Pauli's Principle in Probe Microscopy

Exceptionally clear images of intramolecular structure can be attained in dynamic force microscopy through the combination of a passivated tip apex and operation in what has become known as the "Pauli exclusion regime" of the tip-sample interaction. We discuss, from an experimentalist's perspective, a number of aspects of the exclusion principle which underpin this ability to achieve submolecular resolution. Our particular focus is on the origins, history, and interpretation of Pauli's principle in the context of interatomic and intermolecular interactions.Comment: This is a chapter from "Imaging and Manipulation of Adsorbates using Dynamic Force Microscopy", a book which is part of the "Advances in Atom and Single Molecule Machines" series published by Springer [http://www.springer.com/series/10425]. To be published late 201

From DNA sequence to application: possibilities and complications

The development of sophisticated genetic tools during the past 15 years have facilitated a tremendous increase of fundamental and application-oriented knowledge of lactic acid bacteria (LAB) and their bacteriophages. This knowledge relates both to the assignments of open reading frames (ORF’s) and the function of non-coding DNA sequences. Comparison of the complete nucleotide sequences of several LAB bacteriophages has revealed that their chromosomes have a fixed, modular structure, each module having a set of genes involved in a specific phase of the bacteriophage life cycle. LAB bacteriophage genes and DNA sequences have been used for the construction of temperature-inducible gene expression systems, gene-integration systems, and bacteriophage defence systems. The function of several LAB open reading frames and transcriptional units have been identified and characterized in detail. Many of these could find practical applications, such as induced lysis of LAB to enhance cheese ripening and re-routing of carbon fluxes for the production of a specific amino acid enantiomer. More knowledge has also become available concerning the function and structure of non-coding DNA positioned at or in the vicinity of promoters. In several cases the mRNA produced from this DNA contains a transcriptional terminator-antiterminator pair, in which the antiterminator can be stabilized either by uncharged tRNA or by interaction with a regulatory protein, thus preventing formation of the terminator so that mRNA elongation can proceed. Evidence has accumulated showing that also in LAB carbon catabolite repression in LAB is mediated by specific DNA elements in the vicinity of promoters governing the transcription of catabolic operons. Although some biological barriers have yet to be solved, the vast body of scientific information presently available allows the construction of tailor-made genetically modified LAB. Today, it appears that societal constraints rather than biological hurdles impede the use of genetically modified LAB.

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease

Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association studies (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of 185 thousand CAD cases and controls, interrogating 6.7 million common (MAF>0.05) as well as 2.7 million low frequency (0.005<MAF<0.05) variants. In addition to confirmation of most known CAD loci, we identified 10 novel loci, eight additive and two recessive, that contain candidate genes that newly implicate biological processes in vessel walls. We observed intra-locus allelic heterogeneity but little evidence of low frequency variants with larger effects and no evidence of synthetic association. Our analysis provides a comprehensive survey of the fine genetic architecture of CAD showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect siz

The Hubbard model within the equations of motion approach

The Hubbard model has a special role in Condensed Matter Theory as it is considered as the simplest Hamiltonian model one can write in order to describe anomalous physical properties of some class of real materials. Unfortunately, this model is not exactly solved except for some limits and therefore one should resort to analytical methods, like the Equations of Motion Approach, or to numerical techniques in order to attain a description of its relevant features in the whole range of physical parameters (interaction, filling and temperature). In this manuscript, the Composite Operator Method, which exploits the above mentioned analytical technique, is presented and systematically applied in order to get information about the behavior of all relevant properties of the model (local, thermodynamic, single- and two- particle ones) in comparison with many other analytical techniques, the above cited known limits and numerical simulations. Within this approach, the Hubbard model is shown to be also capable to describe some anomalous behaviors of the cuprate superconductors.Comment: 232 pages, more than 300 figures, more than 500 reference

Canadian Arctic sea ice reconstructed from bromine in the Greenland NEEM ice core

Reconstructing the past variability of Arctic sea ice provides an essential context for recent multi-year sea ice decline, although few quantitative reconstructions cover the Holocene period prior to the earliest historical records 1,200 years ago. Photochemical recycling of bromine is observed over first-year, or seasonal, sea ice in so-called "bromine explosions" and we employ a 1-D chemistry transport model to quantify processes of bromine enrichment over first-year sea ice and depositional transport over multi-year sea ice and land ice. We report bromine enrichment in the Northwest Greenland Eemian NEEM ice core since the end of the Eemian interglacial 120,000 years ago, finding the maximum extension of first-year sea ice occurred approximately 9,000 years ago during the Holocene climate optimum, when Greenland temperatures were 2 to 3 degrees C above present values. First-year sea ice extent was lowest during the glacial stadials suggesting complete coverage of the Arctic Ocean by multi-year sea ice. These findings demonstrate a clear relationship between temperature and first-year sea ice extent in the Arctic and suggest multi-year sea ice will continue to decline as polar amplification drives Arctic temperatures beyond the 2 degrees C global average warming target of the recent COP21 Paris climate agreement

