Studying Energy Transfer In Light-Harvesting Protein Complexes By Methodologies Of Quantum Dissipation

Photosynthesis,known as one of the most important biological processes,provides the basis for survival of almost all lives on the planet.Therefore,it is of great significance to understand the physical mechanism behind it.In the primary steps of photosynthesis,the sunlight is captured by the light-harvesting protein complex and converted into electron excitation energy.Then the en-ergy is transferred in the network of pigment molecules with a high efficiency up to 90%towards the reaction center,where it is converted into chemical energy.In recent years,the experiments of two-dimensional electronic spectroscopy have determined long-lived quantum beating in various light-harvesting protein complexes,suggesting that quantum coherence may play an important role in the energy transfer process.In order to study this process,it is theoretically necessary to use the method of quantum dissipative dynamics.In this thesis,we extended the hierarchy equation of motion(HEOM)to study the spin-boson model under Ohmic/sub-Ohmic noise at arbitrary temper-ature,developed the clustered-based generalized quantum kinetic expansion(GQKE)method for an energy transfer network,and numerically applied these methods to study the light-harvesting protein complexes.The thesis is organized as follows:(1)In chapter 1,we introduce the background of the energy transfer process in the light-harvesting protein complexes,and give the outline of our work done in this thesis.(2)In chapter 2,we introduce the physical picture of the energy transfer process and the light-harvesting protein complexes studied in this thesis,and then review the common theoreti-cal and experimental research methods in studying the energy transfer process of the light-harvesting protein complexes.(3)In chapter 3,we focus on the study of the HEOM,which is an exact method for quantum dissipative dynamics.Since the original HEOM is difficult to deal with the low temperature condition and the slow,e.g.,the power-law decaying bath,we developed the extend HEOM by expanding an arbitrary bath correlation function over a complete set of orthonormal func-tions.As a demonstration,we verified the reliability of the extended HEOM by studying the spin-boson model under high temperature classical and zero temperature quantum noises.(4)In chapter 4,we develop the GQKE method for a pair of donor and acceptor clusters based on the matrix structure of the HEOM.For the local cluster equilibrium initial state,we ver-ified that the lowest second order GQKE rate recover the MCFT rate and the higher-order corrections can be systematically obtained.For the system-bath factorized initial state,the time-integrated site-to-site rate matrix and the site kinetics revealed the time scale separation is between short-time intra-cluster and long-time inter-cluster kinetics.(5)In chapter 5,we further extend the GQKE method to a general multi-cluster energy transfer network following similar matrix formulation discussed in the previous chapter.Due to the spatial inhomogeneity of the energy transfer network,we proposed a systematic approach of accumulating corrections of multi-cluster cooperation from a series of subnetworks to get the converged rate constants.The reliability of the GQKE method is verified in the studies of the Fenna-Matthews-Olson(FMO)protein complex and the light-harvesting system II(LHCII)protein complex.(6)In chapter 6,we discuss the partition of clusters and propose the minimal model analysis technique.In the minimal model analysis,we determine the minimal number of clusters based on the final state and quantitatively construct the spatially overlapped quantum kinetic clusters.Moreover,the overlap of the quantum kinetic clusters help us identify the crucial hub sites in the network.As a demonstration,we present the procedure and verify the relia-bility of the minimal model analysis by studying the FMO and LHCII.(7)In chapter 7,a summary and the prospect of our work is given.