Helix and hairpin nucleation in short peptides using centrally positioned conformationally constrained dipeptide segments

The effect of incorporation of a centrally positioned Ac(6)c-Xxx segment where Xxx = (L)Val/(D)Val into a host oligopeptide composed of L-amino acid residues has been investigated. Studies of four designed octapeptides Boc-Leu-Phe-Val-Ac(6)c-Xxx-Leu-Phe-Val-OMe (Xxx = (D)Val 1, (L)Val 2) Boc-Leu-Val-Val-Ac(6)c-Xxx-Leu-Val-Val-OMe (Xxx = (D)Val 3, (L)Val 4) are reported. Diagnostic nuclear Overhouse effects characteristic of hairpin conformations are observed for Xxx = (D)Val peptides (1 and 3) while continuous helical conformation characterized by sequential NiH <-> Ni+1H NOEs are favored for Xxx = (L)Val peptides (2 and 4) in methanol solutions. Temperature co-efficient of NH chemical shifts are in agreement with distinctly different conformational preferences upon changing the configuration of the residue at position 5. Crystal structures of peptides 2 and 4 (Xxx = (L)Val) establish helical conformations in the solid state, in agreement with the structures deduced from NMR data. The results support the design principle that centrally positioned type I beta-turns may be used to nucleate helices in short peptides, while type I' beta-turns can facilitate folding into beta-hairpins.

Motion Analysis for Short and Long Jump

Motion analysis is very essential in sport activities to enhance the performance of an athlete and to ensure the correctness of regimes. Expensive methods of motion analysis involving the use of sophisticated technology has led to limited application of motion analysis in sports. Towards this, in this paper we have integrated a low-cost method for motion analysis using three axis accelerometer, three axis magnetometer and microcontroller which are very accurate and easy to use. Seventeen male subjects performed two experiments, standing short jumps and long jumps over a wide range of take-off angles. During take-off and landing the acceleration and angles at different joints of the body are recorded using accelerometers and magnetometers, and the data is captured using Lab VIEW software. Optimum take-off angle in these jumps are calculated using the recorded data, to identify the optimum projection angle that maximizes the distance achieved in a jump. The results obtained for optimum take off angle in short jump and long jump is in agreement with those obtained using other methodologies and theoretical calculations assuming jump to be a projectile motion. The impact force (acceleration) is also analysed and is found to progressively decrease from foot to neck.

Short- and long-term temporal variations in salinity and the oxygen, carbon and hydrogen isotopic compositions of the Hooghly Estuary water, India

The Hooghly River estuary provides a unique experimental site to understand the effect of monsoonal river discharge on freshwater and seawater mixing. Water samples collected bi-weekly for a duration of 17 months were analyzed for salinity, delta O-18,delta C-13(DIC), as well as delta D to investigate the differential mixing of freshwater and seawater. The differences in salinity and delta O-18 of samples collected during low and high tides on the same day are strongly correlated suggesting a well mixed water column at our sampling site. Low salinity and depleted delta O-18 during monsoon is consistent with increased river discharge as well as high rainfall. We identified different slopes in a delta O-18 versus salinity plot for the estuary water samples collected during monsoon and non-monsoon seasons. This is driven by composition of the freshwater source which is dominated by rainwater during monsoon and rivers during non-monsoon months. Selected delta D analyses of samples indicate that groundwater contributes significantly to the Hooghly Estuary during low rainfall times of the year. delta C-13(DIC) measured in the water recorded low values towards the end of monsoon indicating low productivity (i.e. increased organic respiration) while progressively increasing delta C-13(DIC) values from October till January as well as during some of the pre-monsoon months can be explained by increasing productivity. Very low delta C-13(DIC) (similar to-20%0) suggests involvement of carbon derived from anaerobic oxidation of organics and/or methane with potential contribution from increased anthropogenic water supply. An estimate of seawater incursion into the Hooghly Estuary at different times of the year is obtained by using salinity data in a two-component mixing model. Presence of seawater was found maximum (31-37%) during February till July and lowest (less than or equal to 6%) from September till November. We notice a temporal offset between Ganges River discharge farther upstream at Farakka and salinity variation at the Hooghly Estuary. We believe that this time lag is a result of the physical distance between Farakka and Kakdweep (our sampling location) and put constraints on the travel time of river water during early monsoon. (c) 2012 Published by Elsevier B.V.

Generation of a short-duration ultrawideband chirped-pulse using CRLH transmission lines

In this paper we present the various design issues related to CRLH-Transmission lines for the generation of short duration Ultra-Wideband chirped-pulse. The major parameters of the CRLH Transmission lines affecting the BandWidth are discussed and methods to increase BandWidth are also suggested. Also presented is the role of components of CRLH Transmission lines in determining the chirp duration. The techniques of controlling the chirp duration by regulating these components are also discussed. Simulations results are also included.

Conformationally restricted short peptides inhibit human islet amyloid polypeptide (hIAPP) fibrillization

hIAPP fibrillization implicated in Type 2 diabetes pathology involves formation of oligomers toxic to insulin producing pancreatic beta-cells. We report design, synthesis, 3D structure and functional characterization of dehydrophenylalanine (Delta F) containing peptides which inhibit hIAPP fibrillization. The inhibitor protects beta-cells from hIAPP induced toxicity.

