A standard reference frame for the description of Nucleic Acid Base-Pair Geometry

A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to con¯icting interpretations of the same structure.1 For example, parts of a structure that appear ``normal'' according to one computational scheme may be highly unusual according to another and vice versa. It is thus dif®cult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures

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.

Influence of the Blade Hub Geometry on the Performance of Low-Head Axial Flow Turbines

The influence of geometric parameters, such as blade profile and hub geometry on axial flow turbines for micro hydro application remains poorly characterized. This paper first introduces a holistic theoretical model for studying the hydraulic phenomenon resulting from geometric modification to the blades. It then describes modification carried out on two runner stages, of which one has untwisted blades and the other has twisted blades obtained by modifying the inlet hub. The experimental results showed that the performance of the untwisted blade runner was satisfactory with a maximum efficiency of 68%. However, positive effects of twisted blades were clearly evident with an efficiency rise of more than 2%. This study also looks into the possible limitations of the model and suggests the extension of the experimental work and the use of computational tools to conduct a progressive validation of all experimental findings, especially on the flow physics within the hub region and the slip phenomena. The paper finally underlines the importance of developing a standardization philosophy for axial flow turbines specific for micro hydro requirements. DOI:10.1061/(ASCE)EY.1943-7897.0000060. (C) 2012 American Society of Civil Engineers.

Air oxygenation chemistry of 4-TBC catalyzed by chloro bridged dinuclear copper(II) complexes of pyrazole based tridentate ligands: synthesis, structure, magnetic and computational studies

Four dinuclear bis(mu-Cl) bridged copper(II) complexes, Cu-2(mu-Cl)(2)(L-X)(2)](ClO4)(2) (L-X = N,N-bis(3,5-dimethylpyrazole-1-yl)-methyl]benzylamine with X = H(1), OMe(2), Me(3) and Cl(4)), have been synthesized and characterized by the single crystal X-ray diffraction method. In these complexes, each copper(II) center is penta-coordinated with square-pyramidal geometry. In addition to the tridentate L-X ligand, a chloride ion occupies the last position of the square plane. This chloride ion is also bonded to the neighboring Cu(II) site in its axial position forming an SP-I dinuclear Cu(II) unit that exhibits small intramolecular ferromagnetic interactions and supported by DFT calculations. The complexes 1-3 exhibit methylmonooxygenase (pMMO) behaviour and oxidise 4-tert-butylcatechol (4-TBCH2) with molecular oxygen in MeOH or MeCN to 4-tert-butyl-benzoquinone (4-TBQ), 5-methoxy-4-tert-butyl-benzoquinone (5-MeO-4-TBQ) as the major products along with 6,6'-Bu-t-biphenyl-3,4,3',4'-tetraol and others as minor products. These are further confirmed by ESI- and FAB-mass analyses. A tentative catalytic cycle has been framed based on the mass spectral analysis of the products and DFT calculations on individual intermediates that are energetically feasible.

Computational fluid dynamics simulation of open ended thermoacoustic prime mover with straight and tapered resonator

A thermoacoustic refrigerator driven by a thermoacoustic primemover is an effective way to produce durable and long lasting refrigeration due to high reliability, no exotic materials, and no moving parts. Resonator geometry is also one of the important factors that influence the performance of a thermoacoustic prime mover, namely, frequency. Computational fluid dynamics simulation of performance comparison of thermoacoustic prime mover with a straight and tapered resonator is chosen for the present study under an identical stack condition with the air as a working fluid. The frequency and pressure amplitude of oscillations obtained from simulation results were found to be more in the tapered resonator than the straight resonator. Apart from computational fluid dynamics simulation, the simulation studies have also been conducted using design environment for low-amplitude thermoacoustic energy conversion, which predicts the performance of thermoacoustic primemover comparatively well. Simulation results from computational fluid dynamics and design environment for low-amplitude thermoacoustic energy conversion were compared and found to be matching well, representing the good validity of computational fluid dynamics modeling.

