1
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Ganguly S, Sarkar S, Mondal K, Maiti SK. Phenomenon of multiple reentrant localization in a double-stranded helix with transverse electric field. Sci Rep 2024; 14:3059. [PMID: 38321060 PMCID: PMC10847133 DOI: 10.1038/s41598-024-52579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/20/2024] [Indexed: 02/08/2024] Open
Abstract
The present work explores the potential for observing multiple reentrant localization behavior in a double-stranded helical (DSH) system, extending beyond the conventional nearest-neighbor hopping (NNH) interaction. The DSH system is considered to have hopping dimerization in each strand, while also being subjected to a transverse electric field. The inclusion of an electric field serves the dual purpose of inducing quasi-periodic disorder and strand-wise staggered site energies. Two reentrant localization regions are identified: one exhibiting true extended behavior in the thermodynamic limit, while the second region shows quasi-extended characteristics with partial spreading within the helix. The DSH system exhibits three distinct single-particle mobility edges linked to localization transitions present in the system. The analysis in this study involves examining various parameters such as the single-particle energy spectrum, inverse participation ratio, local probability amplitude, and more. Our proposal, combining achievable hopping dimerization and induced correlated disorder, presents a unique opportunity to study phenomenon of reentrant localization, generating significant research interest.
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Affiliation(s)
- Sudin Ganguly
- Department of Physics, School of Applied Sciences, University of Science and Technology Meghalaya, Ri-Bhoi, 793101, India
| | - Suparna Sarkar
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata, 700108, India
| | - Kallol Mondal
- School of Physical Sciences, National Institute of Science Education and Research Bhubaneswar, Jatni, Odisha, 752050, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India.
| | - Santanu K Maiti
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata, 700108, India
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2
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Mohammad H, Anantram MP. Charge transport through DNA with energy-dependent decoherence. Phys Rev E 2023; 108:044403. [PMID: 37978586 DOI: 10.1103/physreve.108.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, USA
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3
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Chen C, Zeng Y, Gao G, Sun T, Shen L. Flexibility Analysis of DNA Nanotubes with Prescribed Circumferences and Their Pearl-Necklace Assemblies with Gold Nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37413975 DOI: 10.1021/acs.langmuir.3c01042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
DNA has been demonstrated as a powerful platform for the construction of inorganic nanoparticles (NPs) into complex three-dimensional assemblies. Despite extensive research, the physical fundamental details of DNA nanostructures and their assemblies with NPs remain obscure. Here, we report the identification and quantification of the assembly details of programmable DNA nanotubes with monodisperse circumferences of a 4, 5, 6, 7, 8, or 10 DNA helix and their pearl-necklace-like assemblies with ultrasmall gold nanoparticles, Au25 nanoclusters (AuNCs), liganded by -S(CH2)nNH3+ (n = 3, 6, 11). The flexibilities of DNA nanotubes, analyzed via statistical polymer physics analysis through atomic force microscopy (AFM), demonstrate that ∼2.8 power exponentially increased with the DNA helix number. Moreover, the short-length liganded AuS(CH2)3NH3+ NCs were observed to be able to form pearl-necklace-like DNA-AuNC assemblies stiffened than neat DNA nanotubes, while long-length liganded AuS(CH2)6NH3+ and AuS(CH2)11NH3+ NCs could fragment DNA nanotubular structures, indicating that DNA-AuNC assembling can be precisely manipulated by customizing the hydrophobic domains of the AuNC nanointerfaces. We prove the advantages of polymer science concepts in unraveling useful intrinsic information on physical fundamental details of DNA-AuNC assembling, which facilitates DNA-metal nanocomposite construction.
