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.

井间地震速度层析成像方法与软件系统

Crosshole Seismic tomography has been broadly studied and applied in the fields of resource exploration and engineering exploration because of its special observing manner and better resolution than normal seismic exploration. This thesis will state the theory and method of Crosshole Seismic tomography. Basing on the previous studies，the thesis studied the initial velocity model，ray-tracing method, and developed the three-dimension tomography software. All the cells that a ray passes through are of the same velocities if the paths from transmitters to receivers are straight. The cells that the each ray passes through are recorded, and rays that pass through each cell are calculated. The ray average velocity which passes through a cell is set as the cell velocity. Analogously we can make a initial node velocity model because the velocity sum is calculated on the all cells which own to a certain node, and the cell number is summed about each nodes，the ratio of the velocity sum to the all cells number is set as the node velocity. The inversion result from the initial node velocity model is better than that of the average velocity model. Ray-bending and Shortest Path for Rays (SPR) have shortcomings and limitations respectively. Using crooked rays obtained from SPR rather than straight lines as the starting point can not only avoid ray bending converging to the local minimum travel time path, but also settle the no smooth ray problem obtained by SPR. The hybrid method costs much computation time, which is roughly equal to the time that SPR expends. The Delphi development tool based on the Object Pascal language standard has an advantage of object-oriented. TDTOM (Three Dimensions Tomography) was developed by using Delphi from the DOS version. Improvement on the part of inversion was made, which bring faster convergence velocity. TDTOM can be used to do velocity tomography from the first arrival travel time of the seismic wave, and it has the good qualities of friendly user interface and convenient operation. TDTOM is used to reconstruct the velocity image for a set of crosshole data from Karamay Oil Field. The geological explanation is then given by comparing the inversion effects of different ray-tracing methods. High velocity zones mean the cover of oil reservoir, and low velocity zones correspond to the reservoir or the steam flooding layer.

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.

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

On the Scalability-Performance Tradeoffs in MPLS and IP Routing

MPLS (Multi-Protocol Label Switching) has recently emerged to facilitate the engineering of network traffic. This can be achieved by directing packet flows over paths that satisfy multiple requirements. MPLS has been regarded as an enhancement to traditional IP routing, which has the following problems: (1) all packets with the same IP destination address have to follow the same path through the network; and (2) paths have often been computed based on static and single link metrics. These problems may cause traffic concentration, and thus degradation in quality of service. In this paper, we investigate by simulations a range of routing solutions and examine the tradeoff between scalability and performance. At one extreme, IP packet routing using dynamic link metrics provides a stateless solution but may lead to routing oscillations. At the other extreme, we consider a recently proposed Profile-based Routing (PBR), which uses knowledge of potential ingress-egress pairs as well as the traffic profile among them. Minimum Interference Routing (MIRA) is another recently proposed MPLS-based scheme, which only exploits knowledge of potential ingress-egress pairs but not their traffic profile. MIRA and the more conventional widest-shortest path (WSP) routing represent alternative MPLS-based approaches on the spectrum of routing solutions. We compare these solutions in terms of utility, bandwidth acceptance ratio as well as their scalability (routing state and computational overhead) and load balancing capability. While the simplest of the per-flow algorithms we consider, the performance of WSP is close to dynamic per-packet routing, without the potential instabilities of dynamic routing.

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.

