Electrical Conductance of Molecular Wires

Molecular wires (MW) are the fundamental building blocks for molecular electronic devices. They consist of a molecular unit connected to two continuum reservoirs of electrons (usually metallic leads). We rely on Landauer theory as the basis for studying the conductance properties of MW systems. This relates the lead to lead current to the transmission probability for an electron to scatter through the molecule. Two different methods have been developed for the study of this scattering. One is based on a solution of the Lippmann-Schwinger equation and the other solves for the {\bf t} matrix using Schroedinger's equation. We use our methodology to study two problems of current interest. The first MW system consists of 1,4 benzene-dithiolate (BDT) bonded to two gold nanocontacts. Our calculations show that the conductance is sensitive to the chemical bonding between the molecule and the leads. The second system we study highlights the interesting phenomenon of antiresonances in MW. We derive an analytic formula predicting at what energies antiresonances should occur in the transmission spectra of MW. A numerical calculation for a MW consisting of filter molecules attached to an active molecule shows the existence of an antiresonance at the energy predicted by our formula.Comment: 14 pages, 5 figure

Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

AbstractLocal structure of the homopurine·homopyrimidine tract in a supercoiled plasmid pEJ4 was studied using chemical probes at single-nucleotide resolution. The conformation of the homopyrimidine strand was probed by osmium tetroxide, pyridine (Os,py) while that of the homopurine strand was tested by diethyl pyrocarbonate (DEPC), i.e. by probes reacting preferentially with single-stranded DNA. At weakly acidic pH values, a strong Os,py attack on three nucleotides at the centre of the (dC-dT)16 block and a weaker attack on two nucleotides at the end of the block were observed. DEPC modified adenines in the 5′-half of the homopurine strand. Os,py modification at the centre of the block corresponded to the loop of the hairpin formed by the homopyrimidine tract, while DEPC modification corresponded to the unstructured half of the homopurine strand in the model of protonated triplex H form of DNA

The multiple gene duplication problem revisited

Motivation: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known

Analysis of Collectivism and Egoism Phenomena within the Context of Social Welfare

Comparative benefits provided by the basic social strategies including collectivism and egoism are investigated within the framework of democratic decision-making. In particular, we study the mechanism of growing "snowball" of cooperation.Comment: 12 pages, 5 figures. Translated from Russian. Original Russian Text published in Problemy Upravleniya, 2008, No. 4, pp. 30-3

Field-effect transistors assembled from functionalized carbon nanotubes

We have fabricated field effect transistors from carbon nanotubes using a novel selective placement scheme. We use carbon nanotubes that are covalently bound to molecules containing hydroxamic acid functionality. The functionalized nanotubes bind strongly to basic metal oxide surfaces, but not to silicon dioxide. Upon annealing, the functionalization is removed, restoring the electronic properties of the nanotubes. The devices we have fabricated show excellent electrical characteristics.Comment: 5 pages, 6 figure

Towards a Tetravalent Chemistry of Colloids

We propose coating spherical particles or droplets with anisotropic nano-sized objects to allow micron-scale colloids to link or functionalize with a four-fold valence, similar to the sp3 hybridized chemical bonds associated with, e.g., carbon, silicon and germanium. Candidates for such coatings include triblock copolymers, gemini lipids, metallic or semiconducting nanorods and conventional liquid crystal compounds. We estimate the size of the relevant nematic Frank constants, discuss how to obtain other valences and analyze the thermal distortions of ground state configurations of defects on the sphere.Comment: Replaced to improve figures. 4 figures Nano Letter

Structural correlations in heterogeneous electron transfer at monolayer and multilayer graphene electrodes

As a new form of carbon, graphene is attracting intense interest as an electrode material with widespread applications. In the present study, the heterogeneous electron transfer (ET) activity of graphene is investigated using scanning electrochemical cell microscopy (SECCM), which allows electrochemical currents to be mapped at high spatial resolution across a surface for correlation with the corresponding structure and properties of the graphene surface. We establish that the rate of heterogeneous ET at graphene increases systematically with the number of graphene layers, and show that the stacking in multilayers also has a subtle influence on ET kinetics. © 2012 American Chemical Society

Partial derivative automata formalized in Coq

In this paper we present a computer assisted proof of the correctness of a partial derivative automata construction from a regular expression within the Coq proof assistant. This proof is part of a for- malization of Kleene algebra and regular languages in Coq towards their usage in program certification.Fundação para a Ciência e Tecnologia (FCT) Program POSI, RESCUE (PTDC/EIA/65862/2006), SFRH/BD/33233/2007

Pseudo-single crystal electrochemistry on polycrystalline electrodes : visualizing activity at grains and grain boundaries on platinum for the Fe2+/Fe3+ redox reaction

The influence of electrode surface structure on electrochemical reaction rates and mechanisms is a major theme in electrochemical research, especially as electrodes with inherent structural heterogeneities are used ubiquitously. Yet, probing local electrochemistry and surface structure at complex surfaces is challenging. In this paper, high spatial resolution scanning electrochemical cell microscopy (SECCM) complemented with electron backscatter diffraction (EBSD) is demonstrated as a means of performing ‘pseudo-single-crystal’ electrochemical measurements at individual grains of a polycrystalline platinum electrode, while also allowing grain boundaries to be probed. Using the Fe2+/3+ couple as an illustrative case, a strong correlation is found between local surface structure and electrochemical activity. Variations in electrochemical activity for individual high index grains, visualized in a weakly adsorbing perchlorate medium, show that there is higher activity on grains with a significant (101) orientation contribution, compared to those with (001) and (111) contribution, consistent with findings on single-crystal electrodes. Interestingly, for Fe2+ oxidation in a sulfate medium a different pattern of activity emerges. Here, SECCM reveals only minor variations in activity between individual grains, again consistent with single-crystal studies, with a greatly enhanced activity at grain boundaries. This suggests that these sites may contribute significantly to the overall electrochemical behavior measured on the macroscale

Regular Expressions and Transducers over Alphabet-invariant and User-defined Labels

We are interested in regular expressions and transducers that represent word relations in an alphabet-invariant way---for example, the set of all word pairs u,v where v is a prefix of u independently of what the alphabet is. Current software systems of formal language objects do not have a mechanism to define such objects. We define transducers in which transition labels involve what we call set specifications, some of which are alphabet invariant. In fact, we give a more broad definition of automata-type objects, called labelled graphs, where each transition label can be any string, as long as that string represents a subset of a certain monoid. Then, the behaviour of the labelled graph is a subset of that monoid. We do the same for regular expressions. We obtain extensions of a few classic algorithmic constructions on ordinary regular expressions and transducers at the broad level of labelled graphs and in such a way that the computational efficiency of the extended constructions is not sacrificed. For regular expressions with set specs we obtain the corresponding partial derivative automata. For transducers with set specs we obtain further algorithms that can be applied to questions about independent regular languages, in particular the witness version of the independent property satisfaction question