 4 we report the creation, detection and control of ultrafast quantum dynamics in single organic molecules at room temperature. We show that manipulation of superposition states is possible in these systems within a coherence dephasing time of ~50 fs. This leads to the first observation of rabi-oscillations in room temperature single molecules, to ultrafast operation of an organic qubit, and to the creation of non-stationary superposition states (vibrational wavepackets). We probe the influence of the local environment on the composition and dynamics of these wavepackets and show we can optimize the state preparation protocol for each individual molecule in its own nanoenvironment, leading to high fidelity coherent control. In these chapters we lay out the proof of principle work of detecting the quantumdynamics of a complex system in interaction with its environment at room temperature. In chapter 5 we discuss application of these techniques to the investigation of long lived coherence in photosynthetic systems. We show that electronic coherence between different rings of the LH2 system persists to time scales of 100s of femtoseconds at room temperature. Moreover we show that the energy transfer pathways in LH2 adapt to environmentally induced changes in the molecule and that the nature of the transfer remains coherent for each pathway, providing strong evidence that coherent energy transfer is the optimum process for energy transfer in photosynthesis. Finally, in chapter 6 we take the technical development one step further and report on the creation of a framework based on plasmonic antennas that allows for control of the amplitude-phase characteristics in nanometric sized hotspot fields. We show for the first time that the ultrafast characteristics of plasmonic hotspots can directly be engineered through design of the plasmonic system and experimentally demonstrate two much-anticipated examples: a sub-diffraction resolution phase shaper and an ultrafast plasmonic switch for pump probe experiments. The results presented in this thesis form the first creation and observation of ultrafast coherent dynamics in individual molecular systems at room temperature. This is a necessary step to be able to do true quantum tomography in complex systems, resolve the influence of the environment on molecular dynamics, and investigate the physics that determines evolutionary optimization and functionality in biomolecules.