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Taher-Ghahramani F, Zheng F, Eisfeld A. Gaussian process regression for absorption spectra analysis of molecular dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121091. [PMID: 35306303 DOI: 10.1016/j.saa.2022.121091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/05/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
A common task is the determination of system parameters from spectroscopy, where one compares the experimental spectrum with calculated spectra, that depend on the desired parameters. Here we discuss an approach based on a machine learning technique, where the parameters for the numerical calculations are chosen from Gaussian Process Regression (GPR). This approach does not only quickly converge to an optimal parameter set, but in addition provides information about the complete parameter space, which allows for example to identify extended parameter regions where numerical spectra are consistent with the experimental one. We consider as example dimers of organic molecules and aim at extracting in particular the interaction between the monomers, and their mutual orientation. We find that indeed the GPR gives reliable results which are in agreement with direct calculations of these parameters using quantum chemical methods.
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Affiliation(s)
- Farhad Taher-Ghahramani
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str 38, Dresden, Germany.
| | - Fulu Zheng
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany.
| | - Alexander Eisfeld
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str 38, Dresden, Germany.
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Zheng F, Chen L, Gao J, Zhao Y. Fully Quantum Modeling of Exciton Diffusion in Mesoscale Light Harvesting Systems. MATERIALS (BASEL, SWITZERLAND) 2021; 14:3291. [PMID: 34198704 PMCID: PMC8232211 DOI: 10.3390/ma14123291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022]
Abstract
It has long been a challenge to accurately and efficiently simulate exciton-phonon dynamics in mesoscale photosynthetic systems with a fully quantum mechanical treatment due to extensive computational resources required. In this work, we tackle this seemingly intractable problem by combining the Dirac-Frenkel time-dependent variational method with Davydov trial states and implementing the algorithm in graphic processing units. The phonons are treated on the same footing as the exciton. Tested with toy models, which are nanoarrays of the B850 pigments from the light harvesting 2 complexes of purple bacteria, the methodology is adopted to describe exciton diffusion in huge systems containing more than 1600 molecules. The superradiance enhancement factor extracted from the simulations indicates an exciton delocalization over two to three pigments, in agreement with measurements of fluorescence quantum yield and lifetime in B850 systems. With fractal analysis of the exciton dynamics, it is found that exciton transfer in B850 nanoarrays exhibits a superdiffusion component for about 500 fs. Treating the B850 ring as an aggregate and modeling the inter-ring exciton transfer as incoherent hopping, we also apply the method of classical master equations to estimate exciton diffusion properties in one-dimensional (1D) and two-dimensional (2D) B850 nanoarrays using derived analytical expressions of time-dependent excitation probabilities. For both coherent and incoherent propagation, faster energy transfer is uncovered in 2D nanoarrays than 1D chains, owing to availability of more numerous propagating channels in the 2D arrangement.
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Affiliation(s)
- Fulu Zheng
- Bremen Center for Computational Materials Science, University of Bremen, 28359 Bremen, Germany;
| | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str., 38, 01187 Dresden, Germany;
| | - Jianbo Gao
- Center for Geodata and Analysis, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China;
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Zhao
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
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Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.
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Richter M, Fingerhut BP. Coupled excitation energy and charge transfer dynamics in reaction centre inspired model systems. Faraday Discuss 2019; 216:72-93. [PMID: 31012450 DOI: 10.1039/c8fd00189h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Functional operation conditions of reaction centre core complexes require the tight coupling of exciton states to concomitant charge separation. Rigorous theoretical treatment of such integrated excitation energy transfer (EET) and charge transfer (CT) dynamics is particularly challenging due to (i) appreciable system sizes, (ii) inter-site and system-bath couplings of similar magnitude that render the Born-Markov approximation invalid, (iii) substantial reorganization energies of CT states, and (iv) the presence of complex structured spectral densities due to vibrational modes of the surroundings. We present numerical simulations on bacterial reaction centre (bRC) inspired model systems that utilize the recently developed MACGIC-iQUAPI method [Richter et al., J. Chem. Phys., 2017, 146, 214101]. The simulations demonstrate that the method provides a rigorous framework for the investigation of such integrated EET-CT dynamics. First, the applicability of the MACGIC-iQUAPI method is explored for a transition from monotonically decaying to oscillatory system-bath influence coefficients, a behavior inherently imposed by structured bath spectral densities. Tightly coupled EET and CT dynamics is further addressed for an excitonic subsystem that resembles strong coupling of special pair states and serves as donor towards a generic bridge-acceptor system. By solving the dissipative quantum dynamics of such bRC inspired model systems, the quenching of excitonic coherence on the hundreds of femtoseconds timescale is explored via a variation of the bridge state energetics, resembling a continuous transition from sequential to superexchange mediated CT regimes. Further, the simulations explore the influence of resonant vibrational modes on the quenching of excitonic coherence via CT. The results reveal a moderate influence of vibrational mode on charge separation dynamics in regimes of biologically relevant EET and CT dynamics.