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Sarkar S, Maiti SK. Helical Molecule as an Efficient Rectifier: Effects of Molecular Conformation and Transverse Electric Field. Chemphyschem 2022; 23:e202200485. [PMID: 35938540 DOI: 10.1002/cphc.202200485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/05/2022] [Indexed: 01/05/2023]
Abstract
The phenomenon of charge current rectification is critically investigated using a single stranded helical molecule in presence of transverse electric field. Two different helical molecules, DNA and protein, are taken into account to explore the specific roles of molecular conformation on rectification, which have not been addressed so far to the best of our concern. Sandwiching the molecular system within source and drain electrodes, we compute charge currents for two bias polarities and the degree of current rectification based on non-equilibrium Green's function formalism within a tight-binding framework. At non-zero electric field, site energies of the molecule are modulated in a cosine form, similar to the well known Aubry-André-Harper relation, resulting an atypical and fragmented energy band spectrum. The appearance of non-uniform site energies plays the central role for generating different currents in two bias polarities, and thus, the current rectification. We find that a high degree of current rectification can be established using the helical system and it becomes more effective for the protein molecule than the DNA one. At the end, the rectification operation considering a more general helical structure is discussed to make the present communication a self-contained one. Our proposition may provide a new route of getting controlled current rectification using similar kind of biological molecules and other tailor made helical geometries.
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Affiliation(s)
- Suparna Sarkar
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata, 700 108, India
| | - Santanu K Maiti
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata, 700 108, India
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5
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Lima RPA, Malyshev AV. Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer. Phys Rev E 2022; 106:024414. [PMID: 36109995 DOI: 10.1103/physreve.106.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
We address various regimes of charge transfer in DNA within the framework of the Peyrard-Bishop-Holstein model and analyze them from the standpoint of the characteristic size and timescales of the electronic and vibrational subsystems. It is demonstrated that a polaron is an unstable configuration within a broad range of temperatures and therefore polaronic contribution to the charge transport is irrelevant. We put forward an alternative fluctuation-governed charge transfer mechanism and show that the charge transfer can be quasiballistic at low temperatures, diffusive or mixed at intermediate temperatures, and subdiffusive close to the DNA denaturation transition point. Dynamic fluctuations in the vibrational subsystem is the key ingredient of our proposed mechanism which allows for explanation of all charge transfer regimes at finite temperatures. In particular, we demonstrate that in the most relevant regime of high temperatures (above the aqueous environment freezing point), the electron dynamics is completely governed by relatively slow fluctuations of the mechanical subsystem. We argue also that our proposed analysis methods and mechanisms can be relevant for the charge transfer in other organic systems, such as conjugated polymers, molecular aggregates, α-helices, etc.
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Affiliation(s)
- R P A Lima
- GISC and GFTC, Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970, Brazil
| | - A V Malyshev
- GISC, Departamento de Física de Materiales, Universidad Complutense, E-28040 Madrid, Spain
- Ioffe Physical-Technical Institute, St-Petersburg, Russia
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6
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Zhang M, Li Z, Jia Y, Wang F, Tian J, Zhang C, Han T, Xing R, Ye W, Wang C. Observing Mesoscopic Nucleic Acid Capacitance Effect and Mismatch Impact via Graphene Transistors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105890. [PMID: 35072345 DOI: 10.1002/smll.202105890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/05/2021] [Indexed: 06/14/2023]
Abstract
This work reports a molecular-scale capacitance effect of the double helical nucleic acid duplex structure for the first time. By quantitatively conducting large sample measurements of the electrostatic field effect using a type of high-accuracy graphene transistor biosensor, an unusual charge-transport behavior is observed in which the end-immobilized nucleic acid duplexes can store a part of ionization electrons like molecular capacitors, other than electric conductors. To elucidate this discovery, a cascaded capacitive network model is proposed as a novel equivalent circuit of nucleic acid duplexes, expanding the point-charge approximation model, by which the partial charge-transport observation is reasonably attributed to an electron-redistribution behavior within the capacitive network. Furthermore, it is experimentally confirmed that base-pair mismatches hinder the charge transport in double helical duplexes, and lead to directly identifiable alterations in electrostatic field effects. The bioelectronic principle of mismatch impact is also self-consistently explained by the newly proposed capacitive network model. The mesoscopic nucleic acid capacitance effect may enable a new kind of label-free nucleic acid analysis tool based on electronic transistor devices. The in situ and real-time nucleic acid detections for virus biomarkers, somatic mutations, and genome editing off-target may thus be predictable.