A study on the usefulness of Support Vector Machines for the realtime computational simulation of soft biological organs

Realistic and realtime computational simulation of soft biological organs (e.g., liver, kidney) is necessary when one tries to build a quality surgical simulator that can simulate surgical procedures involving these organs. Since the realistic simulation of these soft biological organs should account for both nonlinear material behavior and large deformation, achieving realistic simulations in realtime using continuum mechanics based numerical techniques necessitates the use of a supercomputer or a high end computer cluster which are costly. Hence there is a need to employ soft computing techniques like Support Vector Machines (SVMs) which can do function approximation, and hence could achieve physically realistic simulations in realtime by making use of just a desktop computer. Present work tries to simulate a pig liver in realtime. Liver is assumed to be homogeneous, isotropic, and hyperelastic. Hyperelastic material constants are taken from the literature. An SVM is employed to achieve realistic simulations in realtime, using just a desktop computer. The code for the SVM is obtained from [1]. The SVM is trained using the dataset generated by performing hyperelastic analyses on the liver geometry, using the commercial finite element software package ANSYS. The methodology followed in the present work closely follows the one followed in [2] except that [2] uses Artificial Neural Networks (ANNs) while the present work uses SVMs to achieve realistic simulations in realtime. Results indicate the speed and accuracy that is obtained by employing the SVM for the targeted realistic and realtime simulation of the liver.

Dynamics of ribonuclease A and ribonuclease S: Computational and experimental studies

RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNaseS and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model, According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.

Void Geometry Driven Spin Crossover in Zeolite-Encapsulated Cobalt Tris(bipyridyl) Complex Ion

The cobalt(II) tris(bipyridyl) complex ion encapsulated in zeolite-Y supercages exhibits a thermally driven interconversion between a low-spin and a high-spin state-a phenomenon not observed for this ion either in solid state or in solution. From a comparative study of the magnetism and optical spectroscopy of the encapsulated and unencapsulated complex ion, supported by molecular modeling, such spin behavior is shown to be intramolecular in origin. In the unencapsulated or free state, the [Co(bipy)(3)](2+) ion exhibits a marked trigonal prismatic distortion, but on encapsulation, the topology of the supercage forces it to adopt a near-octahedral geometry. An analysis using the angular overlap ligand field model with spectroscopically derived parameters shows that the geometry does indeed give rise to a low-spin ground state, and suggests a possible scenario for the spin state interconversion.

Collision-Geometry-Based Pulsed Guidance Law for Exoatmospheric Interception

No abstract is available.

Geometry Of Proline And Hydroxyproline .1. An Analysis Of X-Ray Crystal-Structure Data

We have carried out an analysis of crystal structure data on prolyl and hydroxyprolyl moieties in small molecules. The flexibility of the pyrrolidine ring due to the pyramidal character of nitrogen has been defined in terms of two projection angles δ1 and δ2. The distribution of these parameters in the crystal structures is found to be consistent with results of the energy calculations carried out on prolyl moieties in our laboratory.

Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

A computational algorithm for the verification of tautologies in propositional calculus

A computational algorithm (based on Smullyan's analytic tableau method) that varifies whether a given well-formed formula in propositional calculus is a tautology or not has been implemented on a DEC system 10. The stepwise refinement approch of program development used for this implementation forms the subject matter of this paper. The top-down design has resulted in a modular and reliable program package. This computational algoritlhm compares favourably with the algorithm based on the well-known resolution principle used in theorem provers.

In quest of a reliable and efficient computational test for detection of isomorphism in kinematic chains

The test based on comparison of the characteristic coefficients of the adjancency matrices of the corresponding graphs for detection of isomorphism in kinematic chains has been shown to fail in the case of two pairs of ten-link, simple-jointed chains, one pair corresponding to single-freedom chains and the other pair corresponding to three-freedom chains. An assessment of the merits and demerits of available methods for detection of isomorphism in graphs and kinematic chains is presented, keeping in view the suitability of the methods for use in computerized structural synthesis of kinematic chains. A new test based on the characteristic coefficients of the “degree” matrix of the corresponding graph is proposed for detection of isomorphism in kinematic chains. The new test is found to be successful in the case of a number of examples of graphs where the test based on characteristic coefficients of adjancency matrix fails. It has also been found to be successful in distinguishing the structures of all known simple-jointed kinematic chains in the categories of (a) single-freedom chains with up to 10 links, (b) two-freedom chains with up to 9 links and (c) three-freedom chains with up to 10 links.

The mean geometry of the peptide unit from crystal structure data

The average dimensions of the peptide unit have been obtained from the data reported in recent crystal structure analyses of di- and tripeptides. The bond lengths and bond angles agree with those in common use, except for the bond angle C---N---H, which is about 4° less than the accepted value, and the angle C2α---N---H which is about 4° more. The angle τ (Cα) has a mean value of 114° for glycyl residues and 110° for non-glycyl residues. Attention is directed to these mean values as observed in crystal structures, as they are relevant for model building of peptide chain structures.