Computational studies investigating the effect of sequencing and environment on the conductance of DNA nanowires

2013 ◽  
Vol 1553 ◽  
Author(s):  
Gareth Jones ◽  
Watheq Elias ◽  
M. Elliott ◽  
C. C. Matthai
Keyword(s):  
Electron Transfer ◽  
Molecular Electronics ◽  
Electronic Devices ◽  
Biological Molecules ◽  
Segment Length ◽  
Hamiltonian Matrix ◽  
Base Pairs ◽  
Electron Conduction ◽  
Molecular Systems ◽  
Extended Hückel Approximation

ABSTRACTUnderstanding electron transfer in molecular systems is important, especially in the context of molecular electronics. With the desire to incorporate biological molecules in molecular electronic devices, there is a need to establish the relative importance of the various factors like the environment and the molecular structure (DNA sequence) on the electrical conduction. There has been much debate about mechanisms of electron transfer in biological molecules. We have conducted a systematic study of electron conduction across DNA molecular segments using the non-equilibrium Green function (NEGF) method. The Hamiltonian matrix elements were determined within the framework of the Extended Hückel Approximation. In considering (CG) base pair sequences, we find that the conductance decreases with segment length and that the substitution of (AT) base-pairs also reduces the conductance. When the DNA segments are in aqueous solution, the conductance is found to almost double in magnitude.

Electron Transfer and Transmission at Molecule–Metal and Molecule–Semiconductor Interfaces

2006 ◽  
Author(s):  
Abraham Nitzan
Keyword(s):  
Electron Transfer ◽  
Molecular Electronics ◽  
Transfer Process ◽  
Metal Electrode ◽  
Molecular Systems ◽  
Transfer Processes ◽  
Charge Distributions ◽  
Fundamental Process ◽  
Solid Conductors ◽  
Electron Transfer Processes

This chapter continues our discussion of electron transfer processes, now focusing on the interface between molecular systems and solid conductors. Interest in such processes has recently surged within the emerging field of molecular electronics, itself part of a general multidisciplinary effort on nanotechnology. Notwithstanding new concepts, new experimental and theoretical methods, and new terminology, the start of this interest dates back to the early days of electrochemistry, marked by the famous experiments of Galvani and Volta in the late eighteenth century. The first part of this chapter discusses electron transfer in what might now be called “traditional” electrochemistry where the fundamental process is electron transfer between a molecule or a molecular ion and a metal electrode. The second part constitutes an introduction to molecular electronics, focusing on the problem of molecular conduction, which is essentially electron transfer (in this context better termed electron transmission) between two metal electrodes through a molecular layer or sometimes even a single molecule. In Chapter 16 we have focused on electron transfer processes of the following characteristics: (1) Two electronic states, one associated with the donor species, the other with the acceptor, are involved. (2) Energetics is determined by the electronic energies of the donor and acceptor states and by the electrostatic solvation of the initial and final charge distributions in their electronic and nuclear environments. (3) The energy barrier to the transfer process originates from the fact that electronic and nuclear motions occur on vastly different timescales. (4) Irreversibility is driven by nuclear relaxation about the initial and final electronic charge distributions. How will this change if one of the two electronic species is replaced by a metal? We can imagine an electron transfer process between a metal substrate and a molecule adsorbed on its surface, however the most common process of this kind takes place at the interface between a metal electrode and an electrolyte solution, where the molecular species is an ion residing in the electrolyte, near the metal surface. Electron transfer in this configuration is the fundamental process of electrochemistry.

scholarly journals 1,4-Dithiolbenzene, 1,4-dimethanediolbenzene and 4-thioacetylbiphenyl molecular systems: electronic devices with possible applications in molecular electronics

RSC Advances ◽  
2020 ◽  
Vol 10 (53) ◽  
pp. 32127-32136
Author(s):  
J. H. Ojeda ◽  
Lina K. Piracón Muñoz ◽  
Julian A. Guerra Pinzón ◽  
Jovanny A. Gómez Castaño
Keyword(s):  
Transport Properties ◽  
Molecular Electronics ◽  
Electronic Transport ◽  
Theoretical Study ◽  
Electronic Devices ◽  
Metal Contacts ◽  
Molecular Systems ◽  
Electronic Transport Properties

A theoretical study of the electronic transport properties of the 1,4-dithiolbenzene, 1,4-dimethanediolbenzene and 4-thioacetylbiphenyl molecules coupled to two metal contacts is carried out.

