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Chevizovich D, Michieletto D, Mvogo A, Zakiryanov F, Zdravković S. A review on nonlinear DNA physics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200774. [PMID: 33391787 PMCID: PMC7735367 DOI: 10.1098/rsos.200774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.
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Affiliation(s)
- Dalibor Chevizovich
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Alain Mvogo
- Laboratory of Biophysics, Department of Physics, Faculty of Science, University of Yaounde I, PO Box 812, Cameroon
| | - Farit Zakiryanov
- Bashkir State University, 32 Zali Validi Street, 450076 Ufa, Republic of Bashkortostan, Russia
| | - Slobodan Zdravković
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
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Ribeiro LA, Monteiro FF, da Cunha WF, E Silva GM. Charge Carrier Scattering in Polymers: A New Neutral Coupled Soliton Channel. Sci Rep 2018; 8:6595. [PMID: 29700347 PMCID: PMC5919967 DOI: 10.1038/s41598-018-24948-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/10/2018] [Indexed: 11/22/2022] Open
Abstract
The dynamical scattering of two oppositely charged bipolarons in non-degenerate organic semiconducting lattices is numerically investigated in the framework of a one-dimensional tight-biding-Hubbard model that includes lattice relaxation. Our findings show that it is possible for the bipolaron pair to merge into a state composed of a confined soliton-antisoliton pair, which is characterized by the appearance of states within less than 0.1 eV from the Fermi level. This compound is in a narrow analogy to a meson confining a quark-antiquark pair. Interestingly, solitons are quasi-particles theoretically predicted to arise only in polymer lattices with degenerate ground state: in the general case of non-degenerate ground state polymers, isolated solitons are not allowed.
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Affiliation(s)
- Luiz Antonio Ribeiro
- Department of Physics, Chemistry and Biology, Linköping University, SE-58183, Linköping, Sweden
| | - Fábio Ferreira Monteiro
- International Center for Condensed Matter Physics, University of Brasília, P.O. Box 04531, 70.919-970, Brasília, DF, Brazil
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Ribeiro Junior LA, Ferreira Monteiro F, Enders BG, de Almeida Fonseca AL, E Silva GM, da Cunha WF. Dynamic Formation of Bipolaron-Exciton Complexes in Conducting Polymers. J Phys Chem A 2018; 122:3866-3872. [PMID: 29608859 DOI: 10.1021/acs.jpca.7b12185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recombination dynamics of two oppositely charged bipolarons within a single polymer chain is numerically studied in the scope of a one-dimensional tight-binding model that considers electron-electron and electron-phonon (e-ph) interactions. By scanning among values of e-ph coupling and electric field, novel channels for the bipolaron recombination were yielded based on the interplay between these two parameters. The findings point to the formation of a compound species formed from the coupling between a bipolaron and an exciton. Depending on the electric field and e-ph coupling strengths, the recombination mechanism may yield two distinct products: a trapped (and almost neutral) or a moving (and partially charged) bipolaron-exciton. These results might enlighten the understanding of the electroluminescence processes in organic light-emitting devices.
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Affiliation(s)
- Luiz Antonio Ribeiro Junior
- Department of Physics, Chemistry and Biology , Linköping University , SE-58183 Linköping , Sweden.,Institute of Physics , University of Brasília , 70919-970 Brasília , Brazil
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Ribeiro LA, Ferreira da Cunha W, de Almeida Fonseca AL, E Silva GM. Bloch oscillations in organic and inorganic polymers. J Chem Phys 2017; 146:144903. [PMID: 28411599 DOI: 10.1063/1.4979950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The transport of polarons above the mobility threshold in organic and inorganic polymers is theoretically investigated in the framework of a one-dimensional tight-binding model that includes lattice relaxation. The computational approach is based on parameters for which the model Hamiltonian suitably describes different polymer lattices in the presence of external electric fields. Our findings show that, above critical field strengths, a dissociated polaron moves through the polymer lattice as a free electron performing Bloch oscillations. These critical electric fields are considerably smaller for inorganic lattices in comparison to organic polymers. Interestingly, for inorganic lattices, the free electron propagates preserving charge and spin densities' localization which is a characteristic of a static polaron. Moreover, in the turning points of the spatial Bloch oscillations, transient polaron levels are formed inside the band gap, thus generating a fully characterized polaron structure. For the organic case, on the other hand, no polaron signature is observed: neither in the shape of the distortion-those polaron profile signatures are absent-nor in the energy levels-as no such polaron levels are formed during the simulation. These results solve controversial aspects concerning Bloch oscillations recently reported in the literature and may enlighten the understanding about the charge transport mechanism in polymers above their mobility edge.