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Affiliation(s)
- Mingfeng Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Zhibo Li
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Yuan Jia
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Fuquan Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Jinpeng Tian
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Cuiping Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Tingting Han
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Ruiqing Xing
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Weixiang Ye
- Department of Physics, School of Science, Hainan University, Haikou, 570228, China
- Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, School of Science, Hainan University, Haikou, 570228, China
| | - Cheng Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
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7
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Garagozi M, Fathizadeh S, Nemati F. Investigation and Control of Strain-Induced Spin-Dependent Current in a DNA Chain: A Piezospintronic Approach. J Phys Chem B 2022; 126:1709-1718. [DOI: 10.1021/acs.jpcb.1c09824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Garagozi
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
| | - S. Fathizadeh
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
| | - F. Nemati
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran
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8
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Wang Y, Xie Y, Gao M, Zhang W, Liu L, Qu Y, Wang J, Hu C, Song Z, Wang Z. Electrical conductivity measurement of λDNA molecules by conductive atomic force microscopy. NANOTECHNOLOGY 2021; 33:055301. [PMID: 34134105 DOI: 10.1088/1361-6528/ac0be6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 06/12/2023]
Abstract
Conductive atomic force microscopy (C-AFM) is a powerful tool used in the microelectronics analysis by applying a certain bias voltage between the conducting probe and the sample and obtaining the electrical information of sample. In this work, the surface morphological information and current images of the lambda DNA (λDNA) molecules with different distributions were obtained by C-AFM. The 1 and 10 ngμl-1DNA solutions were dripped onto mica sheets for making randomly distributed DNA and DNA network samples, and another 1 ngμl-1DNA sample was placed in a DC electric field with a voltage of 2 V before being dried for stretching the DNA sample. The results show that the current flowing through DNA networks was significantly higher than the stretched and random distribution of DNA in the experiment. TheI-Vcurve of DNA networks was obtained by changing the bias voltage of C-AFM from -9 to 9 V. The currents flowing through stretched DNA at different pH values were studied. When the pH was 7, the current was the smallest, and the current was gradually increased as the solution became acidic or alkaline.
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Affiliation(s)
- Ying Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Ying Xie
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Mingyan Gao
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Wenxiao Zhang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Lanjiao Liu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Yingmin Qu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Jiajia Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Cuihua Hu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zhengxun Song
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, People's Republic of China
- JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, United Kingdom
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9
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Sarkar S, Maiti SK. Localization to delocalization transition in a double stranded helical geometry: effects of conformation, transverse electric field and dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:505301. [PMID: 33006319 DOI: 10.1088/1361-648x/abb05f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Conformational effect on electronic localization is critically investigated for the first time considering a double-stranded helical geometry (DSHG) subjected to an electric field. In the presence of electric field the DSHG behaves like a correlated disordered system whose site potentials are modulated in a cosine form like the well known Aubry-André-Harper model. The potential distribution can be modulated further by changing the orientation of the incident field. A similar kind of cosine modulation is also introduced in the inter-strand hopping integrals of the DSHG. Suitably adjusting the orientation of the electric field, we can achieve fully extended energy eigenstates or completely localized ones or a mixture of both. The effects of short-range and long-range hopping integrals along with the chirality on localization are thoroughly studied. Finally, we inspect the role of helical dynamics to make the model more realistic. The interplay between the helical geometry and electric field may open up several notable features of electronic localization and can be verified by using different chiral molecules.
