163 research outputs found
Stabilizing single atom contacts by molecular bridge formation
Gold-molecule-gold junctions can be formed by carefully breaking a gold wire
in a solution containing dithiolated molecules. Surprisingly, there is little
understanding on the mechanical details of the bridge formation process and
specifically on the role that the dithiol molecules play themselves. We propose
that alkanedithiol molecules have already formed bridges between the gold
electrodes before the atomic gold-gold junction is broken. This leads to
stabilization of the single atomic gold junction, as observed experimentally.
Our data can be understood within a simple spring model.Comment: 14 pages, 3 figures, 1 tabl
Magnetoresistance through a single molecule
The use of single molecules to design electronic devices is an extremely
challenging and fundamentally different approach to further downsizing
electronic circuits. Two-terminal molecular devices such as diodes were first
predicted [1] and, more recently, measured experimentally [2]. The addition of
a gate then enabled the study of molecular transistors [3-5]. In general terms,
in order to increase data processing capabilities, one may not only consider
the electron's charge but also its spin [6,7]. This concept has been pioneered
in giant magnetoresistance (GMR) junctions that consist of thin metallic films
[8,9]. Spin transport across molecules, i.e. Molecular Spintronics remains,
however, a challenging endeavor. As an important first step in this field, we
have performed an experimental and theoretical study on spin transport across a
molecular GMR junction consisting of two ferromagnetic electrodes bridged by a
single hydrogen phthalocyanine (H2Pc) molecule. We observe that even though
H2Pc in itself is nonmagnetic, incorporating it into a molecular junction can
enhance the magnetoresistance by one order of magnitude to 52%.Comment: To appear in Nature Nanotechnology. Present version is the first
submission to Nature Nanotechnology, from May 18th, 201
Quantum transport through STM-lifted single PTCDA molecules
Using a scanning tunneling microscope we have measured the quantum
conductance through a PTCDA molecule for different configurations of the
tip-molecule-surface junction. A peculiar conductance resonance arises at the
Fermi level for certain tip to surface distances. We have relaxed the molecular
junction coordinates and calculated transport by means of the Landauer/Keldysh
approach. The zero bias transmission calculated for fixed tip positions in
lateral dimensions but different tip substrate distances show a clear shift and
sharpening of the molecular chemisorption level on increasing the STM-surface
distance, in agreement with experiment.Comment: accepted for publication in Applied Physics
The use of multiple displacement amplification to amplify complex DNA libraries
Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple displacement amplification (MDA) has been recently developed as a method for in vitro amplification of DNA. However, MDA has no selection function for the removal of ligation multimers. We developed a novel method of briefly introducing ligation reactions into bacteria to select single insert DNA clones followed by MDA to amplify. We applied these methods to a Gene Identification Signatures with Paired-End diTags (GIS-PET) library, which is a complex transcriptome library created by pairing short tags from the 5′ and 3′ ends of cDNA fragments together, and demonstrated that this selection and amplification strategy is unbiased and efficient
Green function techniques in the treatment of quantum transport at the molecular scale
The theoretical investigation of charge (and spin) transport at nanometer
length scales requires the use of advanced and powerful techniques able to deal
with the dynamical properties of the relevant physical systems, to explicitly
include out-of-equilibrium situations typical for electrical/heat transport as
well as to take into account interaction effects in a systematic way.
