A Semantic Basis for Parallel Algorithm Design

As computing demands increase, emphasis is being placed on parallel architectures- To efficiently use parallel machines, software must be designed to take advantage of these machines. This research concentrates on an abstraction of algorithm design to permit the expression of parallel programs. The abstraction emphasizes thought about algorithms at a high level as opposed to algorithm implementation at a statement level. A model based on data flow allows algorithm expression using flow diagrams. The model specifies operating system requirements that support parallel programming at a module level. Paths are used to carry data between modules. Data enter modules through ports. Module activation is triggered by the satisfaction of data availability conditions. Continual module presence within the system, dynamic activation criteria, and a high level of programming distinguishes this model from other parallel programming systems

A Simple Method for Organizing Nearly Optimal Binary Search Trees

Improving the efficiency of retrieving information concerns users of computer systems involved in many applications- One way of addressing this concern is to organize a sorted sequence into a binary search tree. Knuth\u27s Algorithm K is a bottom-up organization algorithm that always constructs a binary tree which minimizes average search time. However, the cost of executing Algorithm K is prohibitive for a large tree. The aim of this work is to find a less costly method of organizing sorted sequences into nearly-optimal binary search trees. We present a top-down organization method which yields better average search times than top-down methods already available, specifically height-balancing and weight-balancing. The variation in access frequency among the members of a sequence is used to recommend specific values for some of the parameters in this new method of organization. The new method improves considerably on the cost of organization as opposed to the cost of using Algorithm K while producing trees whose average search times are close to minimal. The new algorithm yields an average search time that is usually within 1% of the minimal average search time and for every case attempted has been no worse than 1.5% larger than minimal

Variational states for the spin-Peierls system

We introduce a family of Jastrow pair product states for quasi one-dimensional spin systems. Depending on a parameter they interpolate between the resonating valence bond ground state of the Haldane-Shastry model describing a spin liquid and the (dimerized) valence bond solid ground states of the Majumdar-Ghosh spin chain. These states are found to form an excellent basis for variational studies of Heisenberg chains with next nearest neighbour interaction and bond alternation as realized in the spin-Peierls system CuGeO_3.Comment: RevTeX+epsf macros, 24 pp. incl. figures, some references adde

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics. However, defining the network of inter-converting conformers that underlie the relaxation data remains generally challenging. Here, we combine NMR relaxation experiments with simulation to visualize networks of inter-converting conformers. We demonstrate our approach with the apo Pin1-WW domain, for which NMR has revealed conformational dynamics of a flexible loop in the millisecond range. We sample and cluster the free energy landscape using Markov State Models (MSM) with major and minor exchange states with high correlation with the NMR relaxation data and low NOE violations. These MSM are hierarchical ensembles of slowly interconverting, metastable macrostates and rapidly interconverting microstates. We found a low population state that consists primarily of holo-like conformations and is a “hub” visited by most pathways between macrostates. These results suggest that conformational equilibria between holo-like and alternative conformers pre-exist in the intrinsic dynamics of apo Pin1-WW. Analysis using MutInf, a mutual information method for quantifying correlated motions, reveals that WW dynamics not only play a role in substrate recognition, but also may help couple the substrate binding site on the WW domain to the one on the catalytic domain. Our work represents an important step towards building networks of inter-converting conformational states and is generally applicable

Proceedings of Abstracts, School of Physics, Engineering and Computer Science Research Conference 2022

© 2022 The Author(s). This is an open-access work distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. For further details please see https://creativecommons.org/licenses/by/4.0/. Plenary by Prof. Timothy Foat, ‘Indoor dispersion at Dstl and its recent application to COVID-19 transmission’ is © Crown copyright (2022), Dstl. This material is licensed under the terms of the Open Government Licence except where otherwise stated. To view this licence, visit http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3 or write to the Information Policy Team, The National Archives, Kew, London TW9 4DU, or email: [email protected] present proceedings record the abstracts submitted and accepted for presentation at SPECS 2022, the second edition of the School of Physics, Engineering and Computer Science Research Conference that took place online, the 12th April 2022

2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary.

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2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary.

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