Effect of fault resistance and grid short circuit MVA on impedance seen by distance relays on lines fed from wind turbine generating units (WTGU)

This paper deals with line protection challenges experienced in system having substantial wind generation penetration. Two types of WTGU: Doubly Fed (DFIG) and Squirrel Cage (SCIG) Induction Generators are simulated and connected to grid with single circuit transmission line. The paper summarizes analytical investigations carried out on the impedance seen by distance relays by varying fault resistances and grid short circuit MVA, for the protection of such transmission lines during faults. The results are also compared with systems having conventional synchronous machine connected to the grid.

Performance improvement of short-length regular low-density parity-check codes with low-complexity post-processing

It is well known that extremely long low-density parity-check (LDPC) codes perform exceptionally well for error correction applications, short-length codes are preferable in practical applications. However, short-length LDPC codes suffer from performance degradation owing to graph-based impairments such as short cycles, trapping sets and stopping sets and so on in the bipartite graph of the LDPC matrix. In particular, performance degradation at moderate to high E-b/N-0 is caused by the oscillations in bit node a posteriori probabilities induced by short cycles and trapping sets in bipartite graphs. In this study, a computationally efficient algorithm is proposed to improve the performance of short-length LDPC codes at moderate to high E-b/N-0. This algorithm makes use of the information generated by the belief propagation (BP) algorithm in previous iterations before a decoding failure occurs. Using this information, a reliability-based estimation is performed on each bit node to supplement the BP algorithm. The proposed algorithm gives an appreciable coding gain as compared with BP decoding for LDPC codes of a code rate equal to or less than 1/2 rate coding. The coding gains are modest to significant in the case of optimised (for bipartite graph conditioning) regular LDPC codes, whereas the coding gains are huge in the case of unoptimised codes. Hence, this algorithm is useful for relaxing some stringent constraints on the graphical structure of the LDPC code and for developing hardware-friendly designs.

Observation of trap-assisted space charge limited conductivity in short channel MoS2 transistor

We present temperature dependent I-V measurements of short channel MoS2 field effect devices at high source-drain bias. We find that, although the I-V characteristics are ohmic at low bias, the conduction becomes space charge limited at high V-DS, and existence of an exponential distribution of trap states was observed. The temperature independent critical drain-source voltage (V-c) was also determined. The density of trap states was quantitatively calculated from V-c. The possible origin of exponential trap distribution in these devices is also discussed. (C) 2013 AIP Publishing LLC.

Radiatively inefficient accretion flow simulations with cooling: implications for black hole transients

We study the effects of optically thin radiative cooling on the structure of radiatively inefficient accretion flows (RIAFs). The flow structure is geometrically thick, and independent of the gas density and cooling, if the cooling time is longer than the viscous time-scale (i.e. t(cool) greater than or similar to t(visc)). For higher densities, the gas can cool before it can accrete and forms the standard geometrically thin, optically thick Shakura-Sunyaev disc. For usual cooling processes (such as bremsstrahlung), we expect an inner hot flow and an outer thin disc. For a short cooling time the accretion flow separates into two phases: a radiatively inefficient hot coronal phase and a cold thin disc. We argue that there is an upper limit on the density of the hot corona corresponding to a critical value of t(cool)/t(ff)( similar to 10-100), the ratio of the cooling time and the free-fall time. Based on our simulations, we have developed a model for transients observed in black hole X-ray binaries (XRBs). An XRB in a quiescent hot RIAF state can transition to a cold blackbody-dominated state because of an increase in the mass accretion rate. The transition from a thin disc to a RIAF happens because of mass exhaustion due to accretion; the transition happens when the cooling time becomes longer than the viscous time at inner radii. Since the viscous time-scale for a geometrically thin disc is quite long, the high-soft state is expected to be long-lived. The different time-scales in black hole transients correspond to different physical processes such as viscous evolution, cooling and free fall. Our model captures the overall features of observed state transitions in XRBs.

Hypersonic interference heating on flat plate with short three-dimensional protuberances

Experiments were conducted to measure the heat flux in the vicinity of a three-dimensional protuberance placed on a flat plate facing a hypersonic flow at zero angle of attack. The effects of flow enthalpy and height of the protuberance on the interference heating in its vicinity were studied. Evidence of disturbed flow with highly three-dimensional characteristics and heightened vorticity was observed near the protrusion. A parametric study by changing the deflection angle of the protuberance was also made. Correlations exist in the open literature for enthalpy values lower than 2  MJ/kg. This effort has yielded a new correlation that is valid for enthalpies up to 6  MJ/kg. The Z-type schlieren technique was used to visualize the flow features qualitatively for one of the flow conditions studied.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

Hypersonic interference heating on cones with short three-dimensional protuberances

Heat fluxes around short, three-dimensional protuberances on sharp and blunt cones in hypersonic flow were experimentally measured using platinum thin-film sensors deposited on macor inserts. A parametric study of different protrusion geometries and flow conditions were conducted. Excessive heating was observed at locations near the protrusion where increased vorticity is expected, with the hottest spot being presented at the foot of the protuberance immediately upstream of it. If left unchecked, these hot spots could prove detrimental to hypersonic flight vehicles. Z-type schlieren technique was used to visualize the flow features qualitatively. New correlations to predict the heat flux at the hot spot have been proposed. (C) 2014 Elsevier Inc. All rights reserved.