Search Space Reduction in QoS Routing

To provide real-time service or engineer constrained-based paths, networks require the underlying routing algorithm to be able to find low-cost paths that satisfy given Quality-of-Service (QoS) constraints. However, the problem of constrained shortest (least-cost) path routing is known to be NP-hard, and some heuristics have been proposed to find a near-optimal solution. However, these heuristics either impose relationships among the link metrics to reduce the complexity of the problem which may limit the general applicability of the heuristic, or are too costly in terms of execution time to be applicable to large networks. In this paper, we focus on solving the delay-constrained minimum-cost path problem, and present a fast algorithm to find a near-optimal solution. This algorithm, called DCCR (for Delay-Cost-Constrained Routing), is a variant of the k-shortest path algorithm. DCCR uses a new adaptive path weight function together with an additional constraint imposed on the path cost, to restrict the search space. Thus, DCCR can return a near-optimal solution in a very short time. Furthermore, we use the method proposed by Blokh and Gutin to further reduce the search space by using a tighter bound on path cost. This makes our algorithm more accurate and even faster. We call this improved algorithm SSR+DCCR (for Search Space Reduction+DCCR). Through extensive simulations, we confirm that SSR+DCCR performs very well compared to the optimal but very expensive solution.

THE DIVERGENT PATHS OF OPERA IN THE CLASSICAL PERIOD AS SEEN THROUGH THE OPERATIC WORKS OF CHRISTOPH WILLIBALD GLUCK AND WOLFGANG AMADEUS MOZART

Although evidence of Gluck's influence on Mozart is sometimes discernible, by examining the two operas I have performed and a recital of arias by these two composers we can see clear contrasts in their approach to and expression of classical opera. The two operas discussed are Gluck's Armide and Mozart's Le Nozze di Figaro. Gluck and Mozart were both innovators but in very different ways. Gluck comes from a dramatic background (his principles have been compared to those of Wagner) and Mozart brings together dramatic excellence with the greatness of his musical genius, his gift of melody, and his ensemble writing, which is arguably unequaled in the repertory. A well-rounded performer strives to understand what the composer is really trying to say with his work, what the message to the audience is and what his particular way of conveying it is. The understanding of a composer's approach to drama and character interaction plays a huge role in character development. This applies no matter what role you are preparing whether it is baroque opera or late romantic. Discovering the ideals, style, and purpose of a composer contributes to an effective and rewarding performance experience, for those on stage, those in the pit, and those sitting in the seats.

Isomorphic effects of managerial and directoral career paths

The extensive array of interlocking directorate research remains near-exclusively cross-sectional or comparative cross-sectional in nature. While this has been fruitful in identifying persistent structures of inter-organisational relationships evidence of the impact of these structures on organisational performance or activity has been more limited. This should not be surprising because, by their nature, relationships have strong longitudinal and dynamic qualities that are likely to be difficult to isolate through cross-sectional approaches. Clearly, managerial practice is inevitably strongly conditioned by the specific contingencies of the time and the information available through networks of colleagues and advisers (particularly at board level) at the time. But managerial and directoral capabilities and mental sets are also developed over time, particularly through previous experiences in these roles and the formation of long-lasting 'strong' and 'weak' relationships. This paper tests the influence of three longitudinal dimensions of managers and directors' relationships on a set of indicators of financial performance, drawing from a large dataset of detailing historic board membership of UK firms. It finds evidence of isomorphic processes through these channels and establishes that the longitudinal design considerably enhances the detection of performance effects from directorate interlocks. More broadly, the research has implications for the conception of collective action and the constitution of 'community'.

Divergent Paths of Development: The Modern World-System and Democratization in South Africa and Zambia

This article examines whether a Modern World- Systems (MWS) perspective can provide an improved understanding of the processes of democratization in Africa (and other developing regions of the world) by conducting a comparative case study of South Africa and Zambia in the 1990s, examining the transitions to democracy and divergent processes of democratic consolidation in each country. Semiperipheral South Africa has, due to its more advantageous position in the world-system, been better equipped than peripheral Zambia to safeguard democracy against erosion and reversal. Th e central irony of the MWS is that the weakest states in the MWS can be pushed around by core powers and are more easily forced to democratize while at the same time they are least likely to possess the resources necessary for democratic consolidation. Semiperipheral states can maintain their independence vis-à-vis the core to a higher degree, but if the decision is made to undertake a democratic transition they are more likely to possess the resources necessary for successful consolidation. Th e MWS perspective allows for an improved understanding of the causal pathway of how position in the MWS translates into the ability to consolidate democracy than does approaches that emphasize domestic factors.