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Affiliation(s)
- Suparna Sarkar
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-700 108, India
| | - Santanu K Maiti
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-700 108, India
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10
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Anderson RF, Shinde SS, Maroz A, Reynisson J. The reduction potential of the slipped GC base pair in one-electron oxidized duplex DNA. Phys Chem Chem Phys 2020; 22:642-646. [PMID: 31822872 DOI: 10.1039/c9cp05544d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Redox equilibrium between the low potential aniline radical cation and the guanine in the GC base pair of duplex DNA has been established using pulse radiolysis. We relate the measurement of a radical one-electron reduction potential, E0', of 1.01 ± 0.03 V to the perturbation of the GC base pair to accommodate the neutral guanyl radical in an energetically more stable 'slipped' structure. The formation of the 'slipped' structure is exothermic by -11.4 kcal mol-1 as calculated by DFT, which is inline with our experimental results.
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Affiliation(s)
- Robert F Anderson
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
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11
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Ojeda Silva JH, Maiti SK. Thermal Properties of Ordered and Disordered DNA Chains: Efficient Energy Conversion. Chemphyschem 2019; 20:3346-3353. [PMID: 31549778 DOI: 10.1002/cphc.201900699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/09/2019] [Indexed: 11/11/2022]
Abstract
Considering the numerous possibilities of having suitable thermoelectric energy conversion at nano-scale level, especially for molecular systems, in the present work we put forward a new proposal along this using a flat DNA segment as a functional element. It is modeled by coupling two chains to a form a two-stranded ladder like geometry, with interactions to first neighbors, within the tight-binding prescription. We critically investigate electrical and thermal properties of DNA molecule depending on the length of the system, temperature, molecule-to-lead coupling and the degree of (correlated) disorder. Our analysis might be helpful in analyzing thermoelectric signatures of correlated and uncorrelated disordered systems, and can be verified in laboratory.
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Affiliation(s)
- Judith Helena Ojeda Silva
- Grupo de Física de Materiales, Universidad Pedagógica y Tecnológica de Colombia, 150003, Tunja, Colombia.,Laboratorio de Química Teórica y Computacional, Grupo de Investigación Química-Física Molecular y Modelamiento Computacional (QUIMOL), Facultad de Ciencias, Universidad Pedagógica y Tecnológica de Colombia, 150003, Tunja, Boyacá, Colombia
| | - Santanu K Maiti
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-, 700 108, India
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12
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Collier TP, Portnoi ME. Double-Gated Nanohelix as a Novel Tunable Binary Superlattice. NANOSCALE RESEARCH LETTERS 2019; 14:257. [PMID: 31448386 PMCID: PMC6709081 DOI: 10.1186/s11671-019-3069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
We theoretically investigate the problem of an electron confined to a nanohelix between two parallel gates modelled as charged wires. The double-gated nanohelix system is a binary superlattice with properties highly sensitive to the gate voltages. In particular, the band structure exhibits energy band crossings for certain combinations of gate voltages, which could lead to quasi-relativistic Dirac-like phenomena. Our analysis for optical transitions induced by linearly and circularly polarized light suggests that a double-gated nanohelix can be used for versatile optoelectronic applications.
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Affiliation(s)
- Thomas P. Collier
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL United Kingdom
| | - Mikhail E. Portnoi
- School of Physics, University of Exeter, Stocker Road, Exeter, EX4 4QL United Kingdom
- ITMO University, St. Petersburg, 197101 Russia
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13
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Likhachev VN, Vinogradov GA. Charge Transfer in the Lattice with an Impurity Site. Reflection and Transmission of the Wave Packet. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2018. [DOI: 10.1134/s1990793118030272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Fathizadeh S, Behnia S, Ziaei J. Engineering DNA Molecule Bridge between Metal Electrodes for High-Performance Molecular Transistor: An Environmental Dependent Approach. J Phys Chem B 2018; 122:2487-2494. [DOI: 10.1021/acs.jpcb.7b10034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Fathizadeh
- Department of Physics, Faculty of Science, Urmia University of Technology, Urmia, Iran
| | - S. Behnia
- Department of Physics, Faculty of Science, Urmia University of Technology, Urmia, Iran
| | - J. Ziaei
- Department of Physics, Faculty of Science, Urmia University of Technology, Urmia, Iran
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15
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Plettenberg J, Stockhofe J, Zampetaki AV, Schmelcher P. Local equilibria and state transfer of charged classical particles on a helix in an electric field. Phys Rev E 2017; 95:012213. [PMID: 28208410 DOI: 10.1103/physreve.95.012213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/07/2022]
Abstract
We explore the effects of a homogeneous external electric field on the static properties and dynamical behavior of two charged particles confined to a helix. In contrast to the field-free setup which provides a separation of the center-of-mass and relative motion, the existence of an external force perpendicular to the helix axis couples the center-of-mass to the relative degree of freedom leading to equilibria with a localized center of mass. By tuning the external field various fixed points are created and/or annihilated through different bifurcation scenarios. We provide a detailed analysis of these bifurcations based on which we demonstrate a robust state transfer between essentially arbitrary equilibrium configurations of the two charges that can be induced by making the external force time dependent.
