Optimization of the modeling of the pigment-protein complex optical response

Chesalin D.D., Kurkov V.A.1, Shkirina U.A.2, Pishchalnikov R.Y.

1Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991, Moscow, Russia,

Numerical modeling in applied sciences (physics, chemistry, biology, etc.) is necessary when the problem posed cannot be solved analytically. Pigment-protein complexes of photosynthetic organisms, consisting of many molecules, are one of the demonstrative examples of the successful application of numerical modeling and multi-parameter optimization. However, the effectiveness of optimization algorithms can be demonstrated using a simpler example - the calculation of absorption spectra of carotenoids in organic solvents. Carotenoids are biological pigments that are part of pigment-protein complexes. To calculate the optical response of carotenoids, it is necessary to use semiclassical quantum theory based on the use of a multimode Brownian oscillator model, in which an infinite set of vibrational states of the molecule is approximated by a finite set of vibronic modes. The basis for the modeling was the differential evolution algorithm, designed to find the global minimum of nonlinear and non-differentiable functions of many variables [1]. The function for minimization was chosen to characterize the discrepancy between the experimental and simulated spectrum. Its advantage is that its lower bound is always zero. In the case of experimental data, it may be unattainable, but when replacing the experimental spectrum with a synthetic one, the resulting zero will indicate a complete coincidence of the spectra. As a result, it is possible to learn information about the structure and natural vibrations of a molecule that cannot be obtained experimentally. The found model parameters can be used to find microparameters of the medium that model the interaction of an ensemble of molecules with each other.


1. Chesalin, D.D.; Kulikov, E.A.; Yaroshevich, I.A.; Maksimov, E.G.; Selishcheva, A.A.; Pishchalnikov, R.Y. Differential evolution reveals the effect of polar and nonpolar solvents on carotenoids: A case study of astaxanthin optical response modeling // Swarm and Evolutionary Computation том 75, 2022, 101210, doi:10.1016/j.swevo.2022.101210.


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