Structural characterization of folded pentapeptides containing centrally positioned beta(R)Val, gamma(R)Val and gamma(S)Val residues

A cylindrical pore of similar to 7.5 angstrom diameter containing a one-dimensional water wire, within the confines of a hydrophobic channel lined with the valine side chain, has been observed in crystals of the peptide Boc-D-Pro-Aib-Val-Aib-Val-OMe (1) (Raghavender et al., 2009, 2010). The synthesis and structural characterization in crystals of three backbone homologated analogues Boc-D-Pro-Aib-beta(3)(R) Val-Aib-Val-OMe (2), Boc-D-Pro-Aib-gamma(4)(R)Val-Aib-Val-OMe (3), Boc-D-Pro-Aib-gamma(4)(S)Val-Aib-Val-OMe (4) are described. Crystal structures of peptides 2, 3 and 4 reveal close-packed arrangements in which no pore was formed. In peptides 2 and 3 the N-terminus D-Pro-Aib segment adopted conformations closely related to Type II' beta-turns, while residues 2-4 form one turn of an alpha beta right-handed C-11 helix in 2 and an alpha gamma C-12 helix in 3. In peptide 4, a continuous left-handed helical structure was observed with the D-Pro-Aib segment forming a Type III' beta-turn, followed by one turn of a left-handed alpha gamma C-12 helix. (C) 2012 Elsevier Ltd. All rights reserved.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

High-pressure synchrotron x-ray diffraction study of RMnO3 (R=Eu, Gd, Tb and Dy) upto 50 GPa

We have carried out synchrotron based high-pressure x-ray diffraction study of orthorhombic EuMnO3, GdMnO3, TbMnO3 and DyMnO3 up to 54.4, 41.6, 47.0 and 50.2 GPa, respectively. The diffraction peaks of all the four manganites shift monotonically to higher diffraction angles and the crystals retain the orthorhombic structure till the highest pressure. We have fitted the observed volume versus pressure data with the Birch-Murnaghan equation of state and determined the bulk modulus to be 185 +/- 6 GPa, 190 +/- 16 GPa, 188 +/- 9 GPa and 192 +/- 8 GPa for EuMnO3, GdMnO3, TbMnO3 and DyMnO3, respectively. The bulk modulus of EuMnO3 is comparable to other manganites, in contrast to theoretical predictions.

On the Role of Higher-Order Evanescent Modes in End-Offset Inlet and End-Centered Outlet Elliptical Flow-Reversal Chamber Mufflers

This paper deals with the role of the higher-order evanescent modes generated at the area discontinuities in the acoustic attenuation characteristics of an elliptical end-chamber muffler with an end-offset inlet and end-centered outlet. It has been observed that with an increase in length, the muffler undergoes a transition from being acoustically short to acoustically long. Short end chambers and long end chambers are characterized by transverse plane waves and axial plane waves, respectively, in the low-frequency range. The nondimensional frequency limit k(0)(D-1/2) or k(0)R(0) as well as the chamber length to inlet/outlet pipe diameter ratio, i.e., L/d(0), up to which the muffler behaves like a short chamber and the corresponding limit beyond which the muffler is acoustically long are determined. The limits between which neither the transverse plane-wave model nor the conventional axial plane-wave model gives a satisfactory prediction have also been determined, the region being called the intermediate range. The end-correction expression for this muffler configuration in the acoustically long limit has been obtained using 3-D FEA carried on commercial software, covering most of the dimension range used in the design exercise. Development of a method of combining the transverse plane wave model with the axial plane wave model using the impedance Z] matrix is another noteworthy contribution of this work.

Development of moving magnet type linear motor for dual piston compressor for pulse tube cryocooler

This paper describes the design, fabrication and testing of a moving magnet type linear motor of dual piston configuration for a pulse tube cryocooler for ground applications. Eight radially magnetized segmented magnets were used to form one set of a magnet ring. Four magnet rings of such type were constructed, in which one pair of rings has north-pole on its outer diameter and south-pole on inner diameter, while the other pair is it's complementary. The magnets were mounted with opposite poles together on the magnet holder with an axial moving shaft having a piston mounted on both ends of the shaft. The shaft movement was restricted to the axial direction by using C-clamp type flexures, mounted on both sides of the shaft. The force requirement for driving the compressor was calculated based on which the electrical circuit of motor is designed by proper selection of wire gauge and Ampere-turns. The flexure spring force estimation was done through simulation using ANSYS 11.0 and was verified experimentally; while the magnet spring force was determined experimentally. The motor with mounted piston was tested using a variable voltage and variable frequency power supply capable of driving 140 watts of load.