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Affiliation(s)
- J Plettenberg
- Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - J Stockhofe
- Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A V Zampetaki
- Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - P Schmelcher
- Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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16
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17
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Yoo-Kong S, Liewrian W. Double path integral method for obtaining the mobility of the one-dimensional charge transport in molecular chain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:135. [PMID: 26701710 DOI: 10.1140/epje/i2015-15135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
We report on a theoretical investigation concerning the polaronic effect on the transport properties of a charge carrier in a one-dimensional molecular chain. Our technique is based on the Feynman's path integral approach. Analytical expressions for the frequency-dependent mobility and effective mass of the carrier are obtained as functions of electron-phonon coupling. The result exhibits the crossover from a nearly free particle to a heavily trapped particle. We find that the mobility depends on temperature and decreases exponentially with increasing temperature at low temperature. It exhibits large polaronic-like behaviour in the case of weak electron-phonon coupling. These results agree with the phase transition (A.S. Mishchenko et al., Phys. Rev. Lett. 114, 146401 (2015)) of transport phenomena related to polaron motion in the molecular chain.
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Affiliation(s)
- Sikarin Yoo-Kong
- Theoretical and Computational Physics (TCP) Group, Department of Physics, Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Theoretical and Computational Science Centre (TaCS), Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Ratchaburi Campus, King Mongkut's University of Technology Thonburi, 70510, Ratchaburi, Thailand.
| | - Watchara Liewrian
- Theoretical and Computational Physics (TCP) Group, Department of Physics, Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- Theoretical and Computational Science Centre (TaCS), Faculty of Science, King Mongkut's University of Technology Thonburi, 10140, Bangkok, Thailand.
- ThEP Center, Commission of Higher Education, 328 Si Ayuthaya Rd., 10400, Bangkok, Thailand.
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18
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Behnia S, Fathizadeh S. Modeling the electrical conduction in DNA nanowires: charge transfer and lattice fluctuation theories. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022719. [PMID: 25768543 DOI: 10.1103/physreve.91.022719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Indexed: 06/04/2023]
Abstract
An analytical approach is proposed for the investigation of the conductivity properties of DNA. The charge mobility of DNA is studied based on an extended Peyrard-Bishop-Holstein model when the charge carrier is also subjected to an external electrical field. We have obtained the values of some of the system parameters, such as the electron-lattice coupling constant, by using the mean Lyapunov exponent method. On the other hand, the electrical current operator is calculated directly from the lattice operators. Also, we have studied Landauer resistance behavior with respect to the external field, which could serve as the interface between chaos theory tools and electronic concepts. We have examined the effect of two types of electrical fields (dc and ac) and variation of the field frequency on the current flowing through DNA. A study of the current-voltage (I-V) characteristic diagram reveals regions with a (quasi-)Ohmic property and other regions with negative differential resistance (NDR). NDR is a phenomenon that has been observed experimentally in DNA at room temperature. We have tried to study the affected agents in charge transfer phenomena in DNA to better design nanostructures.
