Multiscale Modeling of a Nanoelectromechanical Shuttle

In this article, we report a theoretical analysis of a nanoelectromechanical shuttle based on a multiscale model that combines microscopic electronic structure data with macroscopic dynamics. The microscopic part utilizes a (static) density functional description to obtain the energy levels and orbitals of the shuttling particle together with the forces acting on the particle. The macroscopic part combines stochastic charge dynamics that incorporates the microscopically evaluated tunneling rates with a Newtonian dynamics. We have applied the multiscale model to describe the shuttling of a single copper atom between two gold-like jellium electrodes. We find that energy spectrum and particle surface interaction greatly influence shuttling dynamics; in the specific example that we studied the shuttling is found to involve only charge states Q=0 and Q=+e. The system is found to exhibit two quasi-stable shuttling modes, a fundamental one and an excited one with a larger amplitude of mechanical motion, with random transitions between them.Comment: 9 pages, 9 figure

酸化物ガラスの塩基度と XPS による O1s 化学シフトの相関に関する考察

O1s binding energy measured by X-ray photoelectron spectroscopy (XPS) is candidate as a new tool to determine a new scale of Lewis basicity of oxide ions in glass. Some mathematical expressions for the basicity or XPS chemical shift, such as charge parameter and optical basicity, were compared with the experimental O1s binding energy in binary alkali oxide glasses. The expressions so far in use needed some modification in parameters. A new empirical expression introduced in this paper gives a new concept and universal scale of basicity

Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

<p>Abstract</p> <p>Background</p> <p>We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions.</p> <p>Findings</p> <p>In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation.</p> <p>Conclusions</p> <p>A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.</p

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735

Gene-specific ACMG/AMP classification criteria for germline APC variants: recommendations from the ClinGen InSIGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel

Purpose The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. Methods Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. Results The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). Conclusion The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use

Does traffic exhaust contribute to the development of asthma and allergic sensitization in children: findings from recent cohort studies

The aim of this review was to assess the evidence from recent prospective studies that long-term traffic pollution could contribute to the development of asthma-like symptoms and allergic sensitization in children. We have reviewed cohort studies published since 2002 and found in PubMed in Oct 2008. In all, 13 papers based on data from 9 cohorts have evaluated the relationship between traffic exposure and respiratory health. All surveys reported associations with at least some of the studied respiratory symptoms. The outcome varied, however, according to the age of the child. Nevertheless, the consistency in the results indicates that traffic exhaust contributes to the development of respiratory symptoms in healthy children. Potential effects of traffic exhaust on the development of allergic sensitization were only assessed in the four European birth cohorts. Long-term exposure to outdoor air pollutants had no association with sensitization in ten-year-old schoolchildren in Norway. In contrast, German, Dutch and Swedish preschool children had an increased risk of sensitization related to traffic exhaust despite fairly similar levels of outdoor air pollution as in Norway. Traffic-related effects on sensitization could be restricted to individuals with a specific genetic polymorphism. Assessment of gene-environment interactions on sensitization has so far only been carried out in a subgroup of the Swedish birth cohort. Further genetic association studies are required and may identify individuals vulnerable to adverse effects from traffic-related pollutants. Future studies should also evaluate effects of traffic exhaust on the development and long term outcome of different phenotypes of asthma and wheezing symptoms