Identifying Proteins of High Designability via Surface-Exposure Patterns

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.Comment: 17 pages, 12 figure

Molecular Spintronics: Spin-Dependent Electron Transport in Molecular Wires

We present a theoretical study of spin-dependent transport through molecular wires bridging ferromagnetic metal nanocontacts. We extend to magnetic systems a recently proposed model that provides a em quantitative explanation of the conductance measurements of Reed et al. on Au break-junctions bridged by self-assembled molecular monolayers (SAMs) of 1,4-benzene-dithiolate (BDT) molecules. Based on our calculations, we predict that spin-valve behavior should be observable in nickel break-junctions bridged by SAM's formed from BDT. We also consider spin transport in systems consisting of a clean ferromagnetic nickel STM tip and SAMs of benzene-thiol molecules on gold and nickel substrates. We find that spin-valve behavior should be possible for the Ni substrate. For the case where the substrate is gold, we show that it should be possible to inject a highly spin-polarized current into the substrate.Comment: 14 pages, 9 figure

The Smallest Molecular Switch

Ab-initio total energy calculations reveal benzene-dithiolate (BDT) molecules on a gold surface, contacted by a monoatomic gold STM tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity these Au/BDT/Au nanowires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. Experiments with a conventional or novel self-assembled STM are proposed to test these predictions.Comment: 8 pages, 3 figure

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

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

Landauer Theory, Inelastic Scattering and Electron Transport in Molecular Wires

In this paper we address the topic of inelastic electron scattering in mesoscopic quantum transport. For systems where only elastic scattering is present, Landauer theory provides an adequate description of transport that relates the electronic current to single-particle transmission and reflection probabilities. A formalism proposed recently by Bonca and Trugman facilitates the calculation of the one-electron transmission and reflection probabilities for inelastic processes in mesoscopic conductors connected to one-dimensional ideal leads. Building on their work, we have developed a self-consistent procedure for the evaluation of the non-equilibrium electron distributions in ideal leads connecting such mesoscopic conductors to electron reservoirs at finite temperatures and voltages. We evaluate the net electronic current flowing through the mesoscopic device by utilizing these non-equilibrium distributions. Our approach is a generalization of Landauer theory that takes account of the Pauli exclusion principle for the various competing elastic and inelastic processes while satisfying the requirement of particle conservation. As an application we examine the influence of elastic and inelastic scattering on conduction through a two site molecular wire with longitudinal phonons using the Su-Schrieffer-Heeger model of electron-phonon coupling.Comment: 25 pages, 8 figure