A computer program for bridge retrofitting

This paper summarizes the work developed in order to establish a framework for seismic retrofitting of bridges. In this context, the first objetive is to find a numerical model to evaluate the damage induced in a structure, under seismic action, as an index of its vulnerability. The model used has the adventage that is based on concepts of fracture mechanics and concentrated plasticity. As a result, the work is based on basic principles. The performance of this model is being evaluated. Some results of the computer program developed for this purpose are shown.

A Structure of Problem Solving Methods for Real Time Decision Support in Traffic Control

This article describes a knowledge-based application in the domain of road traffic management that we have developed following a knowledge modeling approach and the notion of problem-solving method. The article presents first a domain-independent model for real-time decision support as a structured collection of problem solving methods. Then, it is described how this general model is used to develop an operational version for the domain of traffic management. For this purpose, a particular knowledge modeling tool, called KSM (Knowledge Structure Manager), was applied. Finally, the article shows an application developed for a traffic network of the city of Madrid and it is compared with a second application developed for a different traffic area of the city of Barcelona.

Analysis of the railway track as a spatially periodic structure

This article presents a new and computationally efficient method of analysis of a railway track modelled as a continuous beam of 2N spans supported by elastic vertical springs. The main feature of this method is its important reduction in computational effort with respect to standard matrix methods of structural analysis. In this article, the whole structure is considered to be a repetition of a single one. The analysis presented is applied to a simple railway track model, i.e. to a repetitive beam supported on vertical springs (sleepers). The proposed method of analysis is based on the general theory of spatially periodic structures. The main feature of this theory is the possibility to apply Discrete Fourier Transform (DFT) in order to reduce a large system of q(2N + 1) linear stiffness equilibrium equations to a set of 2N + 1 uncoupled systems of q equations each. In this way, a dramatic reduction of the computational effort of solving the large system of equations is achieved. This fact is particularly important in the analysis of railway track structures, in which N is a very large number (around several thousands), and q = 2, the vertical displacement and rotation, is very small. The proposed method allows us to easily obtain the exact solution given by Samartín [1], i.e. the continuous beam railway track response. The comparison between the proposed method and other methods of analysis of railway tracks, such as Lorente de Nó and Zimmermann-Timoshenko, clearly shows the accuracy of the obtained results for the proposed method, even for low values of N. In addition, identical results between the proposed and the Lorente methods have been found, although the proposed method seems to be of simpler application and computationally more efficient than the Lorente one. Small but significative differences occur between these two methods and the one developed by Zimmermann-Timoshenko. This article also presents a detailed sensitivity analysis of the vertical displacement of the sleepers. Although standard matrix methods of structural analysis can handle this railway model, one of the objectives of this article is to show the efficiency of DFT method with respect to standard matrix structural analysis. A comparative analysis between standard matrix structural analysis and the proposed method (DFT), in terms of computational time, input, output and also software programming, will be carried out. Finally, a URL link to a MatLab computer program list, based on the proposed method, is given

Computer simulation of the interplay between fractal structures and surrounding heterogeneous multifractal distributions. Applications

In a large number of physical, biological and environmental processes interfaces with high irregular geometry appear separating media (phases) in which the heterogeneity of constituents is present. In this work the quantification of the interplay between irregular structures and surrounding heterogeneous distributions in the plane is made For a geometric set image and a mass distribution (measure) image supported in image, being image, the mass image gives account of the interplay between the geometric structure and the surrounding distribution. A computation method is developed for the estimation and corresponding scaling analysis of image, being image a fractal plane set of Minkowski dimension image and image a multifractal measure produced by random multiplicative cascades. The method is applied to natural and mathematical fractal structures in order to study the influence of both, the irregularity of the geometric structure and the heterogeneity of the distribution, in the scaling of image. Applications to the analysis and modeling of interplay of phases in environmental scenarios are given.

Computer simulation of random parckings for self-similar particle size distributions in soil and granular materials: porosity and pore size distribution

A 2D computer simulation method of random packings is applied to sets of particles generated by a self-similar uniparametric model for particle size distributions (PSDs) in granular media. The parameter p which controls the model is the proportion of mass of particles corresponding to the left half of the normalized size interval [0,1]. First the influence on the total porosity of the parameter p is analyzed and interpreted. It is shown that such parameter, and the fractal exponent of the associated power scaling, are efficient packing parameters, but this last one is not in the way predicted in a former published work addressing an analogous research in artificial granular materials. The total porosity reaches the minimum value for p = 0.6. Limited information on the pore size distribution is obtained from the packing simulations and by means of morphological analysis methods. Results show that the range of pore sizes increases for decreasing values of p showing also different shape in the volume pore size distribution. Further research including simulations with a greater number of particles and image resolution are required to obtain finer results on the hierarchical structure of pore space.

