A Special Homotopy Continuation Method For A Class of Polynomial Systems

A special homotopy continuation method, as a combination of the polyhedral homotopy and the linear product homotopy, is proposed for computing all the isolated solutions to a special class of polynomial systems. The root number bound of this method is between the total degree bound and the mixed volume bound and can be easily computed. The new algorithm has been implemented as a program called LPH using C++. Our experiments show its efficiency compared to the polyhedral or other homotopies on such systems. As an application, the algorithm can be used to find witness points on each connected component of a real variety

Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex

Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex of photosynthetic green sulphur bacteria, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network model (NNM) provides a computationally inexpensive approach to studying vibrational modes at the microscopic level in large protein structures, whilst incorporating anharmonicity in the inter-residue interactions which can influence protein dynamics. We apply the NNM to the entire trimeric FMO complex and find evidence for the existence of nonlinear discrete breather modes. These modes tend to transfer energy to the highly connected core pigments, potentially opening up alternative excitation energy transfer routes through their influence on pigment properties. Incorporating localised modes based on these discrete breathers in the optical spectra calculations for FMO using ab initio site energies and excitonic couplings can substantially improve their agreement with experimental results.A.W.C. and S.E.M. acknowledge support from the Winton Programme for the Physics of Sustainability. S.E.M. is also supported by an EPSRC doctoral training award. D.J.C. is supported by a Marie Curie International Outgoing Fellowship within the seventh European Community Framework Programme

The correlation of dust and gas emission in star-forming environments

This is the final version of the article. Available from the publisher via the DOI in this record.We present ammonia maps of portions of the W3 and Perseus molecular clouds in order to compare gas emission with submillimetre continuum thermal emission which are commonly used to trace the same mass component in star-forming regions, often under the assumption of local thermodynamic equilibrium (LTE). The Perseus and W3 star-forming regions are found to have significantly different physical characteristics consistent with the difference in size scales traced by our observations. Accounting for the distance of theW3 region does not fully reconcile these differences, suggesting that there may be an underlying difference in the structure of the two regions. Peak positions of submillimetre and ammonia emission do not correlate strongly. Also, the extent of diffuse emission is only moderately matched between ammonia and thermal emission. Source sizes measured from our observations are consistent between regions, although there is a noticeable difference between the submillimetre source sizes with sources in Perseus being significantly smaller than those in W3. Fractional abundances of ammonia are determined for our sources which indicate a dip in the measured ammonia abundance at the positions of peak submillimetre column density. Virial ratios are determined which show that our sources are generally bound in both regions, although there is considerable scatter in both samples. We conclude that sources in Perseus are bound on smaller scales than in W3 in a way that may reflect their previous identification as low-and high-mass, respectively. Our results indicate that assumptions of local thermal equilibrium and/or the coupling of the dust and gas phases in star-forming regions may not be as robust as commonly assumed. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.The authors would like to thank Neal Evans and Erik Rosolowsky for insightful and thorough comments on this work which have considerably improved its quality. The authors acknowledge the data analysis facilities provided by the Starlink Project under continual development by the JAC. In addition, the following Starlink packages have been used: Kappa, Cupid, GAIA, Convert and Coco. We would like to thank the helpful staff of the GBT in the collection of data used in this paper related to the project GBT10C_024. LKM is supported by a STFC postdoctoral grant (ST/G001847/1) and DJE is supported by a STFC PhD studentship. This research would not have been possible without the SIMBAD astronomical data base service operated at CDS, Strasbourg, France and the NASA Astrophysics Data System Bibliographic Services

A wide-spectrum language for verification of programs on weak memory models

Modern processors deploy a variety of weak memory models, which for efficiency reasons may (appear to) execute instructions in an order different to that specified by the program text. The consequences of instruction reordering can be complex and subtle, and can impact on ensuring correctness. Previous work on the semantics of weak memory models has focussed on the behaviour of assembler-level programs. In this paper we utilise that work to extract some general principles underlying instruction reordering, and apply those principles to a wide-spectrum language encompassing abstract data types as well as low-level assembler code. The goal is to support reasoning about implementations of data structures for modern processors with respect to an abstract specification. Specifically, we define an operational semantics, from which we derive some properties of program refinement, and encode the semantics in the rewriting engine Maude as a model-checking tool. The tool is used to validate the semantics against the behaviour of a set of litmus tests (small assembler programs) run on hardware, and also to model check implementations of data structures from the literature against their abstract specifications

