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

Effect of impurities on transport through organic molecular films from first principles

We calculate electron transport through molecular monolayers of saturated alkanes with point defects from first principles. Single defects (incorporated Au ions, kinks, dangling bonds) produce deep localized levels in the gap between occupied and unoccupied molecular levels. Single defects produce steps on the I-V curve, whereas pairs of (unlike and like) defects give negative differential resistance peaks. The results are discussed in relation to the observed unusual transport behavior of organic monolayers and compared with transport through conjugated polythiophenes.Comment: 5 pages, 2 figures. Small typos corrected and text slightly shortened. To appear in Phys. Rev.

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

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

Molecular Cloning and Copy Number Variation of a Ferritin Subunit (Fth1) and Its Association with Growth in Freshwater Pearl Mussel Hyriopsis cumingii

Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5′ untranslated region (UTR) and a 144 bp 3′ UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5′-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii

Genome-Wide Identification of Molecular Pathways and Biomarkers in Response to Arsenic Exposure in Zebrafish Liver

10.1371/journal.pone.0068737PLoS ONE87-POLN

Susceptibility of Pancreatic Beta Cells to Fatty Acids Is Regulated by LXR/PPARα-Dependent Stearoyl-Coenzyme A Desaturase

Chronically elevated levels of fatty acids-FA can cause beta cell death in vitro. Beta cells vary in their individual susceptibility to FA-toxicity. Rat beta cells were previously shown to better resist FA-toxicity in conditions that increased triglyceride formation or mitochondrial and peroxisomal FA-oxidation, possibly reducing cytoplasmic levels of toxic FA-moieties. We now show that stearoyl-CoA desaturase-SCD is involved in this cytoprotective mechanism through its ability to transfer saturated FA into monounsaturated FA that are incorporated in lipids. In purified beta cells, SCD expression was induced by LXR- and PPARα-agonists, which were found to protect rat, mouse and human beta cells against palmitate toxicity. When their SCD was inhibited or silenced, the agonist-induced protection was also suppressed. A correlation between beta cell-SCD expression and susceptibility to palmitate was also found in beta cell preparations isolated from different rodent models. In mice with LXR-deletion (LXRβ-/- and LXRαβ-/-), beta cells presented a reduced SCD-expression as well as an increased susceptibility to palmitate-toxicity, which could not be counteracted by LXR or PPARα agonists. In Zucker fatty rats and in rats treated with the LXR-agonist TO1317, beta cells show an increased SCD-expression and lower palmitate-toxicity. In the normal rat beta cell population, the subpopulation with lower metabolic responsiveness to glucose exhibits a lower SCD1 expression and a higher susceptibility to palmitate toxicity. These data demonstrate that the beta cell susceptibility to saturated fatty acids can be reduced by stearoyl-coA desaturase, which upon stimulation by LXR and PPARα agonists favors their desaturation and subsequent incorporation in neutral lipids