Structure and stability of helices in square-well homopolymers

Recently, it has been demonstrated [Magee et al., Phys. Rev. Lett. 96, 207802 (2006)] that isolated, square-well homopolymers can spontaneously break chiral symmetry and freeze into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics, combined with an optimized parallel tempering scheme, to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a window of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature, however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.Comment: Submitted to Physical Review

The Canary Islands: Their History, Natural History and Scenery

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GRIN2A (NR2A): a gene contributing to glutamatergic involvement in schizophrenia

Involvement of the glutamate system, particularly N-methyl-D-aspartate (NMDA) receptor hypofunction, has long been postulated to be part of the pathophysiology of schizophrenia. An important development is provided by recent data that strongly implicate GRIN2A, the gene encoding the NR2A (GluN2A) NMDA receptor subunit, in the aetiology of the disorder. Rare variants and common variants are both robustly associated with genetic risk for schizophrenia. Some of the rare variants are point mutations likely affecting channel function, but most are predicted to cause protein truncation and thence result, like the common variants, in reduced gene expression. We review the genomic evidence, and the findings from Grin2a mutant mice and other models which give clues as to the likely phenotypic impacts of GRIN2A genetic variation. We suggest that one consequence of NR2A dysfunction is impairment in a form of hippocampal synaptic plasticity, producing deficits in short-term habituation and thence elevated and dysregulated levels of attention, a phenotype of relevance to schizophrenia and its cognitive aspects

Innate immune response to intramammary infection with Serratia marcescens and Streptococcus uberis

Streptococcus uberis and Serratia marcescens are Gram-positive and Gram-negative bacteria, respectively, that induce clinical mastitis. Once initial host barrier systems have been breached by these pathogens, the innate immune system provides the next level of defense against these infectious agents. The innate immune response is characterized by the induction of pro-inflammatory cytokines, as well as increases in other accessory proteins that facilitate host recognition and elimination of the pathogens. The objective of the current study was to characterize the innate immune response during clinical mastitis elicited by these two important, yet less well-studied, Gram-positive and Gram-negative organisms. The pro-inflammatory cytokine response and changes in the levels of the innate immune accessory recognition proteins, soluble CD14 (sCD14) and lipopolysaccharide (LPS)-binding protein (LBP), were studied. Decreased milk output, induction of a febrile response, and increased acute phase synthesis of LBP were all characteristic of the systemic response to intramammary infection with either organism. Infection with either bacteria similarly resulted in increased milk levels of IL-1$\beta$, IL-8, IL-10, IL-12, IFN-$\gamma$, TNF-$\alpha$, sCD14, LBP, and the complement component, C5a. However, the duration of and/or maximal changes in the increased levels of these inflammatory markers were significantly different for several of the inflammatory parameters assayed. In particular, S. uberis infection was characterized by the sustained elevation of higher milk levels of IL-1$\beta$, IL-10, IL-12, IFN-$\gamma$, and C5a, relative to S. marcescens infection. Together, these data demonstrate the variability of the innate immune response to two distinct mastitis pathogens

Transport properties of highly asymmetric hard-sphere mixtures

The static and dynamic properties of binary mixtures of hard spheres with a diameter ratio of sigma(B)/sigma(A)= 0.1 and a mass ratio of m(B)/m(A)= 0.001 are investigated using event driven molecular dynamics. The contact values of the pair correlation functions are found to compare favorably with recently proposed theoretical expressions. The transport coefficients of the mixture, determined from simulation, are compared to the predictions of the revised Enskog theory using both a third-order Sonine expansion and direct simulation Monte Carlo. Overall, the Enskog theory provides a fairly good description of the simulation data, with the exception of systems at the smallest mole fraction of larger spheres (x(A)=0.01) examined. A "fines effect" was observed at higher packing fractions, where adding smaller spheres to a system of large spheres decreases the viscosity of the mixture; this effect is not captured by the Enskog theory

Movers and shakers: Granular damping in microgravity

The response of an oscillating granular damper to an initial perturbation is studied using experiments performed in microgravity and granular dynamics mulations. High-speed video and image processing techniques are used to extract experimental data. An inelastic hard sphere model is developed to perform simulations and the results are in excellent agreement with the experiments. The granular damper behaves like a frictional damper and a linear decay of the amplitude is bserved. This is true even for the simulation model, where friction forces are absent. A simple expression is developed which predicts the optimal damping conditions for a given amplitude and is independent of the oscillation frequency and particle inelasticities.Comment: 9 pages, 9 figure

Evaluating decontamination protocols for the isolation of Mycobacterium ulcerans from swabs

Mycobacterium ulcerans (M. ulcerans) is the causative agent of Buruli Ulcer (BU) disease. In order to inhibit the growth of the microbial contaminants during culture of M. ulcerans, it is necessary to decontaminate BU samples with effective chemical agents. This study aimed at investigating some selected chemicals as potential decontamination agents for the isolation of M. ulcerans from swabs.; Povidone iodine at 0.5 and 1% exhibited the lowest contamination and recovery rate for microbial contaminants and M. ulcerans. The most effective decontamination method was the protocol using 2% cetylpyridinium chloride/4% sodium chloride (recovery rate = 53%, contamination rate = 14%). The observed difference between the recovery rate of 2% CPC/4% NaC and the other protocols was however not statistically significant (p = 0.76).; Two percent (2%) cetylpyridinium chloride/4% sodium chloride can be conveniently used as an alternative decontamination method for the isolation of M. ulcerans from swabs

Using Cold Atoms to Measure Neutrino Mass

We propose a beta decay experiment based on a sample of ultracold atomic tritium. These initial conditions enable detection of the helium ion in coincidence with the beta. We construct a two-dimensional fit incorporating both the shape of the beta-spectrum and the direct reconstruction of the neutrino mass peak. We present simulation results of the feasible limits on the neutrino mass achievable in this new type of tritium beta-decay experiment.Comment: 10 pages, 5 figure

Let\u27s Talk Protecting Endangered Species

The Trump Administration recently changed Endangered Species Act regulations affecting how species are removed from endangered status and streamlining permits for the oil and gas and ranching industries. Environmentalists say the rules weaken protections. How could the new rules change industry and conservation in New Mexico

Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19

The coronavirus disease 2019 (COVID-19) pandemic caused by the new coronavirus (SARS-CoV-2) is currently responsible for more than 3 million deaths in 219 countries across the world and with more than 140 million cases. The absence of FDA-approved drugs against SARS-CoV-2 has highlighted an urgent need to design new drugs. We developed an integrated model of the human cell and SARS-CoV-2 to provide insight into the virus'' pathogenic mechanism and support current therapeutic strategies. We show the biochemical reactions required for the growth and general maintenance of the human cell, first, in its healthy state. We then demonstrate how the entry of SARS-CoV-2 into the human cell causes biochemical and structural changes, leading to a change of cell functions or cell death. A new computational method that predicts 20 unique reactions as drug targets from our models and provides a platform for future studies on viral entry inhibition, immune regulation, and drug optimisation strategies. The model is available in BioModels (https://www.ebi.ac.uk/biomodels/MODEL2007210001) and the software tool, findCPcli, that implements the computational method is available at https://github.com/findCP/findCPcli. © 2021 Bannerman et al