Current-Driven Conformational Changes, Charging and Negative Differential Resistance in Molecular Wires

We introduce a theoretical approach based on scattering theory and total energy methods that treats transport non-linearities, conformational changes and charging effects in molecular wires in a unified way. We apply this approach to molecular wires consisting of chain molecules with different electronic and structural properties bonded to metal contacts. We show that non-linear transport in all of these systems can be understood in terms of a single physical mechanism and predict that negative differential resistance at high bias should be a generic property of such molecular wires.Comment: 9 pages, 4 figure

Quantum Conductance and Electronic Properties of Lower Diamondoid Molecules and Derivatives

Diamondoids and their derivatives have found major applications as templates and as molecular building blocks in nanotechnology. Applying ab initio method, we calculated the quantum conductance and the essential electronic properties of two lower diamondoids (adamantane and diamantane) and three of their important derivatives (amantadine, memantine and rimantadine). We also studies two artificial molecules that are built by substituting one hydrogen ion with one sodium ion in both adamantane and diamantane molecules. Most of our results are based on an infinite Au two-probe system constructed by ATK and VNL software, which comprise TRANSTA-C package. By changing various system structures and molecule orientations in linear Au and 2 by 2 Au probe systems, we found that although the conductance of adamantane and diamantane are very small, the derivatives of the lower diamondoids have considerable conductance at specific orientations and also showed interesting electronic properties. The quantum conductance of such molecules will change significantly by changing the orientations of the molecules, which approves that residues like nitrogen and sodium atoms have great effects on the conductance and electronic properties of single molecule. There are obvious peaks near Fermi energy in the transmission spectrums of artificial molecules, indicating the plateaus in I-V characteristics of such molecules

Antiresonances in Molecular Wires

We present analytic and numerical studies based on Landauer theory of conductance antiresonances of molecular wires. Our analytic treatment is a solution of the Lippmann-Schwinger equation for the wire that includes the effects of the non-orthogonality of the atomic orbitals on different atoms exactly. The problem of non-orthogonality is treated by solving the transport problem in a new Hilbert space which is spanned by an orthogonal basis. An expression is derived for the energies at which antiresonances should occur for a molecular wire connected to a pair of single-channel 1D leads. From this expression we identify two distinct mechanisms that give rise to antiresonances under different circumstances. The exact treatment of non-orthogonality in the theory is found to be necessary to obtain reliable results. Our numerical simulations extend this work to multichannel leads and to molecular wires connected to 3D metallic nanocontacts. They demonstrate that our analytic results also provide a good description of these more complicated systems provided that certain well-defined conditions are met. These calculations suggest that antiresonances should be experimentally observable in the differential conductance of molecular wires of certain types.Comment: 22 pages, 5 figure

Electron Standing Wave Formation in Atomic Wires

Using the Landauer formulation of transport theory and tight binding models of the electronic structure, we study electron transport through atomic wires that form 1D constrictions between pairs of metallic nano-contacts. Our results are interpreted in terms of electron standing waves formed in the atomic wires due to interference of electron waves reflected at the ends of the atomic constrictions. We explore the influence of the chemistry of the atomic wire-metal contact interfaces on these standing waves and the associated transport resonances by considering two types of atomic wires: gold wires attached to gold contacts and carbon wires attached to gold contacts. We find that the conductance of the gold wires is roughly $1 G_0 = 2 e^2/h$ for the wire lengths studied, in agreement with experiments. By contrast, for the carbon wires the conductance is found to oscillate strongly as the number of atoms in the wire varies, the odd numbered chains being more conductive than the even numbered ones, in agreement with previous theoretical work that was based on a different model of the carbon wire and metal contacts.Comment: 14 pages, includes 6 figure