XPS surface analysis of ceria-based materials: Experimental methods and considerations

X-ray photoelectron spectroscopy (XPS) analysis of cerium is ubiquitous amongst the catalytic and materials literature however errors in experimental procedure and data analysis are often easily proliferated. In this work we focus on the best practice for experimental construction when approaching the task of understanding chemical environments in cerium-based materials by XPS

Health outcomes of iron supplementation and/or food fortification in iron-replete children aged 4-24 months: Protocol for a systematic review and meta-analysis

© 2019 The Author(s). Background: Direct supplementation or food fortification with iron are two public health initiatives intended to reduce the prevalence of iron deficiency (ID) and iron deficiency anaemia (IDA) in 4-24-month-old infants. In most high-income countries where IDA prevalence is 40%. Emerging concerns about delayed neurological effects of early-life iron overexposure have raised questions as to whether recommended guidelines in high-income countries are unnecessarily excessive. This systematic review will gather evidence from supplementation/fortification trials, comparing health outcomes in studies where iron-replete children did or did not receive additional dietary iron; and determine if replete children at study outset were not receiving additional iron show changes in haematological indices of ID/IDA over the trial duration. Methods: We will perform a systematic review of the literature, including all studies of iron supplementation and/or fortification, including study arms with confirmed iron-replete infants at the commencement of the trial. This includes both dietary iron intervention or placebo/average dietary intakes. One reviewer will conduct searches in electronic databases of published and ongoing trials (Medline, Web of Science, Scopus, CENTRAL, EBSCO [e.g. CINAHL Complete, Food Science and Technology Abstracts], Embase, ClinicalTrials.gov, ClinicalTrialsRegister.eu and who.it/trialsearch), digital theses and dissertations (WorldCat, Networked Digital Library of Theses and Dissertations, DART-Europe E-theses Portal, Australasian Digital Theses Program, Theses Canada Portal and ProQuest). For eligible studies, one reviewer will use a data extraction form, and a second reviewing entered data for accuracy. Both reviewers will independently perform quality assessments before qualitative and, if appropriate, quantitative synthesis as a meta-analysis. We will resolve any discrepancies through discussion or consult a third author to resolve discrepancies. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement will be used as the basis for reporting. Discussion: Recommended iron supplementation and food fortification practices in high-income countries have been criticised for being both excessive and based on outdated or underpowered studies. This systematic review will build a case for revisiting iron intake guidelines for infants through the design of new trials where health effects of additional iron intake in iron-replete infants are the primary outcome. Systematic review registration: PROSPERO CRD42018093744

Restoration of dystrophin expression using the Sleeping Beauty transposon.

The Sleeping beauty (SB) system is a non-viral DNA based vector that has been used to stably integrate therapeutic genes into disease models. Here we report the SB system is capable of stably integrating the ΔR4-R23/CTΔ micro-dystrophin gene into a conditionally immortal dystrophin deficient muscle cell-line, H2K SF1, a murine cell model for Duchenne muscular dystrophy. Genetically corrected H2K SF1 cells retained their myogenic properties in vitro. Moreover, upon transplantation ΔR4-R23/CTΔ micro-dystrophin expression was detected within mdx nu/nu mice. Our data suggests the SB system is an effective way of stably integrating therapeutic genes into myogenic cells

Properties of kinetic transition networks for atomic clusters and glassy solids

A database of minima and transition states corresponds to a network where the minima represent nodes and the transition states correspond to edges between the pairs of minima they connect via steepest-descent paths. Here we construct networks for small clusters bound by the Morse potential for a selection of physically relevant parameters, in two and three dimensions. The properties of these unweighted and undirected networks are analysed to examine two features: whether they are small-world, where the shortest path between nodes involves only a small number or edges; and whether they are scale-free, having a degree distribution that follows a power law. Small-world character is present, but statistical tests show that a power law is not a good fit, so the networks are not scale-free. These results for clusters are compared with the corresponding properties for the molecular and atomic structural glass formers ortho-terphenyl and binary Lennard-Jones. These glassy systems do not show small-world properties, suggesting that such behaviour is linked to the structure-seeking landscapes of the Morse clusters.JM acknowledges the support of a Sackler Studentship from the University of Cambridge. Part of this work was performed while DM was a member of the Department of Chemistry at the University of Cambridge, financially supported by the Engineering and Physical Sciences Research Council and the European Research Council