We describe a fully GPU-based implementation of the first level trigger for the upgrade of the LHCb detector, due to start data taking in 2021. We demonstrate that our implementation, named Allen, ...can process the 40 Tbit/s data rate of the upgraded LHCb detector and perform a wide variety of pattern recognition tasks. These include finding the trajectories of charged particles, finding proton–proton collision points, identifying particles as hadrons or muons, and finding the displaced decay vertices of long-lived particles. We further demonstrate that Allen can be implemented in around 500 scientific or consumer GPU cards, that it is not I/O bound, and can be operated at the full LHC collision rate of 30 MHz. Allen is the first complete high-throughput GPU trigger proposed for a HEP experiment.
RapidSim is a lightweight application for the fast simulation of phase space decays of beauty and charm quark hadrons, allowing for quick studies of the properties of signal and background decays in ...particle physics analyses. Based upon the TGenPhaseSpace class from the ROOT application it uses externally provided fixed-order next-to-leading-logarithm calculations to boost the initial beauty and charm hadrons to the appropriate energy for the production environment of interest. User-defined momentum resolution functions can be used to mimic the effect of imperfect track reconstruction. User-defined efficiency shapes can be applied during generation to reproduce the effects of geometric and kinematic requirements on final state particles as well as the dynamics of the decay. The effect of mis-identification of the final state particles is simple to configure via configuration files, while the framework can easily be extended to include additional particle types. This paper describes the RapidSim framework, features and some example use cases.
Program Title: RapidSim
Program Files doi:http://dx.doi.org/10.17632/62gg6pz6z7.1
Licensing provisions: MIT
Programming language: C++
Nature of problem: A common problem in the analysis of particle decays is understanding the kinematic properties of the signal decay of interest and the potential backgrounds that can be introduced via other particle decays that have been imperfectly reconstructed in the detector. In particular, it is often crucial to know the shape of the invariant mass of the final state particles (or sub-sets of them) and the corresponding shape of the background decays. One method to study potential background sources is to generate large samples of the decays and pass them through the full detector simulation and reconstruction software chain. By selecting these events as if they are the signal decay, it is possible to study the shape of the backgrounds in the invariant mass distribution of interest. The disadvantage of this approach is the typically long time required to generate, reconstruct and select these background samples and the mass storage requirements to retain these samples. This long turnaround time can hinder progress of the analysis.
Solution method: RapidSim is an application that allows analysts to quickly generate large samples (a few seconds for millions of events) of potential background decays with momentum spectra, invariant mass resolutions and efficiency shapes that are close approximations to what can be obtained from a full detector simulation. The speed of generation allows analysts to quickly perform initial studies that may indicate avenues for further investigation that may need a more detailed simulation.
The substrate specificities of papain-like cysteine proteases (clan CA, family C1) papain, bromelain, and human cathepsins L, V, K, S, F, B, and five proteases of parasitic origin were studied using ...a completely diversified positional scanning synthetic combinatorial library. A bifunctional coumarin fluorophore was used that facilitated synthesis of the library and individual peptide substrates. The library has a total of 160,000 tetrapeptide substrate sequences completely randomizing each of the P1, P2, P3, and P4 positions with 20 amino acids. A microtiter plate assay format permitted a rapid determination of the specificity profile of each enzyme. Individual peptide substrates were then synthesized and tested for a quantitative determination of the specificity of the human cathepsins. Despite the conserved three-dimensional structure and similar substrate specificity of the enzymes studied, distinct amino acid preferences that differentiate each enzyme were identified. The specificities of cathepsins K and S partially match the cleavage site sequences in their physiological substrates. Capitalizing on its unique preference for proline and glycine at the P2 and P3 positions, respectively, selective substrates and a substrate-based inhibitor were developed for cathepsin K. A cluster analysis of the proteases based on the complete specificity profile provided a functional characterization distinct from standard sequence analysis. This approach provides useful information for developing selective chemical probes to study protease-related pathologies and physiologies.