The Potential Energy Surface in Molecular Quantum Mechanics

The idea of a Potential Energy Surface (PES) forms the basis of almost all accounts of the mechanisms of chemical reactions, and much of theoretical molecular spectroscopy. It is assumed that, in principle, the PES can be calculated by means of clamped-nuclei electronic structure calculations based upon the Schr\"{o}dinger Coulomb Hamiltonian. This article is devoted to a discussion of the origin of the idea, its development in the context of the Old Quantum Theory, and its present status in the quantum mechanics of molecules. It is argued that its present status must be regarded as uncertain.Comment: 18 pages, Proceedings of QSCP-XVII, Turku, Finland 201

Near-Field Scanning Optical Microscope Combined with Digital Holography for Three-Dimensional Electromagnetic Field Reconstruction

International audienceNear-field scanning optical microscopy (NSOM) has proven to be a very powerful imaging technique that allows overcoming the diffraction limit and obtaining information on a scale much smaller than what can be achieved by classical optical imaging techniques. This is achieved using nanosized probes that are placed in close proximity to the sample surface, and thus allow the detection of evanescent waves that contain important information about the properties of the sample on a subwavelength scale. In particular, some aperture-based probes use a nanometer-sized hole to locally illuminate the sample. The far-field radiation of such probes is essential to their imaging properties, but cannot be easily estimated since it highly depends on the environment with which it interacts. In this chapter, we tackle this problem by introducing a microscopy method based on full-field off-axis digital holography that allows us to study in details the three-dimensional electromagnetic field scattered by a NSOM probe in different environments. We start by describing the NSOM and holography techniques independently, and continue by highlighting the advantage of combining both methods. We present a comparative study of the reconstructed light from a NSOM tip located in free space or coupled to transparent and plasmonic media. While far-field methods, such as back focal plane imaging, can be used to infer the directionality of angular radiation patterns, the advantage of our technique is that a single hologram contains information on both the amplitude and phase of the scattered light, allowing to reverse numerically the propagation of the electromagnetic field towards the source. We also present Finite Difference Time Domain (FDTD) simulations to model the radiation of the NSOM tip as a superposition of a magnetic and an electric dipole. We finally propose some promising applications that could be performed with this combined NSOM-holography technique

Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity

We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila S2 cells, we generated ChIP-seq datasets for a site-specific transcription factor (Suppressor of Hairy-wing) and a histone modification (H3K36me3). We detected a chromatin state bias, open chromatin regions yielded higher coverage, which led to false positives if not corrected and had a greater effect on detection specificity than any base-composition bias. Paired-end sequencing revealed that single-end data underestimated ChIP library complexity at high coverage. The removal of reads originating at the same base reduced false-positives while having little effect on detection sensitivity. Even at a depth of ~1 read/bp coverage of mappable genome, ~1% of the narrow peaks detected on a tiling array were missed by ChIP-seq. Evaluation of widely-used ChIP-seq analysis tools suggests that adjustments or algorithm improvements are required to handle datasets with deep coverage

Determinants of Aortic Stiffness: 16-Year Follow-Up of the Whitehall II Study

Aortic stiffness is a strong predictor of cardiovascular disease endpoints. Cross-sectional studies have shown associations of various cardiovascular risk factors with aortic pulse wave velocity, a measure of aortic stiffness, but the long-term impact of these factors on aortic stiffness is unknown.In 3,769 men and women from the Whitehall II cohort, a wide range of traditional and novel cardiovascular risk factors were determined at baseline (1991-1993) and aortic pulse wave velocity was measured at follow-up (2007-2009). The prospective associations between each baseline risk factor and aortic pulse wave velocity at follow-up were assessed through sex stratified linear regression analysis adjusted for relevant confounders. Missing data on baseline determinants were imputed using the Multivariate Imputation by Chained Equations.Among men, the strongest predictors were waist circumference, waist-hip ratio, heart rate and interleukin 1 receptor antagonist, and among women, adiponectin, triglycerides, pulse pressure and waist-hip ratio. The impact of 10 centimeter increase in waist circumference on aortic pulse wave velocity was twice as large for men compared with women (men: 0.40 m/s (95%-CI: 0.24;0.56); women: 0.17 m/s (95%-CI: -0.01;0.35)), whereas the opposite was true for the impact of a two-fold increase in adiponectin (men: -0.30 m/s (95%-CI: -0.51;-0.10); women: 0.61 m/s (95%-CI: -0.86;-0.35)).In this large prospective study, central obesity was a strong predictor of aortic stiffness. Additionally, heart rate in men and adiponectin in women predicted aortic pulse wave velocity suggesting that strategies to prevent aortic stiffening should be focused differently by sex