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Affiliation(s)
- S Behnia
- Department of Physics, Urmia University of Technology, Orumieh, Iran
| | - S Fathizadeh
- Department of Physics, Urmia University of Technology, Orumieh, Iran
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19
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Wu L, Liu K, Jie J, Song D, Su H. Direct observation of guanine radical cation deprotonation in G-quadruplex DNA. J Am Chem Soc 2014; 137:259-66. [PMID: 25506785 DOI: 10.1021/ja510285t] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G(+•)) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2-H instead of imino proton N1-H) and slower (1-2 orders of magnitude) deprotonation rate of G(+•) within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, mechanistic insights have been further achieved, showing that it should be the non-hydrogen-bonded free proton to be released during deprotonation in G-quadruplexes, which is the N2-H exposed to solvent for G bases in G-quartets or the free N1-H for G base in the loop. The slower N2-H deprotonation rate can thus ensure less interruption of the hole transfer. The unique deprotonation features observed here for G-quadruplexes open possibilities for their interesting applications as molecular electronic devices, while the elucidated mechanisms can provide illuminations for the rational design of G-quadruplex structures toward such applications and enrich the fundamental understandings of DNA radical chemistry.
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Affiliation(s)
- Lidan Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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20
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Wang K, Hamill J, Zhou J, Guo C, Xu B. Measurement and control of detailed electronic properties in a single molecule break junction. Faraday Discuss 2014; 174:91-104. [DOI: 10.1039/c4fd00080c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch–hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal–molecule junction, providing us insightful clues towards the next step for in-depth study.
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Affiliation(s)
- Kun Wang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Joseph Hamill
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Jianfeng Zhou
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Cunlan Guo
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Bingqian Xu
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
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21
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Mendes G, Albuquerque E, Fulco U, Bezerril L, Caetano E, Freire V. Electronic specific heat of an α3-helical polypeptide and its biochemical variants. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Munárriz J, Domínguez-Adame F, Malyshev AV. Toward graphene-based quantum interference devices. NANOTECHNOLOGY 2011; 22:365201. [PMID: 21836327 DOI: 10.1088/0957-4484/22/36/365201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A new type of quantum interference device based on a graphene nanoring in which all edges are of the same type is studied theoretically. The superposition of the electron wavefunction propagating from the source to the drain along the two arms of the nanoring gives rise to interesting interference effects. We show that a side-gate voltage applied across the ring allows for control of the interference pattern at the drain. The electron current between the two leads can therefore be modulated by the side gate. The latter manifests itself as conductance oscillations as a function of the gate voltage. We study quantum nanorings with two edge types (zigzag or armchair) and argue that the armchair type is more advantageous for applications. We demonstrate finally that our proposed device operates as a quantum interference transistor with high on/off ratio.
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Affiliation(s)
- J Munárriz
- GISC, Departamento de Física de Materiales, Universidad Complutense, Madrid, Spain
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23
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Kang DW, Qu Z, Jiang H, Xie SJ. Transverse electric field modulated tunneling magnetoresistance in a DNA molecular device. Phys Chem Chem Phys 2010; 12:578-82. [PMID: 20066344 DOI: 10.1039/b917050b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum spin-dependent transport in a ferromagnetic(FM)/DNA/ferromagnetic(FM) device is theoretically investigated based on the lattice Green function method and the Landauer-Büttiker theory. The effect of a transverse electric field on magnetoresistance (MR) of the device is investigated. It is predicted that either the direction or strength of the transverse electric field can change the MR of the device. We suggest a possible application of modulating MR of the FM/DNA/FM device by a transverse electric field.
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Affiliation(s)
- Da-Wei Kang
- School of Physics, Shandong University, Jinan, 250100, China
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25
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Malyshev AV, Díaz E, Domínguez-Adame F, Malyshev VA. Effects of the environment on the electric conductivity of double-stranded DNA molecules. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:335105. [PMID: 21828599 DOI: 10.1088/0953-8984/21/33/335105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a theoretical analysis of the effects of the environment on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i) localization of carrier functions due to static disorder and (ii) phonon-induced scattering of the carriers between the localized states, resulting in hopping conductivity. A nonlinear Pauli master equation for populations of localized states is used to describe the hopping transport and calculate the electric current as a function of the applied bias. We demonstrate that, although the electronic gap in the density of states shrinks as the disorder increases, the voltage gap in the I-V characteristics becomes wider. A simple physical explanation of this effect is provided.
