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Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules 2022; 27:molecules27217408. [DOI: 10.3390/molecules27217408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
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2
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Leo A, Peluso A. Electron Transfer Rates in Polar and Non-Polar Environments: a Generalization of Marcus' Theory to Include an Effective Treatment of Tunneling Effects. J Phys Chem Lett 2022; 13:9148-9155. [PMID: 36166392 PMCID: PMC9549518 DOI: 10.1021/acs.jpclett.2c02343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
A multistep kinetic model in which solvent motion is treated in the framework of Marcus theory and the rates of the elementary electron transfer step are evaluated at full quantum mechanical level is proposed and applied to the calculation of the rates of intramolecular electron transfer reactions in rigidly spaced D-Br-A (D = 1,1'-biphenyl radical anion, Br = androstane) compounds, for five acceptors (A) in three organic solvents with different polarity. The calculated rates agree well with experimental ones, and their temperature dependence is almost quantitatively reproduced.
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3
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Landi A, Capobianco A, Peluso A. The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study. Molecules 2021; 26:5497. [PMID: 34576968 PMCID: PMC8465834 DOI: 10.3390/molecules26185497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800-1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.
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Affiliation(s)
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, Italy; (A.L.); (A.P.)
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Chen X, Salim T, Zhang Z, Yu X, Volkova I, Nijhuis CA. Large Increase in the Dielectric Constant and Partial Loss of Coherence Increases Tunneling Rates across Molecular Wires. ACS APPLIED MATERIALS & INTERFACES 2020; 12:45111-45121. [PMID: 32897683 DOI: 10.1021/acsami.0c11106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although the dielectric behavior of monolayers is important in a large range of applications, its role in charge transport studies involving molecular junctions is largely ignored. This paper describes a large increase in the relative static dielectric constant (εr) by simply increasing the thickness of well-organized monolayers of oligoglycine and oligo(ethylene glycol) from 7 up to 14. The resulting large capacitance of 3.5-5.1 μF/cm2 is thickness-independent, which is highly attractive for field-effect transistor applications. This increase of εr results in a linear increase of the thermal activation energy by a factor of 6, which suggests that the mechanism of charge transport gradually changes from coherent to (partially) incoherent tunneling. The comparisons of oligoglycine (which readily forms hydrogen bonds with neighboring molecules) and methyl terminated oligo(ethylene glycol) (which lacks hydrogen bond donors) monolayers, kinetic isotope effects, and relative humidity-dependent measurements all indicate the importance of strong hydrogen bonds involving ionic species and strongly bonded water in the unusual dielectric behavior and the incoherent tunneling mechanism. This partial loss of coherence of the charge carriers can explain the unusually small tunneling decay coefficients across long molecular wires, and the length-dependent increase of εr of monolayers opens up interesting new applications.
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Affiliation(s)
- Xiaoping Chen
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Teddy Salim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Ziyu Zhang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Xiaojiang Yu
- Singapore Synchrotron Light Source, National University of Singapore, 5 Research Link, Singapore 117603, Singapore
| | - Ira Volkova
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Christian A Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre for Advanced 2D Materials and Graphene Research Centre, National University of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
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Landi A, Capobianco A, Peluso A. Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA. J Phys Chem Lett 2020; 11:7769-7775. [PMID: 32830977 PMCID: PMC8154848 DOI: 10.1021/acs.jpclett.0c01996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the framework of a multistep mechanism in which environmental motion triggers comparatively faster elementary electron-transfer steps and stabilizes hole-transfer products, microscopic coherence is crucial for rationalizing the observed yield ratios of oxidative damage to DNA. Interference among probability amplitudes of indistinguishable electron-transfer paths is able to drastically change the final outcome of charge transport, even in DNA oligomers constituted by similar building blocks, and allows for reconciling apparently discordant experimental observations. Properly tailored DNA oligomers appear to be a promising workbench for studying tunneling in the presence of dissipation at the macroscopic level.
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Eshel Y, Peskin U, Amdursky N. Coherence-assisted electron diffusion across the multi-heme protein-based bacterial nanowire. NANOTECHNOLOGY 2020; 31:314002. [PMID: 32259806 DOI: 10.1088/1361-6528/ab8767] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological electron transfer (ET) is one of the most studied biochemical processes due to its immense importance in biology. For many years, biological ET was explained using the classical incoherent transport mechanism, i.e. sequential hopping. One of the relatively recent major observations in this field is long-range extracellular ET (EET), where some bacteria were shown to mediate electrons for extremely long distances on the micrometer length scales across individual nanowires. This fascinating finding has resulted in several suggested mechanisms that might explain this intriguing EET. More recently, the structure of a conductive G. sulfurreducens nanowire has been solved, which showed a highly ordered quasi-1D wire of a hexaheme cytochrome protein, named OmcS. Based on this new structure, we suggest here several electron diffusion models for EET, involving either purely hopping or several degrees of mixed hopping and coherent transport, in which the coherent part is due to a local rigidification of the protein structure, associated with a decrease in the local reorganization energy. The effect is demonstrated for two closely packed heme sites as well as for longer chains containing up to several dozens porphyrins. We show that the pure hopping model probably cannot explain the reported conductivity values of the G. sulfurreducens nanowire using conventional values of reorganization energy and electronic coupling. On the other hand, we show that for a wide range of the latter energy values, the mixed hopping-coherent model results in superior electron diffusion compared to the pure hopping model, and especially for long-range coherent transport, involving multiple porphyrin sites.