Equilibrium Green function techniques and their extension to non-equilibrium
situations via the Keldysh formalism build one of the pillars of current
state-of-the-art approaches to quantum transport which have been implemented in
both model Hamiltonian formulations and first-principle methodologies. We offer
a tutorial overview of the applications of Green functions to deal with some
fundamental aspects of charge transport at the nanoscale, mainly focusing on
applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references,
submitted to Springer series "Lecture Notes in Physics
A Mixture of “Cheats” and “Co-Operators” Can Enable Maximal Group Benefit
It is commonly assumed that the world would be best off if everyone co-operates. Experimental and mathematical analysis of “co-operation” in yeast show why this isn't always the case
Intra-colony channels in E. coli function as a nutrient uptake system
The ability of microorganisms to grow as aggregated assemblages has been known for many years, however their structure has remained largely unexplored across multiple spatial scales. The development of the Mesolens, an optical system which uniquely allows simultaneous imaging of individual bacteria over a 36 mm2 field of view, has enabled the study of mature Escherichia coli macro-colony biofilm architecture like never before. The Mesolens enabled the discovery of intra-colony channels on the order of 10 μm in diameter, that are integral to E. coli macro-colony biofilms and form as an emergent property of biofilm growth. These channels have a characteristic structure and re-form after total mechanical disaggregation of the colony. We demonstrate that the channels are able to transport particles and play a role in the acquisition of and distribution of nutrients through the biofilm. These channels potentially offer a new route for the delivery of dispersal agents for antimicrobial drugs to biofilms, ultimately lowering their impact on public health and industry
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
<p>Abstract</p> <p>Background</p> <p>The yeast <it>Saccharomyces cerevisiae </it>is able to adjust to external oxygen availability by utilizing both respirative and fermentative metabolic modes. Adjusting the metabolic mode involves alteration of the intracellular metabolic fluxes that are determined by the cell's multilevel regulatory network. Oxygen is a major determinant of the physiology of <it>S. cerevisiae </it>but understanding of the oxygen dependence of intracellular flux distributions is still scarce.</p> <p>Results</p> <p>Metabolic flux distributions of <it>S. cerevisiae </it>CEN.PK113-1A growing in glucose-limited chemostat cultures at a dilution rate of 0.1 h<sup>-1 </sup>with 20.9%, 2.8%, 1.0%, 0.5% or 0.0% O<sub>2 </sub>in the inlet gas were quantified by <sup>13</sup>C-MFA. Metabolic flux ratios from fractional [U-<sup>13</sup>C]glucose labelling experiments were used to solve the underdetermined MFA system of central carbon metabolism of <it>S. cerevisiae</it>.</p> <p>While ethanol production was observed already in 2.8% oxygen, only minor differences in the flux distribution were observed, compared to fully aerobic conditions. However, in 1.0% and 0.5% oxygen the respiratory rate was severely restricted, resulting in progressively reduced fluxes through the TCA cycle and the direction of major fluxes to the fermentative pathway. A redistribution of fluxes was observed in all branching points of central carbon metabolism. Yet only when oxygen provision was reduced to 0.5%, was the biomass yield exceeded by the yields of ethanol and CO<sub>2</sub>. Respirative ATP generation provided 59% of the ATP demand in fully aerobic conditions and still a substantial 25% in 0.5% oxygenation. An extensive redistribution of fluxes was observed in anaerobic conditions compared to all the aerobic conditions. Positive correlation between the transcriptional levels of metabolic enzymes and the corresponding fluxes in the different oxygenation conditions was found only in the respirative pathway.</p> <p>Conclusion</p> <p><sup>13</sup>C-constrained MFA enabled quantitative determination of intracellular fluxes in conditions of different redox challenges without including redox cofactors in metabolite mass balances. A redistribution of fluxes was observed not only for respirative, respiro-fermentative and fermentative metabolisms, but also for cells grown with 2.8%, 1.0% and 0.5% oxygen. Although the cellular metabolism was respiro-fermentative in each of these low oxygen conditions, the actual amount of oxygen available resulted in different contributions through respirative and fermentative pathways.</p
Metallic, magnetic and molecular nanocontacts
Scanning tunnelling microscopy and break-junction experiments realize metallic and molecular nanocontacts that act as ideal one-dimensional channels between macroscopic electrodes. Emergent nanoscale phenomena typical of these systems encompass structural, mechanical, electronic, transport, and magnetic properties. This Review focuses on the theoretical explanation of some of these properties obtained with the help of first-principles methods. By tracing parallel theoretical and experimental developments from the discovery of nanowire formation and conductance quantization in gold nanowires to recent observations of emergent magnetism and Kondo correlations, we exemplify the main concepts and ingredients needed to bring together ab initio calculations and physical observations. It can be anticipated that diode, sensor, spin-valve and spin-filter functionalities relevant for spintronics and molecular electronics applications will benefit from the physical understanding thus obtained
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