Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Computer perception of topological symmetry by all-paths algorithm

During the development of our ESESOC system (Expert System for the Elucidation of the Structures of Organic Compounds), computer perception of topological symmetry is essential in searching for the canonical description of a molecular structure, removing the irredundant connections in the structure generation process, and specifying the number of peaks in C-13- and H-1-NMR spectra in the structure evaluation process. In the present paper, a new path identifier is introduced and an algorithm for detection of topological symmetry from a connection table is developed by the all-paths method. (C) 1999 Elsevier Science B.V. All rights reserved.

Developing molecular identification numbers by an all-paths method

A new topological index is devised from an all-paths method. This molecular topological index has highly discriminating power for various kinds of organic compounds such as alkane trees, complex cyclic or polycyclic graphs, and structures containing heteroatoms and thus can be used as a Molecular IDentification number (MID) for chemical documentation. Some published MIDs derived from an all-paths method and their structural selectivity for alkane trees are also reviewed.

Calculation of Blocking Probabilities in Multistage Interconnection Networks with Redundant Paths

The blocking probability of a network is a common measure of its performance. There exist means of quickly calculating the blocking probabilities of Banyan networks; however, because Banyan networks have no redundant paths, they are not inherently fault-tolerant, and so their use in large-scale multiprocessors is problematic. Unfortunately, the addition of multiple paths between message sources and sinks in a network complicates the calculation of blocking probabilities. A methodology for exact calculation of blocking probabilities for small networks with redundant paths is presented here, with some discussion of its potential use in approximating blocking probabilities for large networks with redundant paths.

Methods for Parallelizing Search Paths in Phrasing

Many search problems are commonly solved with combinatoric algorithms that unnecessarily duplicate and serialize work at considerable computational expense. There are techniques available that can eliminate redundant computations and perform remaining operations concurrently, effectively reducing the branching factors of these algorithms. This thesis applies these techniques to the problem of parsing natural language. The result is an efficient programming language that can reduce some of the expense associated with principle-based parsing and other search problems. The language is used to implement various natural language parsers, and the improvements are compared to those that result from implementing more deterministic theories of language processing.

Ethics and Foreign Policy: The Antinomies of New Labour's 'Third Way' in Sub-Saharan Africa

Abrahamsen, Rita, Williams, Paul, 'Ethics and Foreign Policy: The Antinomies of New Labour's 'Third Way' in Sub-Saharan Africa', Political Studies (2002) 49(2) pp.249-264 RAE2008

Labour and the Bomb: The First Eighty Years

Scott, L. (2006). Labour and the Bomb: The First Eighty Years. International Affairs. 82(4), pp.685-700 RAE2008

'We are not Seeking Strength for its Own Sake': The British Labour Party, West Germany and the Cold War, 1951-64

Hughes, R. (2002). 'We are not Seeking Strength for its Own Sake': The British Labour Party, West Germany and the Cold War, 1951-64. Cold War History. 3(1) pp.67-94 RAE2008

Typically Anti-American? The Labour movement, America and Broadcasting in Britain from Beveridge to Pilkington, 1949-62

O'Malley, T. (2007). Typically Anti-American?: The Labour movement, America and Broadcasting in Britain from Beveridge to Pilkington, 1949-62. In J. Wiener and M. Hampton (Eds.), Anglo- American Media Interactions,1850-2000 (pp.234-253). Basingstoke: Palgrave Macmillan. RAE2008

Troublesome Amateurs: Theatre, ethics and the labour of mimesis

Kear, A. 'Troublesome Amateurs: Theatre, ethics and the labour of mimesis', Performance Research (2005) 10 (1), 26-46 RAE2008

In the wake of the war canoe ; a stirring record of forty years' successful labour, peril & adventure amongst the savage Indian tribes of the Pacific coast, and the piratical headhunting Haidas of the Queen Charlotte Islands, B.C., with an introduction by the Lord Bishop of Derry.

http://www.archive.org/details/inwakeofwarcanoe00collrich

By-paths to forgotten folks; stories of real life in Baptist home mission fields, by Coe Hayne. Ed. by the Department of missionary education, Board of education of the Northern Baptist convention.

http://www.archive.org/details/bypathstoforgott00haynrich

Diversity of Forwarding Paths in Pocket Switched Networks

Forwarding in DTNs is a challenging problem. We focus on the specific issue of forwarding in an environment where mobile devices are carried by people in a restricted physical space (e.g. a conference) and contact patterns are not predictable. We show for the first time a path explosion phenomenon between most pairs of nodes. This means that, once the first path reaches the destination, the number of subsequent paths grows rapidly with time, so there usually exist many near-optimal paths. We study the path explosion phenomenon both analytically and empirically. Our results highlight the importance of unequal contact rates across nodes for understanding the performance of forwarding algorithms. We also find that a variety of well-known forwarding algorithms show surprisingly similar performance in our setting and we interpret this fact in light of the path explosion phenomenon.

On the Stable Paths Problem and a Restricted Variant

Interdomain routing on the Internet is performed using route preference policies specified independently, and arbitrarily by each Autonomous System in the network. These policies are used in the border gateway protocol (BGP) by each AS when selecting next-hop choices for routes to each destination. Conflicts between policies used by different ASs can lead to routing instabilities that, potentially, cannot be resolved no matter how long BGP is run. The Stable Paths Problem (SPP) is an abstract graph theoretic model of the problem of selecting nexthop routes for a destination. A stable solution to the problem is a set of next-hop choices, one for each AS, that is compatible with the policies of each AS. In a stable solution each AS has selected its best next-hop given that the next-hop choices of all neighbors are fixed. BGP can be viewed as a distributed algorithm for solving SPP. In this report we consider the stable paths problem, as well as a family of restricted variants of the stable paths problem, which we call F stable paths problems. We show that two very simple variants of the stable paths problem are also NP-complete. In addition we show that for networks with a DAG topology, there is an efficient centralized algorithm to solve the stable paths problem, and that BGP always efficiently converges to a stable solution on such networks.