Thermoelectric properties of B12N12 molecule

2019 ◽  
Vol 16 ◽  
Author(s):  
Mohammad Reza Niazian ◽  
Laleh Farhang Matin ◽  
Mojtaba Yaghobi ◽  
Amir Ali Masoudi
Keyword(s):  
Molecular Electronics ◽  
Thermoelectric Properties ◽  
Electronic Devices ◽  
Thermal Conductance ◽  
Wide Band ◽  
Oscillatory Behavior ◽  
Mapping Technique ◽  
Junction Points ◽  
Inelastic Behaviour ◽  
New Generation

Background: Recently, molecular electronics have attracted the attention of many researchers, both theoretically and applied electronics.Nanostructures have significant thermal properties, which is why they are considered as good options for designing a new generation of integrated electronic devices. Objective: In this paper, the focus is on the thermoelectric properties of the molecular junction points with the electrodes. Also, the influence of the number of atom contacts was investigated on the thermoelectric properties of molecule located between two electrodes metallic.Therefore, the thermoelectric characteristics of the B12 N12 molecule are investigated. Methods: For this purpose, the Green’s function theory as well as mapping technique approach with the wide-band approximation and also the inelastic behaviour is considered for the electron-phonon interactions. Results & Conclusion: Results & Conclusion:It is observed that the largest values of the total part of conductance as well as its elastic (G(e,n)max) depends on the number of atom contacts and are arranged as: G(e,1)max>G(e,4)max>G(e,6)max. Furthermore, the largest values of the electronic thermal conductance, i.e. Kpmax is seen to be in the order of K(p,4)max < K(p,1)max < K(p,6)max that the number of main peaks increases in four-atom contacts at (E<Ef). Furthermore, it is represented that the thermal conductance shows an oscillatory behavior which is significantly affected by the number of atom contacts.

scholarly journals Reduction of the molecular hamiltonian matrix using quantum community detection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Susan M. Mniszewski ◽  
Pavel A. Dub ◽  
Sergei Tretiak ◽  
Petr M. Anisimov ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Community Detection ◽  
Slater Determinant ◽  
Hamiltonian Matrix ◽  
Approximate Methods ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Molecular Hamiltonian ◽  
Structure Problem ◽  
Modularity Maximization ◽  
Chemical Knowledge

AbstractQuantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

HYBRID SILICON-MOLECULAR ELECTRONICS

2008 ◽  
Vol 22 (12) ◽  
pp. 1183-1202 ◽  
Author(s):  
QILIANG LI
Keyword(s):  
Molecular Electronics ◽  
New Technologies ◽  
Electronic System ◽  
Cmos Technology ◽  
Smooth Transition ◽  
Molecular Memory ◽  
Molecular Systems ◽  
Redox Active ◽  
Hybrid Silicon ◽  
Intensive Investigation

As CMOS technology extends beyond the current technology node, many challenges to conventional MOSFET were raised. Non-classical CMOS to extend and fundamentally new technologies to replace current CMOS technology are under intensive investigation to meet these challenges. The approach of hybrid silicon/molecular electronics is to provide a smooth transition technology by integrating molecular intrinsic scalability and diverse properties with the vast infrastructure of traditional MOS technology. Here we discuss: (1) the integration of redox-active molecules into Si -based structures, (2) characterization and modeling of the properties of these Si /molecular systems, (3) single and multiple states of Si /molecular memory, and (4) applications based on hybrid Si /molecular electronic system.