Experimental and theoretical investigation of thermoacoustic prime mover

The thermoacoustic prime mover is part of an interesting class of prime movers that can be used to generate clean energy and to drive cryogenic refrigeration systems. A thermoacoustic prime mover has been built based on the linear thermoacoustic model, which consumes thermal energy and produces acoustic energy. The objective of this article is to design a thermoacoustic prime mover that can be used as a drive for a thermoacoustic refrigerator. It is found that stack plate length and its distance from the closed end have a significant effect on the thermal efficiency of the prime mover. For different stack center positions, there is an optimum length of stack plate that has a significant effect on the performance of the thermoacoustic prime mover in terms of temperature gradient, frequency, and pressure amplitude. In this study, the experiments have been done on the thermoacoustic prime mover by varying stack position and its length with constant blockage ratio and resonator length. The results obtained from the experiments have been compared to the theoretical results acquired from DeltaEc Software.

Spectral analysis on SL(2, R)

Let G be the group . For this group we prove a version of Schwartz's theorem on spectral analysis for the group G. We find the sharp range of Lebesgue spaces L (p) (G) for which a smooth function is not mean periodic unless it is a cusp form. Failure of the Schwartz-like theorem is also proved when C (a)(G) is replaced by L (p) (G) with suitable p. We show that the last result is linked with the failure of the Wiener-tauberian theorem for G.

Interplay of software bloat, hardware energy proportionality and system bottlenecks

In large flexible software systems, bloat occurs in many forms, causing excess resource utilization and resource bottlenecks. This results in lost throughput and wasted joules. However, mitigating bloat is not easy; efforts are best applied where savings would be substantial. To aid this we develop an analytical model establishing the relation between bottleneck in resources, bloat, performance and power. Analyses with the model places into perspective results from the first experimental study of the power-performance implications of bloat. In the experiments we find that while bloat reduction can provide as much as 40% energy savings, the degree of impact depends on hardware and software characteristics. We confirm predictions from our model with selected results from our experimental study. Our findings show that a software-only view is inadequate when assessing the effects of bloat. The impact of bloat on physical resource usage and power should be understood for a full systems perspective to properly deploy bloat reduction solutions and reap their power-performance benefits.

Reuse, recycle to de-bloat software

Most Java programmers would agree that Java is a language that promotes a philosophy of “create and go forth”. By design, temporary objects are meant to be created on the heap, possibly used and then abandoned to be collected by the garbage collector. Excessive generation of temporary objects is termed “object churn” and is a form of software bloat that often leads to performance and memory problems. To mitigate this problem, many compiler optimizations aim at identifying objects that may be allocated on the stack. However, most such optimizations miss large opportunities for memory reuse when dealing with objects inside loops or when dealing with container objects. In this paper, we describe a novel algorithm that detects bloat caused by the creation of temporary container and String objects within a loop. Our analysis determines which objects created within a loop can be reused. Then we describe a source-to-source transformation that efficiently reuses such objects. Empirical evaluation indicates that our solution can reduce upto 40% of temporary object allocations in large programs, resulting in a performance improvement that can be as high as a 20% reduction in the run time, specifically when a program has a high churn rate or when the program is memory intensive and needs to run the GC often.

Prioritizing constraint evaluation for efficient points-to analysis

Pervasive use of pointers in large-scale real-world applications continues to make points-to analysis an important optimization-enabler. Rapid growth of software systems demands a scalable pointer analysis algorithm. A typical inclusion-based points-to analysis iteratively evaluates constraints and computes a points-to solution until a fixpoint. In each iteration, (i) points-to information is propagated across directed edges in a constraint graph G and (ii) more edges are added by processing the points-to constraints. We observe that prioritizing the order in which the information is processed within each of the above two steps can lead to efficient execution of the points-to analysis. While earlier work in the literature focuses only on the propagation order, we argue that the other dimension, that is, prioritizing the constraint processing, can lead to even higher improvements on how fast the fixpoint of the points-to algorithm is reached. This becomes especially important as we prove that finding an optimal sequence for processing the points-to constraints is NP-Complete. The prioritization scheme proposed in this paper is general enough to be applied to any of the existing points-to analyses. Using the prioritization framework developed in this paper, we implement prioritized versions of Andersen's analysis, Deep Propagation, Hardekopf and Lin's Lazy Cycle Detection and Bloom Filter based points-to analysis. In each case, we report significant improvements in the analysis times (33%, 47%, 44%, 20% respectively) as well as the memory requirements for a large suite of programs, including SPEC 2000 benchmarks and five large open source programs.

