Searching for a Unique Exciton Model of Photosynthetic Pigment–Protein Complexes: Photosystem II Reaction Center Study by Differential Evolution

Chesalin, Denis D; Pishchalnikov, Roman Y.

doi:10.3390/math10060959

Cited by 8 publications

(13 citation statements)

References 39 publications

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“…A detailed description of the quantum model of PSIIRC without taking into account of the inhomogeneous broadening has been given in our previous published paper [40]. Considering the multimode Brownian oscillator model to calculate the spectral density and the lineshape function for cofactors of PSIIRC, and the exciton theory to simulate the optical response of a system of coupling pigments [9], the final expressions in terms of the modified Redfield theory [43,44] for absorption ( ), linear ( ), circular ( ) dichroism and steady-state fluorescence ( ) of PSIIRC were written as follows:…”

Section: Theory Of the Optical Response With Inhomogeneous Broadeningmentioning

confidence: 99%

“…To fit the PSIIRC linear spectroscopy data, the classical version of DE was used [31]. The developed software, together with the spectra simulation procedures, contains the implementation of four steps of DE data processing: (1) initialization of the parameter population, (2) creating the mutation vectors, (3) crossover and (4) parameters selection for the new generation [40,41]. Previously, DE has been successfully applied to fit the linear optical response of monomeric Chls, bacteriochlorophylls and carotenoids in different solvents.…”

Section: Differential Evolutionmentioning

confidence: 99%

“…However, these modifications in the case of PPC optical properties modeling have no significant effect on the convergence rate and the spectra fitting results. To deal with this situation, we have developed software combining the DE algorithm and procedures for the calculation of the spectra of photosynthetic pigments and pigment-protein complexes [40,41]. Starting with the modeling of linear absorption of monomeric Chl, bacteriochlorophyll and carotenoids in different solvents, the best DE strategy and its optimal settings have been found [41,42].…”

Section: Introductionmentioning

confidence: 99%

“…The next step was to explore the prospect of using DE to fit the linear spectroscopy of a small PPC, such as PSIIRC. Having a set of artificially simulated spectra as experimental data, we were able to match the DE settings with which the algorithm found the required parameters of the exciton model of PSIIRC [40]. However, it makes no sense to use such a model to fit experimentally measured spectra, since it does not take into account the inhomogeneous broadening of the PSIIRC excited states (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

“…However, it makes no sense to use such a model to fit experimentally measured spectra, since it does not take into account the inhomogeneous broadening of the PSIIRC excited states (Figure 1). Thus, the aim of this study is to enhance the previously published PSIIRC exciton model and the quality of linear optical properties modeling [40] by adding the procedure of inhomogeneous broadening by means of MCM. It must be stressed that MCM is a probabilistic method which provides only an approximate solution to a problem.…”

Section: Introductionmentioning

confidence: 99%

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Monte Carlo Simulation Affects Convergence of Differential Evolution: A Case of Optical Response Modeling

et al. 2022

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It is known that the protein surrounding, as well as solvent molecules, has a significant influence on optical spectra of organic pigments by modulating the transition energies of their electronic states. These effects manifest themselves by a broadening of the spectral lines. Most semiclassical theories assume that the resulting lineshape of an electronic transition is a combination of homogeneous and inhomogeneous broadening contributions. In the case of the systems of interacting pigments such as photosynthetic pigment–protein complexes, the inhomogeneous broadening can be incorporated in addition to the homogeneous part by applying the Monte Carlo method (MCM), which implements the averaging over static disorder of the transition energies. In this study, taking the reaction center of photosystem II (PSIIRC) as an example of a quantum optical system, we showed that differential evolution (DE), a heuristic optimization algorithm, used to fit the experimentally measured data, produces results that are sensitive to the settings of MCM. Applying the exciton theory to simulate the PSIIRC linear optical response, the number of minimum required MCM realizations for the efficient performance of DE was estimated. Finally, the real linear spectroscopy data of PSIIRC were fitted using DE considering the necessary modifications to the implementation of the optical response modeling procedures.

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