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Affiliation(s)
- Luiz Antonio Ribeiro
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
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Ribeiro Junior LA, da Cunha WF. Nonadiabatic dynamics of injected holes in conjugated polymers. Phys Chem Chem Phys 2017; 19:10000-10008. [PMID: 28362447 DOI: 10.1039/c7cp00729a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of injected holes in short transient times that precede polaron formation is numerically studied in the framework of a tight-binding electron-phonon interacting approach aimed at describing organic one-dimensional lattices. In particular, the direct impact of internal and external factors on the conversion of injected holes into polarons is carefully investigated. The results show that a hole injected at levels lower than the highest occupied molecular orbital forms self-trapped bound structures that can merge spontaneously to form a polaron after, at least, one picosecond. On the other hand, the life-time of such structures substantially decreases (up to a few hundreds of femtoseconds) when the influence of external electric fields, temperature effects and impurities is considered. Importantly, the critical values of the aforementioned factors in promoting the quenching of the self-trapped structures are obtained. These findings may enlighten the understanding of the mechanism of charge carrier generation in Polymer Light Emitting Diodes when several kinds of excitations are present.
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Ribeiro Junior LA, da Cunha WF, de Almeida Fonseca AL, Gargano R, e Silva GM. Concentration effects on intrachain polaron recombination in conjugated polymers. Phys Chem Chem Phys 2015; 17:1299-308. [PMID: 25423278 DOI: 10.1039/c4cp04514a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of different charge carrier concentrations on the recombination dynamics between oppositely charged polarons is numerically investigated using a modified version of the Su–Schrieffer–Heeger (SSH) model that includes an external electric field and electron–electron interactions.
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Affiliation(s)
| | | | | | - Ricardo Gargano
- Department of Chemistry and Physics
- University of Florida
- Gainesville
- USA
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da Cunha WF, Ribeiro Junior LA, Gargano R, e Silva GM. Critical temperature and products of intrachain polaron recombination in conjugated polymers. Phys Chem Chem Phys 2014; 16:17072-80. [DOI: 10.1039/c4cp02184c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intrachain recombination dynamics between oppositely charged polarons is theoretically investigated through the use of a version of the Su–Schrieffer–Heeger (SSH) model modified to include an external electric field, an extended Hubbard model, Coulomb interactions, and temperature effects in the framework of a nonadiabatic evolution method.
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Čevizović D, Ivić Z, Pržulj Ž, Tekić J, Kapor D. Interchain coupling effects on large acoustic polaron in two parallel molecular chains. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Zhang YL, Liu XJ, Sun Z, An Z. Dynamics of exciton transfer in coupled polymer chains. J Chem Phys 2013; 138:174906. [DOI: 10.1063/1.4803163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Yuan XJ, Dong XF, Li DM, Liu DS. Effects of disordered interchain interactions on polaron dynamics in semiconducting polymers. J Chem Phys 2011; 134:244901. [PMID: 21721658 DOI: 10.1063/1.3600666] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Polaron dynamics in a system of two randomly coupled polymer chains is simulated using a nonadiabatic evolution method. The simulations are performed within the framework of the Su-Schrieffer-Heeger model modified to include disordered interchain interactions and an external electric field. By analysing the polaron velocity statistically, we find that the polaron motion is determined by the competition between the electric field and the disordered interchain interactions. Polaron dynamics are classified into two types, weak-coupling dynamics and strong-coupling dynamics. It is found that the strength of interchain interactions is the dominant factor controlling charge propagation in weak-coupling dynamics, whereas the effects of disorder are dominant in strong-coupling dynamics. The charge carriers tend to have higher mobility for stronger interchain coupling, and interchain coupling disorder can be favorable for charge transport depending on the coupling strength and the electric field.