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Affiliation(s)
- Martin Richter
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany.
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany.
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Mallus MI, Shakya Y, Prajapati JD, Kleinekathöfer U. Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Rätsep M, Timpmann K, Kawakami T, Wang-Otomo ZY, Freiberg A. Spectrally Selective Spectroscopy of Native Ca-Containing and Ba-Substituted LH1-RC Core Complexes from Thermochromatium tepidum. J Phys Chem B 2017; 121:10318-10326. [PMID: 29058423 DOI: 10.1021/acs.jpcb.7b07841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LH1-RC core complex from the thermophilic photosynthetic purple sulfur bacterium Thermochromatium tepidum has recently attracted interest of many researchers because of its several unique properties, such as increased robustness against environmental hardships and the much red-shifted near-infrared absorption spectrum of the LH1 antenna exciton polarons. The known near-atomic-resolution crystal structure of the complex well supported this attention. Yet several mechanistic aspects of the complex prominence remained to be understood. In this work, samples of the native, Ca2+-containing core complexes were investigated along with those destabilized by Ba2+ substitution, using various spectrally selective steady-state and picosecond time-resolved spectroscopic techniques at physiological and cryogenic temperatures. As a result, the current interpretation of exciton spectra of the complex was significantly clarified. Specifically, by evaluating the homogeneous and inhomogeneous compositions of the spectra, we showed that there is little to no effect of cation substitution on the dynamic or kinetic properties of antenna excitons. Reasons of the extra red shift of absorption/fluorescence spectra observed in the Ca-LH1-RC and not in the Ba-LH1-RC complex should thus be searched in subtle structural differences following the inclusion of different cations into the core complex scaffold.
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Affiliation(s)
- Margus Rätsep
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | - Kõu Timpmann
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia
| | | | | | - Arvi Freiberg
- Institute of Physics, University of Tartu , W. Ostwald Str. 1, 50411 Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu , Riia 23, 51010 Tartu, Estonia
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Sakamoto S, Tanimura Y. Exciton-Coupled Electron Transfer Process Controlled by Non-Markovian Environments. J Phys Chem Lett 2017; 8:5390-5394. [PMID: 29039960 DOI: 10.1021/acs.jpclett.7b01535] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We theoretically investigate an exciton-coupled electron transfer (XCET) process that is conversion of an exciton into a charge transfer state. This conversion happens in an exciton transfer (XT) process, and the electron moves away in an electron transfer (ET) process in multiple environments (baths). This XCET process plays an essential role in the harvesting of solar energy in biological and photovoltaic materials. We develop a practical theoretical model to study the efficiency of the XCET process that occurs either in consecutive or concerted processes under the influence of non-Markovian baths. The role of quantum coherence in the XT-ET system and the baths is investigated using reduced hierarchal equations of motion (HEOM). This model includes independent baths for each XT and ET state, in addition to a XCET bath for the conversion process. We found that, while quantum system-bath coherence is important in the XT and ET processes, coherence between the XT and ET processes must be suppressed in order to realize that an efficient irreversible XCET process through the weak off-diagonal interaction between the XT and ET bridge sites arises from an XCET bath.
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Affiliation(s)
- Souichi Sakamoto
- Department of Chemistry, Graduate School of Science, Kyoto University , Sakyoku, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University , Sakyoku, Kyoto 606-8502, Japan
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Mallus MI, Schallwig M, Kleinekathöfer U. Relation between Vibrational Dephasing Time and Energy Gap Fluctuations. J Phys Chem B 2017. [PMID: 28625060 DOI: 10.1021/acs.jpcb.7b02693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dephasing processes are present in basically all applications in which quantum mechanics plays a role. These applications certainly include excitation energy and charge transfer in biological systems. In a previous study, we have analyzed the vibrational dephasing time as a function of energy gap fluctuation for a large set of molecular simulations. In that investigation, individual molecular subunits were the focus of the calculations. The set of studied molecules included bacteriochlorophylls in Fenna-Matthews-Olson and light-harvesting system 2 complexes as well as bilins in PE545 aggregates. The present work extends this study to entire complexes, including the respective intermolecular couplings. Again, it can be concluded that a universal and inverse proportionality exists between dephasing time and variance of the excitonic energy gap fluctuations, whereas the respective proportionality constants can be rationalized using the energy gap autocorrelation functions. Furthermore, these findings can be extended to the gaps between higher-lying neighboring excitonic states.
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Affiliation(s)
- Maria Ilaria Mallus
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Maximilian Schallwig
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , Campus Ring 1, 28759 Bremen, Germany
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Anda A, De Vico L, Hansen T. Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies. J Phys Chem B 2017; 121:5499-5508. [PMID: 28485594 DOI: 10.1021/acs.jpcb.7b02071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.
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Affiliation(s)
- André Anda
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Luca De Vico
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53100 Siena, Italy
| | - Thorsten Hansen
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
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