Role of feedback in mammalian vision: a new hypothesis and a computational model

This paper presents a novel hypothesis on the function of massive feedback pathways in mammalian visual systems. We propose that the cortical feature detectors compete not for the right to represent the output at a point, but for exclusive rights to abstract and represent part of the underlying input. Feedback can do this very naturally. A computational model that implements the above idea for the problem of line detection is presented and based on that we suggest a functional role for the thalamo-cortical loop during perception of lines. We show that the model successfully tackles the so called Cross problem. Based on some recent experimental results, we discuss the biological plausibility of our model. We also comment on the relevance of our hypothesis (on the role of feedback) to general sensory information processing and recognition. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

The restriction mapping problem revisited

In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction. In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n(2) log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n(4)) worst-case algorithm that can provably tolerate an absolute error of O(Delta/n) (where Delta is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule. Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest-the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al. (C) 2002 Elsevier Science (USA). All rights reserved.

Three-dimensional computational modeling of momentum, heat, and mass transfer in a laser surface alloying process

A three- dimensional, transient model is developed for studying heat transfer, fluid flow, and mass transfer for the case of a single- pass laser surface alloying process. The coupled momentum, energy, and species conservation equations are solved using a finite volume procedure. Phase change processes are modeled using a fixed-grid enthalpy-porosity technique, which is capable of predicting the continuously evolving solid- liquid interface. The three- dimensional model is able to predict the species concentration distribution inside the molten pool during alloying, as well as in the entire cross section of the solidified alloy. The model is simulated for different values of various significant processing parameters such as laser power, scanning speed, and powder feedrate in order to assess their influences on geometry and dynamics of the pool, cooling rates, as well as species concentration distribution inside the substrate. Effects of incorporating property variations in the numerical model are also discussed.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

Computational and experimental studies of fluid flow and heat transfer in a Calandria based reactor

CFD investigations are carried out to study the heat flux and temperature distribution in the calandria using a 3–Dimensional RANS code. Internal flow computations and experimental studies are carried out for a calandria embedded with a matrix of tubes working together as a reactor. Numerical investigations are carried on the Calandria reactor vessel with horizontal inlets and outlets located on top and the bottom to study the flow pattern and the associated temperature distribution. The computations have been carried out to simulate fluid flow and convective heat transfer for assigned near–to working conditions with different moderator injection rates and reacting heat fluxes. The results of computations provide an estimate of the tolerance bands for safe working limits for the heat dissipation at different working conditions by virtue of prediction of the hot spots in the calandria. The isothermal CFD results are validated by a set of experiments on a specially designed scaled model conducted over a range of flows and simulation parameters. The comparison of CFD results with experiments show good agreement.

Incentive Compatible Mechanisms for Resource Procurement in Computational Grids with Rational resource Providers

In a computational grid, the presence of grid resource providers who are rational and intelligent could lead to an overall degradation in the efficiency of the grid. In this paper, we design incentive compatible grid resource procurement mechanisms which ensure that the efficiency of the grid is not affected by the rational behavior of resource providers.In particular, we offer three elegant incentive compatible mechanisms for this purpose: (1) G-DSIC (Grid-Dominant Strategy Incentive Compatible) mechanism (2) G-BIC (Grid-Bayesian Nash Incentive Compatible) mechanism (3) G-OPT(Grid-Optimal) mechanism which minimizes the cost to the grid user, satisfying at the same time, (a) Bayesian incentive compatibility and (b) individual rationality. We evaluate the relative merits and demerits of the above three mechanisms using game theoretical analysis and numerical experiments.

Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts

Among the many different objectives of large scale structural genomics projects are expanding the protein fold space, enhancing understanding of a model or disease-related organism, and providing foundations for structure-based drug discovery. Systematic analysis of protein structures of Mycobacterium tuberculosis has been ongoing towards meeting some of these objectives. Indian participation in these efforts has been enthusiastic and substantial. The proteins of M. tuberculosis chosen for structural analysis by the Indian groups span almost all the functional categories. The structures determined by the Indian groups have led to significant improvement in the biochemical knowledge on these proteins and consequently have started providing useful insights into the biology of M. tuberculosis. Moreover, these structures form starting points for inhibitor design studies, early results of which are encouraging. The progress made by Indian structural biologists in determining structures of M. tuberculosis proteins is highlighted in this review. (C) 2011 Elsevier Ltd. All rights reserved.

Systems biology of tuberculosis

Systems biology seeks to study biological systems as a whole, by adopting an integrated approach to study and understand the function of biological systems, particularly, the response of such systems to various perturbations. In this article, we focus on the Indian efforts towards systems-level studies of Mycobacterium tuberculosis and its interaction with the host. Availability of a variety of genome-scale experimental data, providing first level `omics' descriptions of the pathogen, render it feasible to study it at a systems level. Various aspects of the pathogen, from metabolic pathways to protein-protein interaction networks have been modelled and simulated, while host-pathogen interactions have been studied experimentally using siRNA-based techniques. These studies have been useful in obtaining a global perspective of the pathogen and its interactions with the host in many ways. For example, significant insights have been gained about different aspects such as proteins essential for bacterial survival, proteins that are highly influential in the network, pathways that are highly connected, host factors responsible for maintaining the TB infection and key factors involved in autophagy and pathogenesis. A rational pipeline developed for drug target identification incorporating analyses of the interactome, reactome, genome, pocketome and the transcriptome is discussed. Finally, exploring host factors as drug targets and insights about the emergence of drug resistance are also discussed. (C) 2011 Elsevier Ltd. All rights reserved.