A Model of Anomalous Enzyme-Catalyzed Gel Degradation Kinetics

We show that a model of target location involving n noninteracting particles moving subdiffusively along a line segment (a generalization of a model introduced by Sokolov et al. [Biophys. J. 2005, 89, 895.]) provides a basis for understanding recent experiments by Pelta et al. [Phys. Rev. Lett. 2007, 98, 228302.] on the kinetics of diffusion-limited gel degradation. These experiments find that the time t(c) taken by the enzyme thermolysin to completely hydrolyze a gel varies inversely as roughly the 3/2 power of the initial enzyme concentration [E]. In general, however, this time would be expected to vary either as [E](-1) or as [E](-2), depending on whether the Brownian diffusion of the enzyme to the site of cleavage took place along the network chains (1-d diffusion) or through the pore spaces (3-d diffusion). In our model, the unusual dependence of t(c) on [E] is explained in terms of a reaction-diffusion equation that is formulated in terms of fractional rather than ordinary time derivatives.

A new approach for simple and rapid shape measurement of objects with surface discontinuities

A new approach for unwrapping phase maps, obtained during the measurement of 3-D surfaces using sinusoidal structured light projection technique, is proposed. "Takeda's method" is used to obtain the wrapped phase map. Proposed method of unwrapping makes use of an additional image of the object captured under the illumination of a specifically designed color-coded pattern. The new approach demonstrates, for the first time, a method of producing reliable unwrapping of objects even with surface discontinuities from a single-phase map. It is shown to be significantly faster and reliable than temporal phase unwrapping procedure that uses a complete exponential sequence. For example, if a measurement with the accuracy obtained by interrogating the object with S fringes in the projected pattern is carried out with both the methods, new method requires only 2 frames as compared to (log(2)S +1) frames required by the later method.

Carbohydrate binding specificity of the basic lectin from winged bean (Psophocarpus tetragonolobus)

The carbohydrate binding specificity of the basic lectin from winged bean (Psophocarpus tetragonolobus) was investigated by quantitative precipitin analysis using blood group A, B, H, Le and I substances and by precipitation inhibition with various mono- and oligosaccharides. The lectin precipitated best with A1 substances and moderately with B and A2 substances, but not with H or Le substances. Inhibition assays of lectin-blood group A1 precipitation demonstration that A substance-derived oligosaccharides having the common structure: d-Ga1NAcα(1 → 3)d-Gal-(β1 → Image ) to a d-Glc, were the best inhibitors and about 8 and 4 times more active than d-Ga1NAc and d-Ga1NAcα(1 → 3)d-Ga1, respectively. A difucosyl A-specific oligosaccharide (A-penta), a monofucosyl (A-tetra) and a non-fucosyl containing (A5 II) oligosaccharide, d-Ga1NAcα(1 → 3)d-Ga1β(1 → 3)d-G1cNAc, had almost the same reactivity, suggesting that the fucose linked to the sub-terminal d-Ga1 or to the third sugar, d-GlcNAc, from the non-reducing end made no contribution to the carbohydrate binding. Although a terminal non-reducing d-Ga1NAc or d-Ga1 residue was indispensible for binding, the lectin bound not only to these terminal non-reducing galactopyranosyl residues, but also showed increased binding to oligosaccharides in which it was bonded to a sub-terminal d-Ga1 joined to a d-GlcNAc residue, as in blood group A or B substances. This defines the site, thus far, as complementary to a disaccharide plus the β linkage to the third sugar (d-Glc or d-GlcNAc) from the non-reducing end. The role of the β(1 → 3) or β(1 → 4) linkage of the sub-terminal non-reducing d-Gal to the d-GlcNAc requires further study.

Analysis of Ridge-Loaded Folded-Waveguide Slow-Wave Structures for Broadband Traveling-Wave Tubes

An E-plane serpentine folded-waveguide slow-wave structure with ridge loading on one of its broad walls is proposed for broadband traveling-wave tubes (TWTs) and studied using a simple quasi-transverse-electromagnetic analysis for the dispersion and interaction impedance characteristics, including the effects of the beam-hole discontinuity. The results are validated against cold test measurements, an approximate transmission-line parametric analysis, an equivalent circuit analysis, and 3-D electromagnetic modeling using CST Microwave Studio. The effect of the structure parameters on widening the bandwidth of a TWT is also studied.

HFinFET: A Scalable, High Performance, Low Leakage Hybrid n-Channel FET

In this letter, we propose the design and simulation study of a novel transistor, called HFinFET, which is a hybrid of an HEMT and a FinFET, to obtain excellent performance and good OFF-state control. Followed by the description of the design, 3-D device simulation has been performed to predict the characteristics of the device. The device has been benchmarked against published state of the art HEMT as well as planar and nonplanar Si n-MOSFET data of comparable gate length using standard benchmarking techniques.

Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Parallelization of an unstructured data based cell centre finite volume code, HIFUN-3D

This work describes the parallelization of High Resolution flow solver on unstructured meshes, HIFUN-3D, an unstructured data based finite volume solver for 3-D Euler equations. For mesh partitioning, we use METIS, a software based on multilevel graph partitioning. The unstructured graph used for partitioning is associated with weights both on its vertices and edges. The data residing on every processor is split into four layers. Such a novel procedure of handling data helps in maintaining the effectiveness of the serial code. The communication of data across the processors is achieved by explicit message passing using the standard blocking mode feature of Message Passing Interface (MPI). The parallel code is tested on PACE++128 available in CFD Center

Prediction of breakout noise from an elliptical duct of finite length

This paper describes a predictive model for breakout noise from an elliptical duct or shell of finite length. The transmission mechanism is essentially that of ``mode coupling'', whereby higher structural modes in the duct walls get excited because of non-circularity of the wall. Effect of geometry has been taken care of by evaluating Fourier coefficients of the radius of curvature. The noise radiated from the duct walls is represented by that from a finite vibrating length of a semi infinite cylinder in a free field. Emphasis is on understanding the physics of the problem as well as analytical modeling. The analytical model is validated with 3-D FEM. Effects of the ovality, curvature, and axial terminations of the duct have been demonstrated. (C) 2010 Institute of Noise Control Engineering.

Cryptosin, a cardenolide from the leaves of Cryptolepis buchanani

A new cardenolide named cryptosin was isolated from the leaves of Cryptolepis buchanani. By spectral studies and single crystal X-ray crystallography, cryptosin was found to possess a novel structure. The structure thus established was 3β-(d-deoxy glucose-oxy)-14β,11β-dihydroxy-7α,8α-epoxy-12-oxo-5β- card-20 (22)-enolide.

New phase unwrapping strategy for rapid and dense 3D data acquisition in structured light approach

Sinusoidal structured light projection (SSLP) technique, specifically-phase stepping method, is in widespread use to obtain accurate, dense 3-D data. But, if the object under investigation possesses surface discontinuities, phase unwrapping (an intermediate step in SSLP) stage mandatorily require several additional images, of the object with projected fringes (of different spatial frequencies), as input to generate a reliable 3D shape. On the other hand, Color-coded structured light projection (CSLP) technique is known to require a single image as in put, but generates sparse 3D data. Thus we propose the use of CSLP in conjunction with SSLP to obtain dense 3D data with minimum number of images as input. This approach is shown to be significantly faster and reliable than temporal phase unwrapping procedure that uses a complete exponential sequence. For example, if a measurement with the accuracy obtained by interrogating the object with 32 fringes in the projected pattern is carried out with both the methods, new strategy proposed requires only 5 frames as compared to 24 frames required by the later method.

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Background: Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive. Results: In the present analysis, starting from C alpha positions of low resolution cryo electron microscopic structures the residue level details of protein-protein interaction interfaces of dengue virus coat proteins have been predicted. By comparing the preexisting structures of virus in different phases of life cycle, the changes taking place in these predicted protein-protein interaction interfaces were followed as a function of maturation process of the virus. Besides changing the current notion about the presence of only homodimers in the mature viral coat, the present analysis indicated presence of a proline-rich motif at the protein-protein interaction interface of the coat protein. Investigating the conservation status of these seemingly functionally crucial residues across other members of flaviviridae family enabled dissecting common mechanisms used for infections by these viruses. Conclusions: Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens.

High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of C-13 and H-1 chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their C-13 chemical shifts with that of the neighboring, directly attached, C-13 nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D H-1-TOCSY-HCCH and (c) (4,3)D C-13-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.

Effect of wall thickness on the end corrections of the extended inlet and outlet of a double-tuned expansion chamber

Simple expansion chambers, the simplest of the muffler configurations, have very limited practical application due to the presence of periodic troughs in the transmission loss spectrum which drastically lower the overall transmission loss of the muffler. Tuned extended inlet and outlet can be designed to nullify three-fourths of these troughs, making use of the plane wave theory. These cancellations would not occur unless one altered the geometric lengths for the extended tube in order to incorporate the effect of evanescent higher-order modes (multidimensional effect) through end corrections or lumped inertance approximation at the area discontinuities or junctions. End corrections of the extended inlet and outlet have been studied by several researchers. However the effect of wall thickness of the inlet/outlet duct on end correction has not been studied explicitly. This has significant effect on the tuning of an extended inlet/outlet expansion chamber. It is investigated here experimentally as well as numerically (through use of 3-D FEM software) for stationary medium. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved.

Evidence for O-H.cntdot..cntdot..cntdot.C and N-H.cntdot..cntdot..cntdot.C hydrogen bonding in crystalline alkynes, alkenes, and aromatics

Attempts have been made to understand the nature and significance of hydrogen bonds of the type X-H-C (X = 0, N) . These unusual interactions have been discussed recently. Crystallographic studies on 17a-ethynylandrosta- 2,4-dieno[2,3-d]dihydroxazol1-7 8-01 (donazole) provide direct evidence of such an 0-H.0-C interaction. Ab initio computations, IR spectroscopy, and database studies show that these hydrogen bonds, while uncommon, are energetically and structurally significant.

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.