sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

Computational Fluid Dynamics in Combustion

Computational fluid dynamics has reached a stage where flow field in practical situation can be predicted to aid the design and to probe into the fundamental flow physics to understand and resolve the issues in fundamental fluid mechanics The study examines the computation of reacting flows After exploring the conservation equations for species and energy, the methods of closing the reaction rate terms in turbulent flow have been examined briefly Two cases of computation where combustion-flow interaction plays important role, have been discussed to illustrate the computational aspects and the physical insight that can be gained by the reacting flow computation

A study of symbolic processing and computational aspects in helicopter dynamics

Even research models of helicopter dynamics often lead to a large number of equations of motion with periodic coefficients; and Floquet theory is a widely used mathematical tool for dynamic analysis. Presently, three approaches are used in generating the equations of motion. These are (1) general-purpose symbolic processors such as REDUCE and MACSYMA, (2) a special-purpose symbolic processor, DEHIM (Dynamic Equations for Helicopter Interpretive Models), and (3) completely numerical approaches. In this paper, comparative aspects of the first two purely algebraic approaches are studied by applying REDUCE and DEHIM to the same set of problems. These problems range from a linear model with one degree of freedom to a mildly non-linear multi-bladed rotor model with several degrees of freedom. Further, computational issues in applying Floquet theory are also studied, which refer to (1) the equilibrium solution for periodic forced response together with the transition matrix for perturbations about that response and (2) a small number of eigenvalues and eigenvectors of the unsymmetric transition matrix. The study showed the following: (1) compared to REDUCE, DEHIM is far more portable and economical, but it is also less user-friendly, particularly during learning phases; (2) the problems of finding the periodic response and eigenvalues are well conditioned.

A simple computational model for predicting .pi.-facial selectivity in reductions of sterically unbiased ketones. Relative importance of electrostatic and orbital interactions

Various factore controlling the preferred facial selectivity in the reductions of a number of sterically unbiased ketones have been evaluated using a semiempirical MO procedure. MNDO optimized geometries do not reveal any significant ground-state distortions which can be correlated with the observed face selectivities. Electrostatic effecta due to an approaching reagent were modeled by placing a test negative charge at a fixed distance from the carbonyl carbon on each of the two faces. A second series of calculations was carried out using the hydride ion as a test nucleophile. The latter calculations effectively include orbital interactions involving the u and u* orbitals of the newly formed bond in the reaction. The computed energy differences with the charge model are generally much larger compared to those with the hydride ion. However, both models lead to predictions which are qualitatively consistent with the experimentally determined facial preferences for most of the systems. Thus, electrostatic interactions between the nucleophile and the substrate seem to effectively determine the face selectivities in these molecules. However, there are a few exceptions in which orbital interactions are found to contribute significantly and occasionally reverse the preference dictated by electrostatic effecta. The remarkable succew of the hydride model calculations, in spite of retaining the unperturbed geometries of the substrates, points to the unimportance of torsional effeds and orbital distortions associated with the pyramidalized carbonyl unit in the transition state in most of the substrates considered. Additional experimental results are reported which provide useful calibration for the present computational approach.

Selectivity in Garratt-Braverman Cyclization: An Experimental and Computational Study

Bispropargyl sulfones equipped with aromatic rings of dissimilar nature were synthesized. Under basic conditions, these sulfones isomerized to the bisallenic sulfones, creating a competitive scenario between two alternate Garratt-Braverman (GB) cyclization pathways. The observed product distribution ruled out the involvement of any ionic intermediate and supported the diradical mechanism with greater involvement of the electron-rich aromatic ring via the more nucleophilic radical. DFT-based calculations supported the diradical mechanism along with the observed selectivity.

Theoretical and Computational Analysis of Static and Dynamic Anomalies in Water-DMSO Binary Mixture at Low DMSO Concentrations

Experiments have repeatedly observed both thermodynamic and dynamic anomalies in aqueous binary mixtures, surprisingly at low solute concentration. Examples of such binary mixtures include water-DMSO, water-ethanol, water-tertiary butyl alcohol (TBA), and water-dioxane, to name a few. The anomalies have often been attributed to the onset of a structural transition, whose nature, however, has been left rather unclear. Here we study the origin of such anomalies using large scale computer simulations and theoretical analysis in water-DMSO binary mixture. At very low DMSO concentration (below 10%), small aggregates of DMSO are solvated by water through the formation of DMSO-(H2O)(2) moieties. As the concentration is increased beyond 10-12% of DMSO, spanning clusters comprising the same moieties appear in the system. Those clusters are formed and stabilized not only through H-bonding but also through the association of CH3 groups of DMSO. We attribute the experimentally observed anomalies to a continuum percolation-like transition at DMSO concentration X-DMSO approximate to 12-15%. The largest cluster size of CH3-CH3 aggregation clearly indicates the formation of such percolating clusters. As a result, a significant slowing down is observed in the decay of associated rotational auto time correlation functions (of the S = O bond vector of DMSO and O-H bond vector of water). Markedly unusual behavior in the mean square fluctuation of total dipole moment again suggests a structural transition around the same concentration range. Furthermore, we map our findings to an interacting lattice model which substantiates the continuum percolation model as the reason for low concentration anomalies in binary mixtures where the solutes involved have both hydrophilic and hydrophobic moieties.

