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Shirmovsky SE, Chizhov AV. Modeling of the entangled states transfer processes in microtubule tryptophan system. Biosystems 2023; 231:104967. [PMID: 37400052 DOI: 10.1016/j.biosystems.2023.104967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
The paper simulates the process of the migration of a single energy excitation along a chain of tryptophans in cell microtubules connected by dipole-dipole interaction. The paper shows that the excited states propagation rate falls within the range of nerve impulse velocity. It was shown that such a process also causes a transfer of quantum entanglement between tryptophans, so that microtubules can be considered as signaling system, the basis for transmitting information via the quantum channel. The conditions under which the migration of entangled states in the microtubule is possible are obtained. In a certain sense, it allows us to argue that the signal function of tryptophans works as an analogue of a quantum repeater that transmits entangled states over microtubule by relaying through intermediate tryptophans. Thus, the paper shows that the tryptophan system can be considered as an environment that supports the existence of entangled states during the time comparable with the time of the processes in biosystems.
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Affiliation(s)
- S Eh Shirmovsky
- Far Eastern Federal University, Institute of Mathematics and Computer Technologies, Department of Information Security, 10Ajax settlement, Russkiy Island, Vladivostok, Primorsky Region, 690922, Russia.
| | - A V Chizhov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Dubna, Moscow region, 141980, Russia; Dubna State University, Dubna, Moscow region, 141980, Russia.
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2
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Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA, Lakhno VD. Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Photosynthesis is the basic process used by plants to convert light energy in reaction centers into chemical energy. The high efficiency of this process is not yet understood today. Using the formalism for the description of open quantum systems by means of a non-Hermitian Hamilton operator, we consider initially the interplay of gain (acceptor) and loss (donor). Near singular points it causes fluctuations of the cross section which appear without any excitation of internal degrees of freedom of the system. This process occurs therefore very quickly and with high efficiency. We then consider the excitation of resonance states of the system by means of these fluctuations. This second step of the whole process takes place much slower than the first one, because it involves the excitation of internal degrees of freedom of the system. The two-step process as a whole is highly efficient, and the decay is biexponential. We provide, if possible, the results of analytical studies, otherwise characteristic numerical results. The similarities of the obtained results to light harvesting in photosynthetic organisms are discussed.
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Affiliation(s)
- Hichem Eleuch
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Ingrid Rotter
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
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Lakhno VD, Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA. Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin. DOKL BIOCHEM BIOPHYS 2017; 471:435-439. [PMID: 28058680 DOI: 10.1134/s1607672916060168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/23/2022]
Abstract
A quantum-classical model of photoisomerization of the visual pigment rhodopsin chromophore is proposed. At certain (and more realistic) parameter value combinations, the model is shown to accurately reproduce a number of independent experimental data on the photoreaction dynamics: the quantum yield, the time to reach the point of conical intersection of potential energy surfaces, the termination time of the evolution of quantum subsystem, as well as the characteristic low frequencies of retinal molecular lattice fluctuations during photoisomerization. In addition, the model behavior is in good accordance with experimental data about coherence and local character of quantum transition.
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Affiliation(s)
- V D Lakhno
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences-branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia
| | - A S Shigaev
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences-branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia.
| | - T B Feldman
- Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
| | - V A Nadtochenko
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - M A Ostrovsky
- Moscow State University, Moscow, 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia
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Shirmovsky SE. Quantum dynamics of a hole migration through DNA: A single strand DNA model. Biophys Chem 2016; 217:42-57. [PMID: 27497061 DOI: 10.1016/j.bpc.2016.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 11/24/2022]
Abstract
A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.
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Affiliation(s)
- S Eh Shirmovsky
- Far Eastern Federal University, 8 Sukhanov St., Vladivostok 690950, Russia.
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6
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Abstract
The influence of the competition between polaron formation and population injection on exciton dissociation.