Genetic definition of a protein-splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution

Inteins are protein-splicing elements, most of which contain conserved sequence blocks that define a family of homing endonucleases. Like group I introns that encode such endonucleases, inteins are mobile genetic elements. Recent crystallography and computer modeling studies suggest that inteins consist of two structural domains that correspond to the endonuclease and the protein-splicing elements. To determine whether the bipartite structure of inteins is mirrored by the functional independence of the protein-splicing domain, the entire endonuclease component was deleted from the Mycobacterium tuberculosis recA intein. Guided by computer modeling studies, and taking advantage of genetic systems designed to monitor intein function, the 440-aa Mtu recA intein was reduced to a functional mini-intein of 137 aa. The accuracy of splicing of several mini-inteins was verified. This work not only substantiates structure predictions for intein function but also supports the hypothesis that, like group I introns, mobile inteins arose by an endonuclease gene invading a sequence encoding a small, functional splicing element.

Computer-based analysis of the binding steps in protein complex formation

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components—an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple “ball-and-stick” structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and Kds and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.

Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors

The telomerase enzyme is a potential therapeutic target in many human cancers. A series of potent inhibitors has been designed by computer modeling, which exploit the unique structural features of quadruplex DNA. These 3,6,9-trisubstituted acridine inhibitors are predicted to interact selectively with the human DNA quadruplex structure, as a means of specifically inhibiting the action of human telomerase in extending the length of single-stranded telomeric DNA. The anilino substituent at the 9-position of the acridine chromophore is predicted to lie in a third groove of the quadruplex. Calculated relative binding energies predict enhanced selectivity compared with earlier 3,6-disubstituted compounds, as a result of this substituent. The ranking order of energies is in accord with equilibrium binding constants for quadruplex measured by surface plasmon resonance techniques, which also show reduced duplex binding compared with the disubstituted compounds. The 3,6,9-trisubstututed acridines have potent in vitro inhibitory activity against human telomerase, with EC50 values of up to 60 nM.

A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes.

Several recent reports indicate that mobile elements are frequently found in and flanking many wild-type plant genes. To determine the extent of this association, we performed computer-based systematic searches to identify mobile elements in the genes of two "model" plants, Oryza sativa (domesticated rice) and Arabidopsis thaliana. Whereas 32 common sequences belonging to nine putative mobile element families were found in the noncoding regions of rice genes, none were found in Arabidopsis genes. Five of the nine families (Gaijin, Castaway, Ditto, Wanderer, and Explorer) are first described in this report, while the other four were described previously (Tourist, Stowaway, p-SINE1, and Amy/LTP). Sequence similarity, structural similarity, and documentation of past mobility strongly suggests that many of the rice common sequences are bona fide mobile elements. Members of four of the new rice mobile element families are similar in some respects to members of the previously identified inverted-repeat element families, Tourist and Stowaway. Together these elements are the most prevalent type of transposons found in the rice genes surveyed and form a unique collection of inverted-repeat transposons we refer to as miniature inverted-repeat transposable elements or MITEs. The sequence and structure of MITEs are clearly distinct from short or long interspersed nuclear elements (SINEs or LINEs), the most common transposable elements associated with mammalian nuclear genes. Mobile elements, therefore, are associated with both animal and plant genes, but the identity of these elements is strikingly different.

Computer speech synthesis: its status and prospects.

Computer speech synthesis has reached a high level of performance, with increasingly sophisticated models of linguistic structure, low error rates in text analysis, and high intelligibility in synthesis from phonemic input. Mass market applications are beginning to appear. However, the results are still not good enough for the ubiquitous application that such technology will eventually have. A number of alternative directions of current research aim at the ultimate goal of fully natural synthetic speech. One especially promising trend is the systematic optimization of large synthesis systems with respect to formal criteria of evaluation. Speech recognition has progressed rapidly in the past decade through such approaches, and it seems likely that their application in synthesis will produce similar improvements.

Repacking protein cores with backbone freedom: structure prediction for coiled coils.

Progress in homology modeling and protein design has generated considerable interest in methods for predicting side-chain packing in the hydrophobic cores of proteins. Present techniques are not practically useful, however, because they are unable to model protein main-chain flexibility. Parameterization of backbone motions may represent a general and efficient method to incorporate backbone relaxation into such fixed main-chain models. To test this notion, we introduce a method for treating explicitly the backbone motions of alpha-helical bundles based on an algebraic parameterization proposed by Francis Crick in 1953 [Crick, F. H. C. (1953) Acta Crystallogr. 6, 685-689]. Given only the core amino acid sequence, a simple calculation can rapidly reproduce the crystallographic main-chain and core side-chain structures of three coiled coils (one dimer, one trimer, and one tetramer) to within 0.6-A root-mean-square deviations. The speed of the predictive method [approximately 3 min per rotamer choice on a Silicon Graphics (Mountain View, CA) 4D/35 computer] permits it to be used as a design tool.

A study in the design of an arithmetic element for serial processing in a linear iterative structure /

Vita.

A graph-structure transformation model for picture parsing,

"COO-2118-0031."

On the structure and automorphisms of finite automata /

Issued also as thesis, University of Illinois.

Random generation of sentences from context free and context sensitive phrase structure grammars.

Bibliography: p. 67.