The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

ICADA: Intelligent computer aided defect analysis for castings

An intelligent computer aided defect analysis (ICADA) system, based on artificial intelligence techniques, has been developed to identify design, process or material parameters which could be responsible for the occurrence of defective castings in a manufacturing campaign. The data on defective castings for a particular time frame, which is an input to the ICADA system, has been analysed. It was observed that a large proportion, i.e. 50-80% of all the defective castings produced in a foundry, have two, three or four types of defects occurring above a threshold proportion, say 10%. Also, a large number of defect types are either not found at all or found in a very small proportion, with a threshold value below 2%. An important feature of the ICADA system is the recognition of this pattern in the analysis. Thirty casting defect types and a large number of causes numbering between 50 and 70 for each, as identified in the AFS analysis of casting defects-the standard reference source for a casting process-constituted the foundation for building the knowledge base. Scientific rationale underlying the formation of a defect during the casting process was identified and 38 metacauses were coded. Process, material and design parameters which contribute to the metacauses were systematically examined and 112 were identified as rootcauses. The interconnections between defects, metacauses and rootcauses were represented as a three tier structured graph and the handling of uncertainty in the occurrence of events such as defects, metacauses and rootcauses was achieved by Bayesian analysis. The hill climbing search technique, associated with forward reasoning, was employed to recognize one or several root causes.

Real-time Computer Simulation of Three Dimensional Elastostatics using the Finite Point Method

Real-time simulation of deformable solids is essential for some applications such as biological organ simulations for surgical simulators. In this work, deformable solids are approximated to be linear elastic, and an easy and straight forward numerical technique, the Finite Point Method (FPM), is used to model three dimensional linear elastostatics. Graphics Processing Unit (GPU) is used to accelerate computations. Results show that the Finite Point Method, together with GPU, can compute three dimensional linear elastostatic responses of solids at rates suitable for real-time graphics, for solids represented by reasonable number of points.

Open-source tools for enhancing full-text searching of OPACs Use of Koha, Greenstone and Fedora

Purpose - There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text searching. Most of the available open-source digital library software facilitates indexing and searching of full-text documents in different formats. This paper makes an effort to enable full-text search features in the widely used open-source library automation package Koha, by integrating it with two open-source digital library software packages, Greenstone Digital Library Software (GSDL) and Fedora Generic Search Service (FGSS), independently. Design/methodology/approach - The implementation is done by making use of the Search and Retrieval by URL (SRU) feature available in Koha, GSDL and FGSS. The full-text documents are indexed both in Koha and GSDL and FGSS. Findings - Full-text searching capability in Koha is achieved by integrating either GSDL or FGSS into Koha and by passing an SRU request to GSDL or FGSS from Koha. The full-text documents are indexed both in the library automation package (Koha) and digital library software (GSDL, FGSS) Originality/value - This is the first implementation enabling the full-text search feature in a library automation software by integrating it into digital library software.

Translational and rotational motion in molecular liquids: A computer simulation study of Lennard-Jones ellipsoids

In order to understand the translational and rotational motion in dense molecular liquids, detailed molecular dynamics simulations of Lennard-Jones ellipsoids have been carried out for three different values of the aspect ratio kappa. For ellipsoids with an aspect ratio equal to 2, the product of the translational diffusion coefficient (D-T) and the average orientational correlation time of the l-th rank harmonics (tau(lR)), converges to a nearly constant value at high density. Surprisingly, this density independent value of D-T tau(lR) is within 5% of the hydrodynamic prediction with the slip boundary condition. This is despite the fact that both D-T and tau(lR) themselves change nearly by an order of magnitude in the density range considered, and the rotational correlation function itself is strongly nonexponential. For small aspect ratios (kappa less than or equal to 1.5), the rotational correlation function remains largely Gaussian even at a very large density, while for a large aspect ratio (kappa greater than or equal to 3), the transition to the nematic liquid-crystalline phase precludes the hydrodynamic regime. Thus, the rotational dynamics of ellipsoids show great sensitivity to the aspect ratio. At low density, tau(lR) goes through a minimum value, indicating the role of interactions in enhancing the rate of orientational relaxation. (C) 1997 American Institute of Physics. [S0021-9606(97)50142-5].

Computer-Based Design Synthesis Research: An Overview

One of the hallmarks of engineering design is the design synthesis phase where the creativity of the designer most prominently comes into play as solutions are generated to meet underlying needs. Over the past decades, methodologies for generating concepts and design solutions have matured to the point that computation-based synthesis provides a means to explore a wider variety of solutions and take over more tedious design tasks. This paper reviews advances in function-based, grammar-based, and analogy-based synthesis approaches and their contributions to computational design synthesis research in the last decade. DOI: 10.1115/1.3593409]

A Flexure-based Deployable Stereo Vision Mechanism and Temperature and Force Sensors for Laparoscopic Tools

This paper presents concepts, designs, and working prototypes of enhanced laparoscopic surgical tools. The enhancements are in equipping the tool with force and temperature sensing as well as image acquisition for stereo vision. Just as the pupils of our eyes are adequately spaced out and the distance between them is adjustable, two minute cameras mounted on a mechanism in our design can be moved closer or farther apart inside the inflated abdomen during the surgery. The cameras are fitted to a deployable mechanism consisting of flexural joints so that they can be inserted through a small incision and then deployed and moved as needed.A temperature sensor and a force sensor are mounted on either of the gripping faces of the surgical grasping tool to measure the temperature and gripping force, which need to be controlled for safe laparoscopic surgery. The sensors are small enough and hence they do not cause interference during surgery and insertion.Prototyping and working of the enhanced laparoscopic tool are presented with details

Java Memory Model aware Software validation

The Java Memory Model (JMM) provides a semantics of Java multithreading for any implementation platform. The JMM is defined in a declarative fashion with an allowed program execution being defined in terms of existence of "commit sequences" (roughly, the order in which actions in the execution are committed). In this work, we develop OpMM, an operational under-approximation of the JMM. The immediate motivation of this work lies in integrating a formal specification of the JMM with software model checkers. We show how our operational memory model description can be integrated into a Java Path Finder (JPF) style model checker for Java programs.

Structural Alignment based Kernels for Protein Structure Classification

Structural alignments are the most widely used tools for comparing proteins with low sequence similarity. The main contribution of this paper is to derive various kernels on proteins from structural alignments, which do not use sequence information. Central to the kernels is a novel alignment algorithm which matches substructures of fixed size using spectral graph matching techniques. We derive positive semi-definite kernels which capture the notion of similarity between substructures. Using these as base more sophisticated kernels on protein structures are proposed. To empirically evaluate the kernels we used a 40% sequence non-redundant structures from 15 different SCOP superfamilies. The kernels when used with SVMs show competitive performance with CE, a state of the art structure comparison program.

Real-time Computer Simulation of Three Dimensional Elastostatics using the Finite Point Method

Real-time simulation of deformable solids is essential for some applications such as biological organ simulations for surgical simulators. In this work, deformable solids are approximated to be linear elastic, and an easy and straight forward numerical technique, the Finite Point Method (FPM), is used to model three dimensional linear elastostatics. Graphics Processing Unit (GPU) is used to accelerate computations. Results show that the Finite Point Method, together with GPU, can compute three dimensional linear elastostatic responses of solids at rates suitable for real-time graphics, for solids represented by reasonable number of points.