Modelling Carbon Nanotube Based Bio-Nano Systems: A Molecular Dynamics Study

2003 ◽  
Vol 773 ◽  
Author(s):  
Yong Kong ◽  
Daxiang Cui ◽  
Cengiz S. Ozkan ◽  
Huajian Gao
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Electronics ◽  
Dominant Role ◽  
Biological Molecules ◽  
Molecular Cluster ◽  
Aqueous Environment ◽  
Higher Temperature ◽  
Dynamics Simulations ◽  
Insertion Process

AbstractMolecular dynamics simulations were performed to study dynamics of carbon nanotube (CNT) interacting with biological molecules (DNA oligonucleotide and protein polypeptide) in an aqueous environment. Our results showed that an oligonucleotide or a polypeptide could be spontaneously inserted into a CNT, provided that the tube size is large enough and the oligonucleotide/polypeptide is appropriately aligned with CNT. The van der Waals and hydrophobic forces were found to be important for the insertion process, with the former playing a more dominant role in the CNT-oligonucleotide and CNT-polypeptide interaction. We discussed temperature effect on the filling process and found that higher temperature can accelerate encapsulation of biological molecules. Our study has general implications on filling nanoporous materials with water solutes of molecular cluster or nanoparticles. The encapsulated CNT-oligonucleotide/polypeptide or other CNT based bio-nano-complex can be further exploited for applications such as molecular electronics, sensors, electronic DNA sequencing, and nanotechnology of gene/drug delivery systems.

scholarly journals Nanofabrication Techniques in Large-Area Molecular Electronic Devices

2020 ◽  
Vol 10 (17) ◽  
pp. 6064
Author(s):  
Lucía Herrer ◽  
Santiago Martín ◽  
Pilar Cea
Keyword(s):  
Molecular Electronics ◽  
Global Economy ◽  
Electronic Devices ◽  
Functional Materials ◽  
Large Area ◽  
Molecular Electronic ◽  
Hybrid Technology ◽  
Top Contact ◽  
Silicon Based ◽  
Molecular Electronic Devices

The societal impact of the electronics industry is enormous—not to mention how this industry impinges on the global economy. The foreseen limits of the current technology—technical, economic, and sustainability issues—open the door to the search for successor technologies. In this context, molecular electronics has emerged as a promising candidate that, at least in the short-term, will not likely replace our silicon-based electronics, but improve its performance through a nascent hybrid technology. Such technology will take advantage of both the small dimensions of the molecules and new functionalities resulting from the quantum effects that govern the properties at the molecular scale. An optimization of interface engineering and integration of molecules to form densely integrated individually addressable arrays of molecules are two crucial aspects in the molecular electronics field. These challenges should be met to establish the bridge between organic functional materials and hard electronics required for the incorporation of such hybrid technology in the market. In this review, the most advanced methods for fabricating large-area molecular electronic devices are presented, highlighting their advantages and limitations. Special emphasis is focused on bottom-up methodologies for the fabrication of well-ordered and tightly-packed monolayers onto the bottom electrode, followed by a description of the top-contact deposition methods so far used.

Comparing statistical predictions of quantum particle transit times in molecular systems to experimental measurements

2019 ◽  
Vol 18 (08) ◽  
pp. 1950039
Author(s):  
Gloria Bazargan ◽  
Evan Curtin ◽  
Karl Sohlberg
Keyword(s):  
Electron Transfer ◽  
Quantum Particle ◽  
Essential Feature ◽  
Probabilistic Method ◽  
Intramolecular Proton Transfer ◽  
Nanoscale Systems ◽  
Molecular Systems ◽  
Quantum Particles ◽  
Transit Times ◽  
Transfer Times

The movement of quantum particles between distinct spatial regions is an essential feature of nanoscale devices. Consequently, theoretical methods for characterizing the transit time associated with this movement may aid in identifying and refining nanoscale systems with desirable transport properties. Herein, we explore the utility and range of validity of a recently reported probabilistic method for quantifying the timescale of quantum particle transit. The method is applied to intramolecular proton transfer in dicarbonyl compounds, and electron transfer in donor-bridge-acceptor molecules. Direct comparison is made between statistical predictions of proton and electron transfer times and corresponding transfer times deduced from the previously reported experimental observables. Insights provided by the method into the path of flow of probability density are discussed.

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