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Affiliation(s)
- Xiao-Juan Yuan
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan, China
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Di B, Meng Y, Wang YD, Liu XJ, An Z. Formation and Evolution Dynamics of Bipolarons in Conjugated Polymers. J Phys Chem B 2011; 115:964-71. [DOI: 10.1021/jp110875b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B. Di
- College of Physics, and Hebei Advanced Thin Films Laboratory, Hebei Normal University, Shijiazhuang 050016, China
| | - Y. Meng
- College of Physics, and Hebei Advanced Thin Films Laboratory, Hebei Normal University, Shijiazhuang 050016, China
| | - Y. D. Wang
- College of Physics, and Hebei Advanced Thin Films Laboratory, Hebei Normal University, Shijiazhuang 050016, China
| | - X. J. Liu
- College of Physics, and Hebei Advanced Thin Films Laboratory, Hebei Normal University, Shijiazhuang 050016, China
| | - Z. An
- College of Physics, and Hebei Advanced Thin Films Laboratory, Hebei Normal University, Shijiazhuang 050016, China
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Ding LJ, Yao KL, Fu HH. Field-controlled magnetic order with insulator–metal transitions in a periodic Anderson-like organic polymer. Phys Chem Chem Phys 2011; 13:328-36. [DOI: 10.1039/c0cp00185f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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de Oliveira Neto PH, da Cunha WF, Roncaratti LF, Gargano R, e Silva GM. Thermal effects on photogeneration of free carriers in organic conductors. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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de Oliveira Neto PH, da Cunha WF, Gargano R, Magela e Silva G. Molecular dynamics investigation of charge carrier density influence over mobility in conjugated polymers. J Phys Chem A 2009; 113:14975-8. [PMID: 20028178 DOI: 10.1021/jp905095a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge carrier mobility is known to be one of the most important efficiency delimiting factors in conducting polymer-based electronic devices. As the transport mechanism in this class of material is nonconventional, many works have tried to elucidate the charge carrier's interaction with temperature, external electric field, and the collective effects they present. Even though the multiple trap-and-release model is often used to describe these effects, its applicability is known to be restricted to electronic properties. In this work we make use of a modified version of the Su-Schrieffer-Heeger model, the most used method to describe the important properties of conducting polymer in general, to investigate the influence of temperature and carrier densities over the transport mechanisms. We obtained different regimes of temperature and carriers density influence over the systems mobility, consistent with most of the experimental data available.
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Meng Y, Liu XJ, Di B, An Z. Recombination of polaron and exciton in conjugated polymers. J Chem Phys 2009; 131:244502. [DOI: 10.1063/1.3274680] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Qiu Y, Zhu LP. Field effect on polaron dynamics and charge transport in conducting polymers. J Chem Phys 2009; 131:134903. [PMID: 19814571 DOI: 10.1063/1.3243682] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the formation and motion dynamics of polarons in one-dimensional conjugated polymers within the extended Su-Schrieffer-Heeger model combined with an adiabatic dynamics method. In the presence of external electric fields, the initial location of the polaron is stressed and concerned with the charge transport property of organic semiconductors. Three regimes for the electric fields are categorized in terms of the forming place of the polaron. In the low field strength regime, the polaron is formed around the center of the chain and thus the charge undergoes a long-time travel before being extracted into the electrode because of the strong electron and phonon (e-p) interaction. In the intermediate strength regime, the polaron is formed near the chain end. Due to the chain-end scattering, the electron mobility increases in linear relation with the field strength. In the high strength regime, the polaron is formed at the chain end. This results in a nonlinear enhancement in the electronic mobility, in agreement with the experimental observations on the field dependent transient photocurrent in poly(phenylene vinylene). The electron-electron correlation, as well as the field mode effect on polaron dynamics, is also discussed.
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Affiliation(s)
- Yu Qiu
- Department of Physics, Zhejiang Normal University, Jinhua, 321004 Zhejiang, China.
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