Cyclotides are plant-derived miniproteins that have the unusual features of a head-to-tail cyclized peptide backbone and a knotted arrangement of disulfide bonds. It had been postulated that they ...might be an especially large family of host defense agents, but this had not yet been tested by field data on cyclotide variation in wild plant populations. In this study, we sampled Australian Hybanthus (Violaceae) to gain an insight into the level of variation within populations, within species, and between species. A wealth of cyclotide diversity was discovered: at least 246 new cyclotides are present in the 11 species sampled, and 26 novel sequences were characterized. A new approach to the discovery of cyclotide sequences was developed based on the identification of a conserved sequence within a signal sequence in cyclotide precursors. The number of cyclotides in the Violaceae is now estimated to be >9000. Cyclotide physicochemical profiles were shown to be a useful taxonomic feature that reflected species and their morphological relationships. The novel sequences provided substantial insight into the tolerance of the cystine knot framework in cyclotides to amino acid substitutions and will facilitate protein engineering applications of this framework.
Cognitive ageing research examines the cognitive abilities that are preserved and/or those that decline with advanced age. There is great individual variability in cognitive ageing trajectories. Some ...older adults show little decline in cognitive ability compared with young adults and are thus termed 'optimally ageing'. By contrast, others exhibit substantial cognitive decline and may develop dementia. Human neuroimaging research has led to a number of important advances in our understanding of the neural mechanisms underlying these two outcomes. However, interpreting the age-related changes and differences in brain structure, activation and functional connectivity that this research reveals is an ongoing challenge. Ambiguous terminology is a major source of difficulty in this venture. Three terms in particular - compensation, maintenance and reserve - have been used in a number of different ways, and researchers continue to disagree about the kinds of evidence or patterns of results that are required to interpret findings related to these concepts. As such inconsistencies can impede progress in both theoretical and empirical research, here, we aim to clarify and propose consensual definitions of these terms.
Cyclotides are mini-proteins of 28–37 amino acid residues that have the unusual feature of a head-to-tail cyclic backbone surrounding a cystine knot. This molecular architecture gives the cyclotides ...heightened resistance to thermal, chemical and enzymatic degradation and has prompted investigations into their use as scaffolds in peptide therapeutics. There are now more than 80 reported cyclotide sequences from plants in the families Rubiaceae, Violaceae and Cucurbitaceae, with a wide variety of biological activities observed. However, potentially limiting the development of cyclotide-based therapeutics is a lack of understanding of the mechanism by which these peptides are cyclized
in vivo. Until now, no linear versions of cyclotides have been reported, limiting our understanding of the cyclization mechanism. This study reports the discovery of a naturally occurring linear cyclotide, violacin A, from the plant
Viola odorata and discusses the implications for
in vivo cyclization of peptides. The elucidation of the cDNA clone of violacin A revealed a point mutation that introduces a stop codon, which inhibits the translation of a key Asn residue that is thought to be required for cyclization. The three-dimensional solution structure of violacin A was determined and found to adopt the cystine knot fold of native cyclotides. Enzymatic stability assays on violacin A indicate that despite an increase in the flexibility of the structure relative to cyclic counterparts, the cystine knot preserves the overall stability of the molecule.
We propose a surface ion trap design incorporating microwave control electrodes for near-field single-qubit control. The electrodes are arranged so as to provide arbitrary frequency, amplitude and ...polarization control of the microwave field in one trap zone, whilst a similar set of electrodes is used to null the residual microwave field in a neighbouring zone. The geometry is chosen to reduce the residual field to the 0.5 % level without nulling fields; with nulling, the crosstalk may be kept close to the 0.01 % level for realistic microwave amplitude and phase drift. Using standard photolithography and electroplating techniques, we have fabricated a proof-of-principle electrode array with two trapping zones. We discuss requirements for the microwave drive system and prospects for scalability to a large 2-D trap array.
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