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Affiliation(s)
- Guangqi Li
- Department of Chemistry
- Northwestern University
- Evanston IL
- USA
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Li G, Movaghar B, Nitzan A, Ratner MA. Polaron formation: Ehrenfest dynamics vs. exact results. J Chem Phys 2013; 138:044112. [PMID: 23387573 DOI: 10.1063/1.4776230] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use a one-dimensional tight binding model with an impurity site characterized by electron-vibration coupling, to describe electron transfer and localization at zero temperature, aiming to examine the process of polaron formation in this system. In particular we focus on comparing a semiclassical approach that describes nuclear motion in this many vibronic-states system on the Ehrenfest dynamics level to a numerically exact fully quantum calculation based on the Bonca-Trugman method [J. Bonča and S. A. Trugman, Phys. Rev. Lett. 75, 2566 (1995)]. In both approaches, thermal relaxation in the nuclear subspace is implemented in equivalent approximate ways: In the Ehrenfest calculation the uncoupled (to the electronic subsystem) motion of the classical (harmonic) oscillator is simply damped as would be implied by coupling to a Markovian zero temperature bath. In the quantum calculation, thermal relaxation is implemented by augmenting the Liouville equation for the oscillator density matrix with kinetic terms that account for the same relaxation. In both cases we calculate the probability to trap the electron by forming a polaron and the probability that it escapes to infinity. Comparing these calculations, we find that while both result in similar long time yields for these processes, the Ehrenfest-dynamics based calculation fails to account for the correct time scale for the polaron formation. This failure results, as usual, from the fact that at the early stage of polaron formation the classical nuclear dynamics takes place on an unphysical average potential surface that reflects the distributed electronic population in the system, while the quantum calculation accounts fully for correlations between the electronic and vibrational subsystems.
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Affiliation(s)
- Guangqi Li
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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Zarea M, Powell D, Renaud N, Wasielewski MR, Ratner MA. Decoherence and Quantum Interference in a Four-Site Model System: Mechanisms and Turnovers. J Phys Chem B 2013; 117:1010-20. [DOI: 10.1021/jp3102942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mahdi Zarea
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Daniel Powell
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Nicolas Renaud
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
| | - Mark A. Ratner
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois,
United States
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Renaud N, Powell D, Zarea M, Movaghar B, Wasielewski MR, Ratner MA. Quantum Interferences and Electron Transfer in Photosystem I. J Phys Chem A 2012; 117:5899-908. [DOI: 10.1021/jp308216y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Daniel Powell
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mahdi Zarea
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Bijan Movaghar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
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Guldi DM, Rahman GMA, Sgobba V, Ehli C. Multifunctional molecular carbon materials--from fullerenes to carbon nanotubes. Chem Soc Rev 2006; 35:471-87. [PMID: 16636729 DOI: 10.1039/b511541h] [Citation(s) in RCA: 360] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This critical review covers the timely topic of carbon nanostructures-fullerenes and carbon nanotubes-in combination with metalloporphyrins as integrative components for electron-donor-acceptor ensembles. These ensembles are typically probed in condensed media and at semi-transparent electrode surfaces. In particular, we will present a comprehensive survey of a variety of covalent (i.e., nanoconjugates) and non-covalent linkages (i.e., nanohybrids) to demonstrate how to govern/fine-tune the electronic interactions in the resulting electron-donor-acceptor ensembles. In the context of covalent bridges, different spacers will be discussed, which range from pure "insulators" (i.e., amide bonds, etc.) to sophisticated "molecular wires" (i.e., p-phenylenevinylene units, etc.). Furthermore, we will elucidate the fundamental impact that these vastly different spacers may exert on the rate, efficiency, and mechanism of short- and long-range electron transfer reactions. Additionally, a series of non-covalent motifs will be described: hydrogen bonding, complementary electrostatics, pi-pi stacking and metal coordination-to name a few. These motifs have been successfully employed by us and our collaborators en route towards novel architectures (i.e., linear structures, tubular structures, rotaxanes, catenanes, etc.) that exhibit unique and remarkable charge transfer features.
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Affiliation(s)
- Dirk M Guldi
- Universität Erlangen, Institute for Physical and Theoretical Chemistry, 91058 Erlangen, Germany
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