Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model

Charge-Symmetry Violation in Pion Scattering from Three-Body Nuclei

We discuss the experimental and theoretical status of charge-symmetry violation (CSV) in the elastic scattering of pi+ and pi- on 3H and 3He. Analysis of the experimental data for the ratios r1, r2, and R at Tpi = 142, 180, 220, and 256 MeV provides evidence for the presence of CSV. We describe pion scattering from the three-nucleon system in terms of single- and double-scattering amplitudes. External and internal Coulomb interactions as well as the Delta-mass splitting are taken into account as sources of CSV. Reasonable agreement between our theoretical calculations and the experimental data is obtained for Tpi = 180, 220, and 256 MeV. For these energies, it is found that the Delta-mass splitting and the internal Coulomb interaction are the most important contributions for CSV in the three-nucleon system. The CSV effects are rather sensitive to the choice of pion-nuclear scattering mechanisms, but at the same time, our theoretical predictions are much less sensitive to the choice of the nuclear wave function. It is found, however, that data for r2 and R at Tpi = 142 MeV do not agree with the predictions of our model, which may indicate that there are additional mechanisms for CSV which are important only at lower energies.Comment: 26 pages of RevTeX, 16 postscript figure

Discrete molecular dynamics simulations of peptide aggregation

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure. This structure has an inter-strand distance of 0.48 nm and an inter-sheet distance of 1.0 nm, which agree with experimental observations. In this model, the hydrogen bond interactions give rise to the inter-strand spacing in beta-sheets, while the Go interactions among side chains make beta-strands parallel to each other and allow beta-sheets to pack into layers. The aggregates also contain free edges which may allow for further aggregation of model peptides to form elongated fibrils.Comment: 15 pages, 8 figure

Children with Respiratory Disease Associated with Metapneumovirus in Hong Kong

Human metapneumovirus (HMPV) is a newly discovered pathogen thought to be associated with respiratory disease. We report the results of a study of 587 children hospitalized with respiratory infection over a 13-month period. HMPV was detected in the nasopharyngeal aspirates from 32 (5.5%) children by reverse transcription-polymerase chain reaction. HMPV infection was associated with clinical diagnoses of pneumonia (36%), asthma exacerbation (23%), or acute bronchiolitis (10%). When compared to those with respiratory syncytial virus infection, children with HMPV infection were older, and wheezing was more likely to represent asthma exacerbation rather than acute bronchiolitis. HMPV viral activity peaked during the spring-summer period in Hong Kong. Phylogenetically, all HMPV virus strains from Hong Kong belonged to one of the two genetic lineages previously described. HMPV contributed to 441.6 hospital admissions per 100,000 population <6 years of age

Ecological Invasion, Roughened Fronts, and a Competitor's Extreme Advance: Integrating Stochastic Spatial-Growth Models

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An ecologically superior invader and a resident species compete for space preemptively. Our general model includes the basic contact process and a variant of the Eden model as special cases. We employ the concept of a "roughened" front to quantify effects of discreteness and stochasticity on invasion; we emphasize the probability distribution of the front-runner's relative position. That is, we analyze the location of the most advanced invader as the extreme deviation about the front's mean position. We find that a class of models with different assumptions about neighborhood interactions exhibit universal characteristics. That is, key features of the invasion dynamics span a class of models, independently of locally detailed demographic rules. Our results integrate theories of invasive spatial growth and generate novel hypotheses linking habitat or landscape size (length of the invading front) to invasion velocity, and to the relative position of the most advanced invader.Comment: The original publication is available at www.springerlink.com/content/8528v8563r7u2742

Simulations of the Static Friction Due to Adsorbed Molecules

The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent with macroscopic friction laws. Crystalline alignment, sliding direction, and the number of adsorbed molecules are not controlled in most experiments and are shown to have little effect on the friction. Temperature, molecular geometry and interaction potentials can have larger effects on friction. The observed trends in friction can be understood in terms of a simple hard sphere model.Comment: 13 pages, 13 figure

Geometric Spin Hall Effect of Light at Polarizing Interfaces

The geometric Spin Hall Effect of Light (geometric SHEL) amounts to a polarization-dependent positional shift when a light beam is observed from a reference frame tilted with respect to its direction of propagation. Motivated by this intriguing phenomenon, the energy density of the light beam is decomposed into its Cartesian components in the tilted reference frame. This illustrates the occurrence of the characteristic shift and the significance of the effective response function of the detector. We introduce the concept of a tilted polarizing interface and provide a scheme for its experimental implementation. A light beam passing through such an interface undergoes a shift resembling the original geometric SHEL in a tilted reference frame. This displacement is generated at the polarizer and its occurrence does not depend on the properties of the detection system. We give explicit results for this novel type of geometric SHEL and show that at grazing incidence this effect amounts to a displacement of multiple wavelengths, a shift larger than the one introduced by Goos-H\"anchen and Imbert-Fedorov effects.Comment: 6 pages, 4 figure

Prostate cancer and Hedgehog signalling pathway

[Abstract] The Hedgehog (Hh) family of intercellular signalling proteins have come to be recognised as key mediators in many fundamental processes in embryonic development. Their activities are central to the growth, patterning and morphogenesis of many different regions within the bodies of vertebrates. In some contexts, Hh signals act as morphogens in the dose-dependent induction of distinct cell fates within a target field, in others as mitogens in the regulation of cell proliferation or as inducing factors controlling the form of a developing organ. These diverse functions of Hh proteins raise many intriguing questions about their mode of action. Various studies have now demonstrated the function of Hh signalling in the control of cell proliferation, especially for stem cells and stem-like progenitors. Abnormal activation of the Hh pathway has been demonstrated in a variety of human tumours. Hh pathway activity in these tumours is required for cancer cell proliferation and tumour growth. Recent studies have uncovered the role for Hh signalling in advanced prostate cancer and demonstrated that autocrine signalling by tumour cells is required for proliferation, viability and invasive behaviour. Thus, Hh signalling represents a novel pathway in prostate cancer that offers opportunities for prognostic biomarker development, drug targeting and therapeutic response monitoring

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)—mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations—comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the ‘legacy’ GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as ‘harmonized’ by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve. Gao et al. performed a systematic analysis of the effects of synchronizing the large-scale, widely used, multi-omic dataset of The Cancer Genome Atlas to the current human reference genome. For each of the five molecular data platforms assessed, they demonstrated a very high concordance between the ‘legacy’ GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as ‘harmonized’ by the Genomic Data Commons

One-loop corrections to omega photoproduction near threshold

One-loop corrections to $\omega$ photoproduction near threshold have been investigated by using the approximation that all relevant transition amplitudes are calculated from the tree diagrams of effective Lagrangians. With the parameters constrained by the data of $\gamma N \to \pi N$, $\gamma N \to \rho N$, and $\pi N \to \omega N$ reactions, it is found that the one-loop effects due to the intermediate $\pi N$ and $\rho N$ states can significantly change the differential cross sections and spin observables. The results from this exploratory investigation suggest strongly that the coupled-channel effects should be taken into account in extracting reliable resonance parameters from the data of vector meson photoproduction in the resonance region.Comment: 19 pages, REVTeX, 14 figures, title changed, revised version to appear in Phys. Rev.