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Affiliation(s)
- Yoni Eshel
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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Iv M, Peskin U. Ballistic transport and quantum unfurling in molecular junctions via minimal representations of quantum master equations. J Chem Phys 2020; 152:184112. [PMID: 32414262 DOI: 10.1063/5.0005412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quantum furling and unfurling are inelastic transitions between localized and delocalized electronic states. We predict scenarios where these processes govern charge transport through donor-bridge-acceptor molecular junctions. Like in the case of ballistic transport, the resulting currents are nearly independent of the molecular bridge length. However, currents involving quantum furling and unfurling processes can be controlled by the coupling to vibrations in the intra-molecular and the extra-molecular environment, which can be experimentally tuned. Our study is based on rate equations for exchange of energy (bosons) and particles (fermions) between the molecular bridge and its environment. An efficient algorithm is introduced for a compact representation of the relevant rate equations, which utilizes the redundancies in the rate matrix and the sparsity of the creation and annihilation operators in the molecular Fock space.
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Affiliation(s)
- Michael Iv
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Uri Peskin
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
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8
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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Landi A, Borrelli R, Capobianco A, Peluso A. Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires. J Phys Chem Lett 2019; 10:1845-1851. [PMID: 30939015 DOI: 10.1021/acs.jpclett.9b00650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.
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Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science , University of Torino , Via Leonardo da Vinci 44 , I-10095 Grugliasco , Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
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Korol R, Segal D. Machine Learning Prediction of DNA Charge Transport. J Phys Chem B 2019; 123:2801-2811. [PMID: 30865456 DOI: 10.1021/acs.jpcb.8b12557] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent electrical conductors, is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. We present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3-7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, on-resonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers in the search for promising electronic and thermoelectric materials.
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Affiliation(s)
- Roman Korol
- Department of Chemistry and Centre for Quantum Information and Quantum Control , University of Toronto , 80 Saint George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Dvira Segal
- Department of Chemistry and Centre for Quantum Information and Quantum Control , University of Toronto , 80 Saint George Street , Toronto , Ontario M5S 3H6 , Canada
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11
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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12
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Levine AD, Iv M, Peskin U. Formulation of Long-Range Transport Rates through Molecular Bridges: From Unfurling to Hopping. J Phys Chem Lett 2018; 9:4139-4145. [PMID: 29961322 DOI: 10.1021/acs.jpclett.8b01581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Weak fluctuations about the rigid equilibrium structure of ordered molecular bridges drive charge transfer in donor-bridge-acceptor systems via quantum unfurling, which differs from both hopping and ballistic transfer, yet static disorder (low frequency motions) in the bridge is shown to induce a change of mechanism from unfurling to hopping when local fluctuations along the molecular bridge are uncorrelated. Remarkably, these two different transport mechanisms manifest in similar charge-transfer rates, which are nearly independent of the molecular bridge length. We propose an experimental test for distinguishing unfurling from hopping in DNA models with different helix directionality. A unified formulation explains the apparent similarity in the length dependence of the transfer rate despite the difference in the underlying transport mechanisms.
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13
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Kim H, Segal D. Controlling charge transport mechanisms in molecular junctions: Distilling thermally induced hopping from coherent-resonant conduction. J Chem Phys 2017; 146:164702. [DOI: 10.1063/1.4981022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Hyehwang Kim
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Dvira Segal
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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Wolter M, Elstner M, Kleinekathöfer U, Kubař T. Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details. J Phys Chem B 2017; 121:529-549. [PMID: 28045546 DOI: 10.1021/acs.jpcb.6b11384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an "on-the-fly" calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical-molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor-bridge-acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the "full" atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.
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Affiliation(s)
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , 28759 Bremen, Germany
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Kubař T, Elstner M, Popescu B, Kleinekathöfer U. Polaron Effects on Charge Transport through Molecular Wires: A Multiscale Approach. J Chem Theory Comput 2016; 13:286-296. [DOI: 10.1021/acs.jctc.6b00879] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Bogdan Popescu
- 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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