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Dynamical Aspects (dynamical + aspect)
Selected AbstractsDynamical aspects of molecular recognitionJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2010Martin Karplus No abstract is available for this article. [source] On open-set lattices and some of their applications in semanticsINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 12 2003Mouw-Ching Tjiok In this article, we present the theory of Kripke semantics, along with the mathematical framework and applications of Kripke semantics. We take the Kripke-Sato approach to define the knowledge operator in relation to Hintikka's possible worlds model, which is an application of the semantics of intuitionistic logic and modal logic. The applications are interesting from the viewpoint of agent interactives and process interaction. We propose (i) an application of possible worlds semantics, which enables the evaluation of the truth value of a conditional sentence without explicitly defining the operator "," (implication), through clustering on the space of events (worlds) using the notion of neighborhood; and (ii) a semantical approach to treat discrete dynamic process using Kripke-Beth semantics. Starting from the topological approach, we define the measure-theoretical machinery, in particular, we adopt the methods developed in stochastic process,mainly the martingale,to our semantics; this involves some Boolean algebraic (BA) manipulations. The clustering on the space of events (worlds), using the notion of neighborhood, enables us to define an accessibility relation that is necessary for the evaluation of the conditional sentence. Our approach is by taking the neighborhood as an open set and looking at topological properties using metric space, in particular, the so-called ,-ball; then, we can perform the implication by computing Euclidean distance, whenever we introduce a certain enumerative scheme to transform the semantic objects into mathematical objects. Thus, this method provides an approach to quantify semantic notions. Combining with modal operators Ki operating on E set, it provides a more-computable way to recognize the "indistinguishability" in some applications, e.g., electronic catalogue. Because semantics used in this context is a local matter, we also propose the application of sheaf theory for passing local information to global information. By looking at Kripke interpretation as a function with values in an open-set lattice ,,U, which is formed by stepwise verification process, we obtain a topological space structure. Now, using the measure-theoretical approach by taking the Borel set and Borel function in defining measurable functions, this can be extended to treat the dynamical aspect of processes; from the stochastic process, considered as a family of random variables over a measure space (the probability space triple), we draw two strong parallels between Kripke semantics and stochastic process (mainly martingales): first, the strong affinity of Kripke-Beth path semantics and time path of the process; and second, the treatment of time as parametrization to the dynamic process using the technique of filtration, adapted process, and progressive process. The technique provides very effective manipulation of BA in the form of random variables and ,-subalgebra under the cover of measurable functions. This enables us to adopt the computational algorithms obtained for stochastic processes to path semantics. Besides, using the technique of measurable functions, we indeed obtain an intrinsic way to introduce the notion of time sequence. © 2003 Wiley Periodicals, Inc. [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] The dynamics of heat lows over flat terrainTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 637 2008Thomas Spengler Abstract The numerical model for a heat low developed by Rácz and Smith is extended to include a representation of radiative heating and cooling. The model is run with a higher horizontal resolution than the original version and is used to investigate additional dynamical aspects of the structure and evolution of a heat low over a subcontinental- or continental-scale circular island surrounded by sea. Of particular interest is the diurnal and day-to-day evolution of the upper- and lower-level circulations and the degree of balance that exists in these. The heat low is surmounted by an anticyclone, the development of which is closely tied to the outflow branch of the sea breeze. The anticyclone has a much smaller diurnal variation than the heat low and, unlike the heat low is largely in balance, except in the region affected by the upward-propagating gravity wave induced by the inland-penetrating sea breeze. There is a strong analogy to certain aspects of tropical cyclones, which have a warm core, a shallow unbalanced boundary layer, and which are surmounted also by an anticyclone. Principles governing the absolute angular momentum budget are the same as those relating to the tropical cyclones and to the zonal-mean flow over Antarctica. Implications of these principles for obtaining a realistic steady state in long-term integrations of axisymmetric models are discussed. Copyright © 2008 Royal Meteorological Society [source] Some dynamical aspects of tropical cyclone concentric eyewallsTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 632 2008Christopher M. Rozoff Abstract The intensification of tropical cyclones is often interrupted by an eyewall replacement cycle, a process in which an outer eyewall forms, contracts, and replaces an inner eyewall. The radial distributions of inertial stability and diabatic heating change during such events, impacting the transverse circulation. To examine the effects of such changes, an analytical solution of the transverse circulation equation associated with a balanced vortex model is derived using a parameterization that distinguishes five radial regions subdividing the domain by each region's values of inertial stability and diabatic heating. These regions define the eye, inner eyewall, moat, outer eyewall, and far-field. In mature concentric eyewall situations, the solutions do not support the hypothesis that the inner eyewall collapses as a direct result of subsidence from the outer eyewall. However, the results suggest subsidence and warming temperatures in the moat are governed by enhanced inertial stability associated with a strengthening outer eyewall. The model solutions also illustrate how the diabatic heating in the inner eyewall, imbedded in a region of high inertial stability, induces larger temperature tendencies than the diabatic heating in the outer eyewall, which borders the far-field region of low inertial stability. Thus, as the inner eyewall dies, the storm temporarily loses its ability to produce an intense, localized warm region. This ability is restored during the contraction and intensification of the outer eyewall. These results provide a partial dynamical explanation of how an eyewall replacement cycle can act as a temporary brake on tropical cyclone intensification. Copyright © 2008 Royal Meteorological Society [source] | ||||||||||