Random Networks Tossing Biased Coins

In statistical mechanical investigations on complex networks, it is useful to employ random graphs ensembles as null models, to compare with experimental realizations. Motivated by transcription networks, we present here a simple way to generate an ensemble of random directed graphs with, asymptotically, scale-free outdegree and compact indegree. Entries in each row of the adjacency matrix are set to be zero or one according to the toss of a biased coin, with a chosen probability distribution for the biases. This defines a quick and simple algorithm, which yields good results already for graphs of size n ~ 100. Perhaps more importantly, many of the relevant observables are accessible analytically, improving upon previous estimates for similar graphs

A Model for the Self-Organization of Microtubules Driven by Molecular Motors

We propose a two-dimensional model for the organization of stabilized microtubules driven by molecular motors in an unconfined geometry. In this model two kinds of dynamics are competing. The first one is purely diffusive, with an interaction between the rotational degrees of freedom, the second one is a local drive, dependent on microtubule polarity. As a result, there is a configuration dependent driving field. Applying a molecular field approximation, we are able to derive continuum equations. A study on the solutions shows nonequilibrium steady states. The presence and stability of such self-organized states are investigated in terms of entropy production. Numerical simulations confirm analytical results.Comment: 23 pages, 10 figures, LaTeX, ep

Numerical optimization design of advanced transonic wing configurations

A computationally efficient and versatile technique for use in the design of advanced transonic wing configurations has been developed. A reliable and fast transonic wing flow-field analysis program, TWING, has been coupled with a modified quasi-Newton method, unconstrained optimization algorithm, QNMDIF, to create a new design tool. Fully three-dimensional wing designs utilizing both specified wing pressure distributions and drag-to-lift ration minimization as design objectives are demonstrated. Because of the high computational efficiency of each of the components of the design code, in particular the vectorization of TWING and the high speed of the Cray X-MP vector computer, the computer time required for a typical wing design is reduced by approximately an order of magnitude over previous methods. In the results presented here, this computed wave drag has been used as the quantity to be optimized (minimized) with great success, yielding wing designs with nearly shock-free (zero wave drag) pressure distributions and very reasonable wing section shapes

Functional models for large-scale gene regulation networks: realism and fiction

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different conditions, times, environments. We now possess a certain amount of information about these two levels of description, stored in libraries, databases and ontologies. A current challenge is to bridge the gap between topology and function, i.e. developing quantitative models aimed at characterizing the expression patterns of large sets of genes. However, approaches that work well for small networks become impossible to master at large scales, mainly because parameters proliferate. In this review we discuss the state of the art of large-scale functional network models, addressing the issue of what can be considered as realistic and what the main limitations may be. We also show some directions for future work, trying to set the goals that future models should try to achieve. Finally, we will emphasize the possible benefits in the understanding of biological mechanisms underlying complex multifactorial diseases, and in the development of novel strategies for the description and the treatment of such pathologies.Comment: to appear on Mol. BioSyst. 200

CFD to Flight: Some Recent Success Stories of X-Plane Design to Flight Test at the NASA Dryden Flight Research Center

Several examples from the past decade of success stories involving the design and flight test of three true X-planes will be described: in particular, X-plane design techniques that relied heavily upon computational fluid dynamics (CFD). Three specific examples chosen from the author s personal experience are presented: the X-36 Tailless Fighter Agility Research Aircraft, the X-45A Unmanned Combat Air Vehicle, and, most recently, the X-48B Blended Wing Body Demonstrator Aircraft. An overview will be presented of the uses of CFD analysis, comparisons and contrasts with wind tunnel testing, and information derived from the CFD analysis that directly related to successful flight test. Some lessons learned on the proper application, and misapplication, of CFD are illustrated. Finally, some highlights of the flight-test results of the three example X-planes will be presented. This overview paper will discuss some of the author s experience with taking an aircraft shape from early concept and three-dimensional modeling through CFD analysis, wind tunnel testing, further refined CFD analysis, and, finally, flight. An overview of the key roles in which CFD plays well during this process, and some other roles in which it does not, are discussed. How wind tunnel testing complements, calibrates, and verifies CFD analysis is also covered. Lessons learned on where CFD results can be misleading are also given. Strengths and weaknesses of the various types of flow solvers, including panel methods, Euler, and Navier-Stokes techniques, are discussed. The paper concludes with the three specific examples, including some flight test video footage of the X-36, the X-45A, and the X-48B