Abstract

There is a widely held perception that science today, under the impact of computer science, is on the verge of a revolutionary shift in paradigm. This perception has been elaborated in detail in a recent document: Towards 2020 Science published by Microsoft Research Cambridge, which has been prepared by 34 scientists of international repute. The report examines the value added aspects, involving new conceptual and technological tools, of computer science with respect to mathematical computations and computing power of computers. It goes on to suggest that these aspects make computer science ideally suited for getting embedded into the very methodology of science that is emerging today, particularly in the context of understanding complex multi component information-processing systems, as e. g. seen in the field of biological sciences. The proposition is Computer science is poised to become as fundamental to science, and in particular the natural sciences, as mathematics has become to science, and in particular the physical sciences. Borrowing liberally from the above document, this article reviews some of the advances that are taking place in natural sciences research, as a result of its nexus with computer science.

Abstract

We present gas phase quantum chemical studies on the metabolite binding interactions in two important purine riboswitches, the adenine and guanine riboswitches, at the B3LYP/6-31G(d,p) level of theory. In order to gain insights into the strucutral basis of their discriminative abilities of regulating gene expression, the structural properties and binding energies for the gas phase optimized geometries of the metabolite bound binding pocket are analyzed and compared with their respective crystal geometries. Kitaura-Morokuma analysis has been carried out to calculate and decompose the interaction energy into various components. NBO and AIM analysis has been carried out to understand the strength and nature of binding of the individual aptamer bases with their respective purine metabolites. The Y74 base, U in case of adenine riboswitch and C in case of guanine riboswitch constitutes the only differentiating element between the two binding pockets. As expected, with W:W cis G:C74 interaction contributing more than 50% of the total binding energy, the interaction energy for metabolite binding as calculated for guanine (-46.43 Kcal/mol) is nearly double compared to the corresponding value for that of adenine (-24.73 Kcal/mol) in the crystal context. Variations in the optimized geometries for different models and comparison of relative contribution to metabolite binding involving four conserved bases reveal the possible role of U47:U51 W:H trans pair in the conformational transition of the riboswitch from the metabolite free to metabolite bound state. Our results are also indicative of significant contributions from stacking and magnesium ion interactions toward cooperativity effects in metabolite recognition

Abstract

Schistosoma mansoni, a trematode parasite, which causes schistosomiasis and affects more than 200 million people worldwide, lives in an aerobic environment and therefore needs an effective redox mechanism for surviving reactive oxygen species from its host. Although, the host has two different redox systems: glutaredoxin and thioredoxin , the parasite has only one unique multifunctional enzyme, thioredoxin glutathione reductase (TGR) involving a fusion of two proteins, glutaredoxin (Grx) and thioredoxin reductase (TR), for performing all the redox activities. This dependence of S. mansoni on a single protein, TGR, for its protection from oxidative stress, makes it a promising drug target. Here, we describe a suitably validated, homology model for S. mansoni TGR (SmTGR), developed using both TR and Grx templates, functionally complete in the dimeric form with cofactors NADP(H) and FAD. Comparative analysis of substrate and inhibitor binding pockets of our model with crystal structures of parent TR as well as with that of glutathione reductase (GR), which is an essential component of the Grx system, appears to provide greater insight in to the functioning of TGR. This also augments recent observations reported on the basis of X-ray structure data on SmTGR monomer lacking the C-terminal selenocysteine tail. Keywords: Schistosoma mansoni; Thioredoxin glutathione reductase; Glutathione disulfide; Homology modeling; Docking

Abstract

Design Rule Checking (DRC) in VLSI design involves checking if a given VLSI layout satisfies a given set of rules, and reporting the violations if any. We propose data structures for reporting violations of the minimum extension rule in a query window of interest.

Abstract

Semantic annotation or tagging of images can greatly improve the accuracy and efficiency of image search engines. However, humans rarely annotate images as they find the task of image annotation boring and laborious despites its benefits in terms of search and retrieval. In this paper, we introduce a novel approach of luring users into image annotation: by embedding image annotation into a CAPTCHA design. A CAPTCHA is a standard security mechanism used by popular commercial websites to prevent automated programs from abusing the online services. Millions of users solve CAPTCHAs daily in order to access web content and services. We aim to utilize human effort spent in solving the CAPTCHA into a productive work of image annotation. We introduce iCAPTCHA, a user friendly and productive CAPTCHA design. Our premise is based on the human ability to recognize images and label them in proper categories. Each time a user solves an iCAPTCHA, he/she is helping to label images in proper categories which will in turn improve image search and retrieval.