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Affiliation(s)
- A V Malyshev
- GISC, Departamento de Física de Materiales, Universidad Complutense, E-28040 Madrid, Spain
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Guo AM, Xiong SJ. Violation of the single-parameter scaling hypothesis in human chromosome 22 with charge transfer models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:041924. [PMID: 19518273 DOI: 10.1103/physreve.79.041924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 12/15/2008] [Indexed: 05/27/2023]
Abstract
We investigate transport properties of DNA sequences in human chromosome 22 and compare the results with those of a random artificial DNA sequence based on the single- and double-stranded charge transfer models. The statistical quantities, including the Hurst exponent, the distribution of Lyapunov exponent (LE), the central moments, and the scaling parameter, are numerically calculated by using the transfer-matrix approach. It is found that the existence of satellite DNA segments in human chromosome 22 could result in deviations from usual Gaussian distribution of LE. Our results suggest that the presence of the satellite DNA segments, together with the long-range correlations and the base-pairing correlations could lead to the violation of single-parameter scaling hypothesis which holds for the random artificial DNA sequence although the behaviors of the averaged LEs for both DNA sequences are similar. This provides a viewpoint to analyze differences between the genomic DNA sequences and the nonliving random ones on the basis of localization properties of wave functions in the sequences.
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Affiliation(s)
- Ai-Min Guo
- Department of Physics and National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093, China
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Ramos MMD, Correia HMG. Modelling the effect of structure and base sequence on DNA molecular electronics. NANOTECHNOLOGY 2008; 19:375202. [PMID: 21832544 DOI: 10.1088/0957-4484/19/37/375202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA.
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Affiliation(s)
- M M D Ramos
- Departamento de Física, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Díaz E. Analysis of the interband optical transitions: characterization of synthetic DNA band structure. J Chem Phys 2008; 128:175101. [PMID: 18465940 DOI: 10.1063/1.2901046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze the band structure and interband optical transitions in a dangling backbone ladder DNA model. Using this model, semiconducting synthetic poly(G)-poly(C) DNA is studied by means of a tight-binding model traditionally used for transport studies. Numerical calculations for optical absorption spectra are also presented. By studying the eigenstates' symmetries in uniform and nonuniform DNA chains, we conclude that, in both cases, the transitions are almost vertical in K space. The optical gap turns out larger than the electronic one, and an indirect band gap electronic structure for this DNA model is revealed. The effects of the environment, which are relevant for the wet form of DNA, are taken into account by introducing disorder in the backbone levels. We demonstrate that they affect more the spectra in the case of parallel polarization of the incoming light (with respect to the molecule axis). In such a case, the closure of the gap appears for a large enough disorder. We also consider the natural helix DNA conformation and find unusual selection rules for interband optical transitions. We propose that a comparison between the obtained spectra and the experiments can provide an insight into the electronic band structure of DNA.
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Affiliation(s)
- Elena Díaz
- GISC, Departamento de Física de Materiales, Universidad Complutense, E-28040 Madrid, Spain.
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29
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Wei JH, Liu XJ, Berakdar J, Yan Y. Pathways of polaron and bipolaron transport in DNA double strands. J Chem Phys 2008; 128:165101. [DOI: 10.1063/1.2902279] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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30
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Exploring Electronic Transport in Molecular Junctions by Conducting Atomic Force Microscopy. Top Curr Chem (Cham) 2008; 285:157-202. [DOI: 10.1007/128_2007_25] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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31
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Vlaming SM, Malyshev VA, Knoester J. Nonmonotonic energy harvesting efficiency in biased exciton chains. J Chem Phys 2007; 127:154719. [DOI: 10.1063/1.2784556] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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