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.

Mass diffusion measurements in liquid crystals by a novel optical method

Binary mass diffusion measurements have been performed in fluid media doped with photochromic dye molecules. A periodic concentration of tagged molecules is created by illuminating the sample with a fringe intensity pattern. The photo induced change of refractive index and/or absorption of the dye molecules creates an optical grating which is observed through Bragg diffraction of an auxiliary laser beam. When the flash excitation is switched off. this grating will relax since photoexcited molecules will diffuse into nonphotoexcited zones and vice versa. The main advantages of this method are that: (1) the duration of the experiment is strongly reduced compared to classical tracer methods since diffusion lengths. defined by the fringe spacing. are small (1-100 fLm); (2) the possibility of studying anisotropic diffusion is readily available; and (3) small sample volumes are required. Results are reported on the diffusion of methyl red in a homogeneously aligned sample of MBBA. In the nematic phase. the diffusion is faster along the local optical axis than perpendicular, the anisotropic ratio DU / Dl being 1.6±O.l at 22 "C. in good agreement with previous tracer data. The temperature dependence yields an activation energy of 5.8±O.7 kcallmole for DII and 6.0±O.8 kcallmole for D 1 • In the isotropic phase. the activation energy is found to be \O± 1.5 kcallmole

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

Chiral and herringbone symmetry breaking in water-surface monolayers

We report the observation from monolayers of eicosanoic acid in the L′2 phase of three distinct out-of-plane first-order diffraction peaks, indicating molecular tilt in a nonsymmetry direction and hence the absence of mirror symmetry. At lower pressures the molecules tilt in the direction of their nearest neighbors. In this region we find a structural transition, which we tentatively identify as the rotator-herringbone transition L2d−L2h

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

Characterization and mitigation of gene expression burden in mammalian cells

Despite recent advances in circuit engineering, the design of genetic networks in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here, we demonstrate that transiently expressed genes in mammalian cells compete for limited transcriptional and translational resources. This competition results in the coupling of otherwise independent exogenous and endogenous genes, creating a divergence between intended and actual function. Guided by a resource-aware mathematical model, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the use of endogenous miRNAs as elementary components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells

Prediction of Cellular Burden with Host--Circuit Models

Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits. In this tutorial we discuss the use of computational models that integrate gene circuits and the physiology of host cells. Through various use cases, we illustrate the power of host-circuit models to predict the impact of design parameters on both burden and circuit functionality. Our approach relies on a new generation of computational models for microbial growth that can flexibly accommodate resource bottlenecks encountered in gene circuit design. Adoption of this modelling paradigm can facilitate fast and robust design cycles in synthetic biology

Viral nanomotors for packaging of dsDNA and dsRNA

While capsid proteins are assembled around single-stranded genomic DNA or RNA in rod-shaped viruses, the lengthy double-stranded genome of other viruses is packaged forcefully within a preformed protein shell. This entropically unfavourable DNA or RNA packaging is accomplished by an ATP-driven viral nanomotor, which is mainly composed of two components, the oligomerized channel and the packaging enzymes. This intriguing DNA or RNA packaging process has provoked interest among virologists, bacteriologists, biochemists, biophysicists, chemists, structural biologists and computational scientists alike, especially those interested in nanotechnology, nanomedicine, AAA+ family proteins, energy conversion, cell membrane transport, DNA or RNA replication and antiviral therapy. This review mainly focuses on the motors of double-stranded DNA viruses, but double-stranded RNA viral motors are also discussed due to interesting similarities. The novel and ingenious configuration of these nanomotors has inspired the development of biomimetics for nanodevices. Advances in structural and functional studies have increased our understanding of the molecular basis of biological movement to the point where we can begin thinking about possible applications of the viral DNA packaging motor in nanotechnology and medical applications