Charging induced asymmetry in molecular conductors

We investigate the origin of asymmetry in various measured current-voltage (I-V) characteristics of molecules with no inherent spatial asymmetry, with particular focus on a recent break junction measurement. We argue that such asymmetry arises due to unequal coupling with the contacts and a consequent difference in charging effects, which can only be captured in a self-consistent model for molecular conduction. The direction of the asymmetry depends on the sign of the majority carriers in the molecule. For conduction through highest occupied molecular orbitals (i.e. HOMO or p-type conduction), the current is smaller for positive voltage on the stronger contact, while for conduction through lowest unoccupied molecular orbitals (i.e. LUMO or n-type conduction), the sense of the asymmetry is reversed. Within an extended Huckel description of the molecular chemistry and the contact microstructure (with two adjustable parameters, the position of the Fermi energy and the sulphur-gold bond length), an appropriate description of Poisson's equation, and a self-consistently coupled non-equilibrium Green's function (NEGF) description of transport, we achieve good agreement between theoretical and experimental I-V characteristics, both in shape as well as overall magnitude.Comment: length of the paper has been extended (4 pages to 6 pages), two new figures have been added (3 figures to 5 figures), has been accepted for PR

Designability of alpha-helical Proteins

A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested on structures composed of four alpha-helices connected by short turns. All such natural four-helix bundles that are connected by short turns seen in nature are reproduced to closer than 3.6 Angstroms per residue within the ensemble. Since structures with no natural counterpart may be targets for ab initio structure design, the designability of each structure in the ensemble -- defined as the number of sequences with that structure as their lowest energy state -- is evaluated using a hydrophobic energy. For the case of four alpha-helices, a small set of highly designable structures emerges, most of which have an analog among the known four-helix fold families, however several novel packings and topologies are identified.Comment: 21 pages, 6 figures, to appear in PNA

Theory for transport through a single magnetic molecule: Endohedral N@C60

We consider transport through a single N@C60 molecule, weakly coupled to metallic leads. Employing a density-matrix formalism we derive rate equations for the occupation probabilities of many-particle states of the molecule. We calculate the current-voltage characteristics and the differential conductance for N@C60 in a break junction. Our results reveal Coulomb-blockade behavior as well as a fine structure of the Coulomb-blockade peaks due to the exchange coupling of the C60 spin to the spin of the encapsulated nitrogen atom.Comment: 5 pages, 4 figures, v2: version as publishe

Control of quantum interference in molecular junctions: Understanding the origin of Fano and anti- resonances

We investigate within a coarse-grained model the conditions leading to the appearance of Fano resonances or anti-resonances in the conductance spectrum of a generic molecular junction with a side group (T-junction). By introducing a simple graphical representation (parabolic diagram), we can easily visualize the relation between the different electronic parameters determining the regimes where Fano resonances or anti-resonances in the low-energy conductance spectrum can be expected. The results obtained within the coarse-grained model are validated using density-functional based quantum transport calculations in realistic T-shaped molecular junctions.Comment: 5 pages, 5 figure

Phonon-assisted resonant tunneling through a triple-quantum-dot: a phonon-signal detector

We study the effect of electron-phonon interaction on current and zero-frequency shot noise in resonant tunneling through a series triple-quantum-dot coupling to a local phonon mode by means of a nonperturbative mapping technique along with the Green function formulation. By fixing the energy difference between the first two quantum dots to be equal to phonon frequency and sweeping the level of the third quantum dot, we find a largely enhanced current spectrum due to phonon effect, and in particular we predict current peaks corresponding to phonon-absorption and -emission assisted resonant tunneling processes, which shows that this system can be acted as a sensitive phonon-signal detector or as a cascade phonon generator.Comment: 3 pages, 3 figure

Real space finite difference method for conductance calculations

We present a general method for calculating coherent electronic transport in quantum wires and tunnel junctions. It is based upon a real space high order finite difference representation of the single particle Hamiltonian and wave functions. Landauer's formula is used to express the conductance as a scattering problem. Dividing space into a scattering region and left and right ideal electrode regions, this problem is solved by wave function matching (WFM) in the boundary zones connecting these regions. The method is tested on a model tunnel junction and applied to sodium atomic wires. In particular, we show that using a high order finite difference approximation of the kinetic energy operator leads to a high accuracy at moderate computational costs.Comment: 13 pages, 10 figure