I-V characteristics and differential conductance fluctuations of Au nanowires

Electronic transport properties of Au nano-structure are investigated using both experimental and theoretical analysis. Experimentally, stable Au nanowires were created using mechanically controllable break junction in air, and simultaneous current-voltage (I-V) and differential conductance $\delta I/\delta V$ data were measured. The atomic device scale structures are mechanically very stable up to bias voltage $V_b\sim0.6V$ and have a life time of a few $minutes$. Facilitated by a shape function data analysis technique which finger-prints electronic properties of the atomic device, our data show clearly differential conductance fluctuations with an amplitude $>1$ at room temperature, and a nonlinear I-V characteristics. To understand the transport features of these atomic scale conductors, we carried out {\it ab initio} calculations on various Au atomic wires. The theoretical results demonstrate that transport properties of these systems crucially depend on the electronic properties of the scattering region, the leads, and most importantly the interaction of the scattering region with the leads. For ideal, clean Au contacts, the theoretical results indicate a linear I-V behavior for bias voltage $V_b<0.5V$. When sulfur impurities exist at the contact junction, nonlinear I-V curves emerge due to a tunnelling barrier established in the presence of the S atom. The most striking observation is that even a single S atom can cause a qualitative change of the I-V curve from linear to nonlinear. A quantitatively favorable comparison between experimental data and theoretical results is obtained. We also report other results concerning quantum transport through Au atomic contacts.Comment: 11 pages and 9 figures, submitted to PR

Current rectification by simple molecular quantum dots: an ab-initio study

We calculate a current rectification by molecules containing a conjugated molecular group sandwiched between two saturated (insulating) molecular groups of different length (molecular quantum dot) using an ab-initio non-equilibrium Green's function method. In particular, we study S-(CH2)m-C10H6-(CH2)n-S dithiol with Naphthalene as a conjugated central group. The rectification current ratio ~35 has been observed at m = 2 and n = 10, due to resonant tunneling through the molecular orbital (MO) closest to the electrode Fermi level (lowest unoccupied MO in the present case). The rectification is limited by interference of other conducting orbitals, but can be improved by e.g. adding an electron withdrawing group to the naphthalene.Comment: 8 pages, 9 figure

First-principles investigation of spin polarized conductance in atomic carbon wire

We analyze spin-dependent energetics and conductance for one dimensional (1D) atomic carbon wires consisting of terminal magnetic (Co) and interior nonmagnetic (C) atoms sandwiched between gold electrodes, obtained employing first-principles gradient corrected density functional theory and Landauer's formalism for conductance. Wires containing an even number of interior carbon atoms are found to be acetylenic with sigma-pi bonding patterns, while cumulene structures are seen in wires containing odd number of interior carbon atoms, as a result of strong pi-conjugation. Ground states of carbon wires containing up to 13 C atoms are found to have anti-parallel spin configurations of the two terminal Co atoms, while the 14 C wire has a parallel Co spin configuration in the ground state. The stability of the anti-ferromagnetic state in the wires is ascribed to a super-exchange effect. For the cumulenic wires this effect is constant for all wire lengths. For the acetylenic wires, the super-exchange effect diminishes as the wire length increases, going to zero for the atomic wire containing 14 carbon atoms. Conductance calculations at the zero bias limit show spin-valve behavior, with the parallel Co spin configuration state giving higher conductance than the corresponding anti-parallel state, and a non-monotonic variation of conductance with the length of the wires for both spin configurations.Comment: revtex, 6 pages, 5 figure

First-Principles Analysis of Molecular Conduction Using Quantum Chemistry Software

We present a rigorous and computationally efficient method to do a parameter-free analysis of molecular wires connected to contacts. The self-consistent field approach is coupled with Non-equilibrium Green's Function (NEGF) formalism to describe electronic transport under an applied bias. Standard quantum chemistry software is used to calculate the self-consistent field using density functional theory (DFT). Such close coupling to standard quantum chemistry software not only makes the procedure simple to implement but also makes the relation between the I-V characteristics and the chemistry of the molecule more obvious. We use our method to interpolate between two extreme examples of transport through a molecular wire connected to gold (111) contacts: band conduction in a metallic (gold) nanowire, and resonant conduction through broadened, quasidiscrete levels of a phenyl dithiol molecule. We obtain several quantities of interest like I-V characteristic, electron density and voltage drop along the molecule.Comment: Accepted for publication in J. Chem. Phys. (Special issue on molecular electronics, Ed. Mark Ratner

Ballistic conductance of Ni nanowire with a magnetization reversal

The approach proposed by Choi and Ihm for calculating the ballistic conductance of open quantum systems is generalized to deal with magnetic transition metals. The method has been implemented with ultrasoft pseudopotentials and plane wave basis set in a DFT-LSDA ab-initio scheme. We present the quantum-mechanical conductance calculations for monatomic Ni nanowire with a single spin reversal. We find that a spin reversal blocks the conductance of $d$ electrons at the Fermi energy of the Ni nanowire. On the other hand, two $s$ electrons (one per each spin) are perfectly transmitted in the whole energy window giving $2G_0$ for the total conductance. The relevance of these results in connection with recent experimental data is discussed.Comment: 4 pages, 1 figure, to be published in Surface Scienc