USHA: unified software and hardware architecture for video decoding

Video decoders used in emerging applications need to be flexible to handle a large variety of video formats and deliver scalable performance to handle wide variations in workloads. In this paper we propose a unified software and hardware architecture for video decoding to achieve scalable performance with flexibility. The light weight processor tiles and the reconfigurable hardware tiles in our architecture enable software and hardware implementations to co-exist, while a programmable interconnect enables dynamic interconnection of the tiles. Our process network oriented compilation flow achieves realization agnostic application partitioning and enables seamless migration across uniprocessor, multi-processor, semi hardware and full hardware implementations of a video decoder. An application quality of service aware scheduler monitors and controls the operation of the entire system. We prove the concept through a prototype of the architecture on an off-the-shelf FPGA. The FPGA prototype shows a scaling in performance from QCIF to 1080p resolutions in four discrete steps. We also demonstrate that the reconfiguration time is short enough to allow migration from one configuration to the other without any frame loss.

Evaluation of isopentane, R-245fa and their mixtures as working fluids for organic Rankine cycles

Low grade thermal energy from sources such as solar, geothermal and industrial waste heat in the temperature range of 380-425 K can be converted to electrical energy with reasonable efficiency using isopentane and R-245fa. While the former is flammable and the latter has considerable global warming potential, their mixture in 0.7/0.3 mole fraction is shown to obviate these disadvantages and yet retain dominant merits of each fluid. A realistic thermodynamic analysis is carried out wherein the possible sources of irreversibilities such as isentropic efficiencies of the expander and the pump and entropy generation in the regenerator, boiler and condenser are accounted for. The performance of the system in the chosen range of heat source temperatures is evaluated. A technique of identifying the required source temperature for a given output of the plant and the maximum operating temperature of the working fluid is developed. This is based on the pinch point occurrence in the boiler and entropy generation in the boiling and superheating regions of the boiler. It is shown that cycle efficiencies of 10-13% can be obtained in the range investigated at an optimal expansion ratio of 7-10. (C) 2012 Elsevier Ltd. All rights reserved.

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.

C12-Helix development in ()n sequences - spectroscopic characterization of Boc-Aib-4(R)Val]-OMe oligomers

The solution conformations of the -hybrid oligopeptides Boc-Aib-4(R)Val]n-OMe (n = 1-8) in organic solvents have been probed by NMR, IR, and CD spectroscopic methods. In the solid state, this peptide series favors C12-helical conformations, which are backbone-expanded analogues of 310 helices in -peptide sequences. NMR studies of the six- (n = 3) and 16-residue (n = 8) peptides reveal that only two NH protons attached the N-terminus residues Aib(1) and 4(R)Val(2) are solvent-exposed. Sequential NiH-Ni+1H NOEs characteristic of local helical conformations are also observed at the residues. IR studies establish that chain extension leads to a large enhancement in the intensities of the hydrogen-bonded NH stretching bands (3343-3280 cm-1), which suggest elongation of intramolecularly hydrogen-bonded structures. The development of C12-helical structures upon lengthening of the sequence is supported by the NMR and IR observations. The CD spectra of the ()n peptides reveal a negative maximum at ca. 206 nm and a positive maximum at ca. 192 nm, spectral feature that are distinct from those of 310 helices in -peptides.

Implications of Higgs boson to diphoton decay rate in the bilinear R-parity violating supersymmetric model

The Large Hadron Collider has recently discovered a Higgs-like particle having a mass around 125 GeVand also indicated that there is an enhancement in the Higgs to diphoton decay rate as compared to that in the standard model. We have studied implications of these discoveries in the bilinear R-parity violating supersymmetric model, whose main motivation is to explain the nonzero masses for neutrinos. The R-parity violating parameters in this model are epsilon and b(epsilon), and these parameters determine the scale of neutrino masses. If the enhancement in the Higgs to diphoton decay rate is true, then we have found epsilon greater than or similar to 0.01 GeV and b epsilon similar to 1 GeV2 in order to be compatible with the neutrino oscillation data. Also, in the above mentioned analysis, we can determine the soft masses of sleptons (m(L)) and CP-odd Higgs boson mass (mA). We have estimated that m(L) greater than or similar to 300 GeV and m(A) greater than or similar to 700 GeV. We have also commented on the allowed values of epsilon and b(epsilon), in case there is no enhancement in the Higgs to diphoton decay rate. Finally, we present a model to explain the smallness of epsilon and b(epsilon).