Computation-Based Reliability Analysis in Real Time Applications

Reliability analysis for computing systems in aerospace applications must account for actual computations the system performs in the use environment. This paper introduces a theoretical nonhomogeneous Markov model for such applications.

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

Performance analysis of subspace based method for source localization in shallow water

The present paper aims at studying the performance characteristics of a subspace based algorithm for source localization in shallow water such as coastal water. Specifically, we study the performance of Multi Image Subspace Algorithm (MISA). Through first-order perturbation analysis and computer simulation it is shown that MISA is unbiased and statistically efficient. Further, we bring out the role of multipaths (or images) in reducing the error in the localization. It is shown that the presence of multipaths is found to improve the range and depth estimates. This may be attributed to the increased curvature of the wavefront caused by interference from many coherent multipaths.

The effect of temperature on the surface tension and adsorption functions of the Fe-S-O melts - an analysis based on interaction parameters

The present investigation analyses the thermodynamic behaviour of the surfaces and adsorption as a function of temperature and composition in the Fe-S-O melts based on the Butler's equations. The calculated-values of the surface tensions exhibit an elevation or depression depending on the type of the added solute at a concentration which coincides with that already present in the system. Generally, the desorption of the solutes as a function of temperature results in an initial increase followed by a decrease in the values of the surface tension. The observations are analyzed based on the surface interaction parameters which are derived in the present research.

Physics based basis function for vibration analysis of high speed rotating beams

The natural frequencies of continuous systems depend on the governing partial differential equation and can be numerically estimated using the finite element method. The accuracy and convergence of the finite element method depends on the choice of basis functions. A basis function will generally perform better if it is closely linked to the problem physics. The stiffness matrix is the same for either static or dynamic loading, hence the basis function can be chosen such that it satisfies the static part of the governing differential equation. However, in the case of a rotating beam, an exact closed form solution for the static part of the governing differential equation is not known. In this paper, we try to find an approximate solution for the static part of the governing differential equation for an uniform rotating beam. The error resulting from the approximation is minimized to generate relations between the constants assumed in the solution. This new function is used as a basis function which gives rise to shape functions which depend on position of the element in the beam, material, geometric properties and rotational speed of the beam. The results of finite element analysis with the new basis functions are verified with published literature for uniform and tapered rotating beams under different boundary conditions. Numerical results clearly show the advantage of the current approach at high rotation speeds with a reduction of 10 to 33% in the degrees of freedom required for convergence of the first five modes to four decimal places for an uniform rotating cantilever beam.

A Gradient-Based Comparison Measure for Visual analysis of Multifield Data

We introduce a multifield comparison measure for scalar fields that helps in studying relations between them. The comparison measure is insensitive to noise in the scalar fields and to noise in their gradients. Further, it can be computed robustly and efficiently. Results from the visual analysis of various data sets from climate science and combustion applications demonstrate the effective use of the measure.

DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

A Simulation Based Study and Analysis of Double Gate Tunnel FET Performance for Low Stand-By Power Applications

The conventional metal oxide semiconductor field effect transistor (MOSFET)may not be suitable for future low standby power (LSTP) applications due to its high off-state current as the sub-threshold swing is theoretically limited to 60mV/decade. Tunnel field effect transistor (TFET) based on gate controlled band to band tunneling has attracted attention for such applications due to its extremely small sub-threshold swing (much less than 60mV/decade). This paper takes a simulation approach to gain some insight into its electrostatics and the carrier transport mechanism. Using 2D device simulations, a thorough study and analysis of the electrical parameters of the planar double gate TFET is performed. Due to excellent sub-threshold characteristics and a reverse biased structure, it offers orders of magnitude less leakage current compared to the conventional MOSFET. In this work, it is shown that the device can be scaled down to channel lengths as small as 30 nm without affecting its performance. Also, it is observed that the bulk region of the device plays a major role in determining the sub-threshold characteristics of the device and considerable improvement in performance (in terms of ION/IOFF ratio) can be achieved if the thickness of the device is reduced. An ION/IOFF ratio of 2x1012 and a minimum point sub-threshold swing of 22mV/decade is obtained.

Analysis of a Novel MOEM Race Track Resontor based Vibration Sensor

In this paper we analyze a novel Micro Opto Electro Mechanical Systems (MOEMS) race track resonator based vibration sensor. In this vibration sensor the straight portion of a race track resonator is located at the foot of the cantilever beam with proof mass. As the beam deflects due to vibration, stress induced refractive change in the waveguide located over the beam lead to the wavelength shift providing the measure of vibration. A wavelength shift of 3.19 pm/g in the range of 280 g for a cantilever beam of 1750μm×450m×20μmhas been obtained. The maximum acceleration (breakdown) for these dimensions is 2900g when a safety factor of 2 is taken into account. Since the wavelength of operation is around 1.55μm hybrid integration of source and detector is possible on the same substrate. Also it is less amenable to noise as wavelength shift provides the sensor signal. This type of sensors can be used for aerospace application and other harsh environments with suitable design.