152 research outputs found
Electron transport through rectifying self-assembled monolayer diodes on silicon: Fermi level pinning at the molecule-metal interface
We report the synthesis and characterization of molecular rectifying diodes
on silicon using sequential grafting of self-assembled monolayers of alkyl
chains bearing a pi group at their outer end (Si/sigma-pi/metal junctions). We
investigate the structure-performance relationships of these molecular devices
and we examine to what extent the nature of the pi end-group (change in the
energy position of their molecular orbitals) drives the properties of these
molecular diodes. For all the pi-groups investigated here, we observe
rectification behavior. These results extend our preliminary work using phenyl
and thiophene groups (S. Lenfant et al., Nano Letters 3, 741 (2003)).The
experimental current-voltage curves are analyzed with a simple analytical
model, from which we extract the energy position of the molecular orbital of
the pi-group in resonance with the Fermi energy of the electrodes. We report
the experimental studies of the band lineup in these silicon/alkyl-pi
conjugated molecule/metal junctions. We conclude that Fermi level pinning at
the pi-group/metal interface is mainly responsible for the observed absence of
dependence of the rectification effect on the nature of the pi-groups, even
though they were chosen to have significant variations in their electronic
molecular orbitalsComment: To be published in J. Phys. Chem.
The tale of the river Scheldt as told by historic maps – Building an RShiny ‘side-by-side viewer’ to visualize 16<sup>th</sup>-20<sup>th</sup> century maps
Molecular Chemical Engines: Pseudo-Static Processes and the Mechanism of Energy Transduction
We propose a simple theoretical model for a molecular chemical engine that
catalyzes a chemical reaction and converts the free energy released by the
reaction into mechanical work. Binding and unbinding processes of reactant and
product molecules to and from the engine are explicitly taken into account. The
work delivered by the engine is calculated analytically for infinitely slow
(``pseudo-static'') processes, which can be reversible (quasi-static) or
irreversible, controlled by an external agent. It is shown that the work larger
than the maximum value limited by the second law of thermodynamics can be
obtained in a single cycle of operation by chance, although the statistical
average of the work never exceeds this limit and the maximum work is delivered
if the process is reversible. The mechanism of the energy transductionis also
discussed.Comment: 8 pages, 3 figues, submitted to J. Phys. Soc. Jp
Efficiency of Energy Transduction in a Molecular Chemical Engine
A simple model of the two-state ratchet type is proposed for molecular
chemical engines that convert chemical free energy into mechanical work and
vice versa. The engine works by catalyzing a chemical reaction and turning a
rotor. Analytical expressions are obtained for the dependences of rotation and
reaction rates on the concentrations of reactant and product molecules, from
which the performance of the engine is analyzed. In particular, the efficiency
of energy transduction is discussed in some detail.Comment: 4 pages, 4 fugures; title modified, figures 2 and 3 modified, content
changed (pages 1 and 4, mainly), references adde
Non-isothermal model for the direct isotropic/smectic-A liquid crystalline transition
An extension to a high-order model for the direct isotropic/smectic-A liquid
crystalline phase transition was derived to take into account thermal effects
including anisotropic thermal diffusion and latent heat of phase-ordering.
Multi-scale multi-transport simulations of the non-isothermal model were
compared to isothermal simulation, showing that the presented model extension
corrects the standard Landau-de Gennes prediction from constant growth to
diffusion-limited growth, under shallow quench/undercooling conditions.
Non-isothermal simulations, where meta-stable nematic pre-ordering precedes
smectic-A growth, were also conducted and novel non-monotonic
phase-transformation kinetics observed.Comment: First revision: 20 pages, 7 figure
HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays
<p>Abstract</p> <p>Background</p> <p>HIV-1 infected patients for whom standard gp160 phenotypic tropism testing failed are currently excluded from co-receptor antagonist treatment. To provide patients with maximal treatment options, massively parallel sequencing of the envelope V3 domain, in combination with tropism prediction tools, was evaluated as an alternative tropism determination strategy. Plasma samples from twelve HIV-1 infected individuals with failing phenotyping results were available. The samples were submitted to massive parallel sequencing and to confirmatory recombinant phenotyping using a fraction of the gp120 domain.</p> <p>Results</p> <p>A cut-off for sequence reads interpretation of 5 to10 times the sequencing error rate (0.2%) was implemented. On average, each sample contained 7 different V3 haplotypes. V3 haplotypes were submitted to tropism prediction algorithms, and 4/14 samples returned with presence of a dual/mixed (D/M) tropic virus, respectively at 3%, 10%, 11%, and 95% of the viral quasispecies. V3 tropism prediction was confirmed by gp120 phenotyping, except for two out of 4 D/M predicted viruses (with 3 and 95%) which were phenotypically R5-tropic. In the first case, the result was discordant due to the limit of detection for the phenotyping technology, while in the latter case the prediction algorithms were not computing the viral tropism correctly.</p> <p>Conclusions</p> <p>Although only demonstrated on a limited set of samples, the potential of the combined use of "deep sequencing + prediction algorithms" in cases where routine gp160 phenotype testing cannot be employed was illustrated. While good concordance was observed between gp120 phenotyping and prediction of R5-tropic virus, the results suggest that accurate prediction of X4-tropic virus would require further algorithm development.</p
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