Abstract

In the PSMT problem, a sender S and a receiver R are part of a distributed network and connected through n node disjoint paths, also called as wires among which at most t are controlled by an all powerful Byzantine adversary At. S has a message m, which S intends to send to R. The challenge is to design a protocol, such that at the end, R should correctly output m without any error (perfect reliability) and At should not get any information about m, what so ever, in information theoretic sense (perfect security). The problem of USMT is same as PSMT, except that R should output m with a small probability of error.Sayeed et al. [15] have given a PSMT protocol in an asynchronous network tolerating At, where S and R are connected by n = 2t + 1 wires. However, we show that their protocol does not provide perfect security. We then prove that in an asynchronous network, if all the n wires are directed from S to R, then any PSMT protocol tolerating At is possible iff n > 3t. Surprisingly, we further prove that even if all the n wires are bi-directional, then any PSMT protocol in asynchronous network tolerating At is possible iff n > 3t. This is quite interesting because for synchronous networks, by the results of Dolev et al. [6], if all the wires are unidirectional (directed from S to R), then PSMT tolerating At is possible iff n > 3t, where as if all the wires are bi-directional then PSMT tolerating At is possible iff n > 2t. This shows that synchrony of the network affects the connectivity requirement for PSMT protocols. However, we show that n > 2t wires are necessary and sufficient for the existence of any USMT protocol in asynchronous network tolerating At, irrespective of whether the n wires are unidirectional from S to R or the n wires are bi-directional.

Abstract

This paper proposes a method to cluster documents of variable length. The main idea is to apply (a) automatic identification of 1, 2, and 3 grams (To reduce the dependency on huge background vocabulary support or learning or complex probabilistic approach), (b) order them by some measure of relevance, which is developed with the help of Tf-Idf and Term-Weighting approach, and finally (c) use them (instead of bag of words based approach) to create vector space model and apply some known clustering methods i. e. Bisecting K-means, K-means, hierarchical method (single link) and Graph based method. Our experimental results with publicly available text dataset (Cogprints and NewsGroup20) show remarkable improvements in the performance of these clustering algorithms with this new approach.

Abstract

In this paper, we re-visit the problem of unconditionally secure message transmission (USMT) from a sender S to a receiver R, who are part of a distributed synchronous network, modeled as an arbitrary directed graph. Some of the intermediate nodes between S and R can be under the control of an adversary having unbounded computing power. Desmedt and Wang [4] have given the characterization of USMT in directed networks. However, in their model, the underlying network is abstracted as directed node disjoint paths (also called as wires/channels) between S and R, where the intermediate nodes are oblivious, message passing nodes and perform no other computation. In this work, we first show that the characterization of USMT given by Desmedt et.al [4] does not hold good for arbitrary directed networks, where the intermediate nodes can perform some computation, beside acting as message forwarding nodes. We then give the characterization of USMT in arbitrary directed networks, considering the entire network as a whole. As far our knowledge is concerned, this is the first ever characterization of USMT in arbitrary directed networks.

Abstract

Computing convex hull for a given set of points is one of the most explored problems in the area of computational geometry (CG). If the set of points is distributed among a set of parties who jointly wish to compute the convex hull, each party can send his points to every other party, and can then locally compute the hull using any of the existing algorithms in CG. However such an approach does not work if the parties wish to compute the convex hull securely, i.e., no party wishes to reveal any of his input points to any other party apart from those that are part of the answer. The problem of secure computation of convex hull for two parties was first introduced by Du and Atallah (NSPW '01). The first solution to the problem was given by Wang et. al(ARES '08). However, the proposed solution was based on well known algorithms for computing convex hull in CG which are proven to be sub-optimal. We propose a new solution for secure computation of convex hull with a considerable improvement in computational complexity. We further show how to extend our two-party protocol for the case of any number of parties.

Abstract

This paper examines the Lombard effect on the excitation fea-tures in speech production. These features correspond mostly to the acoustic features at sub segmental (