Recognition of Polycyclic Aromatic Hydrocarbons and Their Derivatives by the 1,3-Dinaphthalimide Conjugate of Calix4]arene: Emission, Absorption, Crystal Structures, and Computational Studies

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants as well as well-known carcinogens. Therefore, it is important to develop an effective receptor for the detection and quantification of such molecules in solution. In view of this, a 1,3-dinaphthalimide derivative of calix4]arene (L) has been synthesized and characterized, and the structure has been established by single crystal XRD. In the crystal lattice, intermolecular arm-to-arm pi center dot center dot center dot pi overlap dominates and thus L becomes a promising receptor for providing interactions with the aromatic species in solution, which can be monitored by following the changes that occur in its fluorescence and absorption spectra. On the basis of the solution studies carried out with about 17 derivatives of the aromatic guest molecular systems, it may be concluded that the changes that occur in the fluorescence intensity seem to be proportional to the number of aromatic rings present and thus proportional to the extent of pi center dot center dot center dot pi interaction present between the naphthalimide moieties and the aromatic portion of the guest molecule. Though the nonaromatic portion of the guest species affects the fluorescence quenching, the trend is still based on the number of rings present in these. Four guest aldehydes are bound to L with K-ass of 2000-6000 M-1 and their minimum detection limit is in the range of 8-35 mu M. The crystal structure of a naphthaldehyde complex, L.2b, exhibits intermolecular arm-to-arm as well as arm-to-naphthaldehyde pi center dot center dot center dot pi interactions. Molecular dynamics studies of L carried out in the presence of aromatic aldehydes under vacuum as well as in acetonitrile resulted in exhibiting interactions observed in the solid state and hence the changes observed in the fluorescence and absorption spectra are attributable for such interactions. Complex formation has also been delineated through ESI MS studies. Thus L is a promising receptor that can recognize PAHs by providing spectral changes proportional to the aromatic conjugation of the guest and the extent of aromatic pi center dot center dot center dot pi interactions present between L and the guest.

Diastereospecific Coupling of Imines by Low-Valent Titanium: An Experimental and Computational Study

The reaction of phenylsilane (PhSiH3) and titanium(IV) isopropoxide Ti(OiPr)(4)] generates low-valent titanium alkoxides that reduce and reductively couple imines. The C-C coupling reaction is diastereospecific, with exclusive formation of the (+/-)-isomer. The yield is dependent on the concentration of titanium(IV) isopropoxide used. Using imines with varying electronic demand revealed that the coupling is most efficient for unsubstituted imines. The involvement of a trimeric titanium biradical species is invoked to explain the observed concentration dependence and diastereospecificity in the reaction. Multilayer ONIOM (''our own n-layered integrated molecular orbital and molecular mechanics'') calculations were carried out on the plausible intermediates involved by using the Guassian 09 suite of programs. Formation of the trimeric biradical species leading to the formation of the (+/-)-isomer is more favored than formation of the trimeric biradical species, which leads to the meso-isomer. Similar calculations with dimeric intermediates do not predict the (+/-)-selectivity. Mass spectral analysis of the reaction mixture indicates the presence of a trimeric titanium alkoxide species.

Particle filters for structural system identification using multiple test and sensor data: A combined computational and experimental study

The problem of structural system identification when measurements originate from multiple tests and multiple sensors is considered. An offline solution to this problem using bootstrap particle filtering is proposed. The central idea of the proposed method is the introduction of a dummy independent variable that allows for simultaneous assimilation of multiple measurements in a sequential manner. The method can treat linear/nonlinear structural models and allows for measurements on strains and displacements under static/dynamic loads. Illustrative examples consider measurement data from numerical models and also from laboratory experiments. The results from the proposed method are compared with those from a Kalman filter-based approach and the superior performance of the proposed method is demonstrated. Copyright (C) 2009 John Wiley & Sons, Ltd.

Metathesis of carbon dioxide and phenyl isocyanate catalysed by group(IV) metal alkoxides: An experimental and computational study

The insertion reactions of zirconium(IV) n-butoxide and titanium(IV) n-butoxide with a heterocumulene like carbodiimide, carbon dioxide or phenyl isocyanate are compared. Both give an intermediate which carries out metathesis at elevated temperatures by inserting a second heterocumulene in a head-to-head fashion. The intermediate metallacycle extrudes a new heterocumulene, different from the two that have inserted leading to metathesis. As the reaction is reversible, catalytic metathesis is feasible. In stoichiometric reactions heterocumulene insertion, metathesis and metathesis cum insertion products are observed. However, catalytic amounts of the metal alkoxide primarily led to metathesis products. It is shown that zirconium alkoxides promote catalytic metathesis (isocyanates, carbon dioxide) more efficiently than the corresponding titanium alkoxide. The difference in the metathetic activity of these alkoxides has been explained by a computational study using model complexes Ti(OMe)(4) (1bTi) and Zr(OMe)(4) (1bZr). The computation was carried out at the B3LYP/LANL2DZ level of theory.

Enhancement in Bath Mixing and Plume area in a New Degassing Process - A Computational Fluid Dynamic Study

Reaction between the various species in slag and metal phase is usually mass transfer controlled. There have been continuous efforts to increase the reaction efficiency in slag-metal system, especially during decarburization of steel to produce the ultra low carbon steel (ULCS) in secondary steelmaking. It has been found that the surface reaction is a dominant factor in the final stage of decarburization. In the initial stage, the inner site reaction is major factor in the refining process. The mixing of bath affects the later reaction. However, the former reaction (surface reaction) is affected by the plume size area at the top of the metal surface. Therefore, a computational study has been made to understand the fluid dynamics of a new secondary steelmaking process called Revolutionary Degasser Activator (REDA) to study the bath mixing and plume area. REDA process has been considered as it is claimed that this process can reduce the carbon content in steel below 10ppm in a less time than the other existing processes such as RH and Tank degasser. This study shows that both bath mixing and plume area are increased in REDA process facilitating it to give the desired carbon content in less time. Qualitative comments are made on slag-metal reaction system based on this finding.

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.

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.