First-Principles Based Matrix-Green's Function Approach to Molecular Electronic Devices: General Formalism

Transport in molecular electronic devices is different from that in semiconductor mesoscopic devices in two important aspects: (1) the effect of the electronic structure and (2) the effect of the interface to the external contact. A rigorous treatment of molecular electronic devices will require the inclusion of these effects in the context of an open system exchanging particle and energy with the external environment. This calls for combining the theory of quantum transport with the theory of electronic structure starting from the first-principles. We present a rigorous yet tractable matrix Green's function approach for studying transport in molecular electronic devices, based on the Non-Equilibrium Green's Function Formalism of quantum transport and the density-functional theory of electronic structure using local orbital basis sets. By separating the device rigorously into the molecular region and the contact region, we can take full advantage of the natural spatial locality associated with the metallic screening in the electrodes and focus on the physical processes in the finite molecular region. This not only opens up the possibility of using the existing well-established technique of molecular electronic structure theory in transport calculations with little change, but also allows us to use the language of qualitative molecular orbital theory to interpret and rationalize the results of the computation. For the device at equilibrium, our method provides an alternative approach for solving the molecular chemisorption problem. For the device out of equilibrium, we show that the calculation of elastic current transport through molecules, both conceptually and computationally, is no more difficult than solving the chemisorption problem.Comment: To appear in Chemical Physic

Living without Oxygen: Anoxia-Responsive Gene Expression and Regulation

Many species of marine mollusks demonstrate exceptional capacities for long term survival without oxygen. Analysis of gene expression under anoxic conditions, including the subsequent translational responses, allows examination of the functional mechanisms that support and regulate natural anaerobiosis and permit noninjurious transitions between aerobic and anoxic states. Identification of stress-specific gene expression can provide important insights into the metabolic adaptations that are needed for anoxia tolerance, with potential applications to anoxia-intolerant systems. Various methods are available to do this, including high throughput microarray screening and construction and screening of cDNA libraries. Anoxia-responsive genes have been identified in mollusks; some have known functions in other organisms but were not previously linked with anoxia survival. In other cases, completely novel anoxia-responsive genes have been discovered, some that show known motifs or domains that hint at function. Selected genes are expressed at different times over an anoxia-recovery time course with their transcription and translation being actively regulated to ensure protein expression at the optimal time. An examination of transcript status over the course of anoxia exposure and subsequent aerobic recovery identifies genes, and the proteins that they encode, that enhance cell survival under oxygen-limited conditions. Analysis of data generated from non-mainstream model systems allows for insight into the response by cells to anoxia stress

Density functional method for nonequilibrium electron transport

We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested Siesta approach (which uses non-local norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (1) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (2) single atom gold wires, and finally (3) large carbon nanotube systems with point defects.Comment: 18 pages, 23 figure

Biosynthetic Study of CcsA and a Polyketide Synthase with Homology to Carnitine Acyltransferase

Polyketides are a class of natural products with large structural and biochemical diversity. Polyketides are assembled by the polymerization of short-chain fatty acids by enzymes named polyketide synthases. Fungal iterative polyketide synthases are notable in that they contain multiple active sites that are used in a cyclical fashion to construct their natural product. There is potential for competing reactions on the growing substrate, and how these enzymes are programmed to synthesize only one final product is not well understood. Cytochalasin E is a fungal polyketide that is currently utilized as an angiogenesis inhibitor in cellular assays. The enzyme responsible for production of cytochalasin E is named CcsA. CcsA is a polyketide synthase that is fused to a non-ribosomal peptide synthetase domain, and both work in tandem to create cytochalasin E. The biosynthetic pathway in the production of cytochalasin E has been proposed, but the pathway has only been partially elucidated. This thesis will first outline the synthetic effort undertaken toward the synthesis of compounds that will be used to study the biosynthesis of cytochalasin E. Progress made toward the synthesis of the proposed octaketide late-stage product of the polyketide synthase will be described. This thesis will then illustrate the discovery of a novel polyketide system that may help to answer pressing questions the polyketide community has concerning enzymatic control of methylation and reduction events. The product of this polyketide system contains an interesting pattern of methylation and reduction, and the enzyme responsible contains a domain with homology to carnitine acyltransferase instead of the standard thioesterase domain for off-loading of the polyketide product. It is hoped that by understanding this fungal polyketide system, the results can be translated to other polyketides assembled by fungal iterative polyketide synthases. The carnitine acyltransferase domain also represents a new mode of polyketide off-loading by polyketide synthases, and adds to the already broad diversity of polyketide natural products