Investigating proline puckering states in diproline segments in proteins

In the current study, the puckering states of the Proline ring occurring in diproline segments (LPro-LPro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/-) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (C-exo/C-exo), (C-exo/Twisted C-exo-C-endo) and (Twisted C-endo-C-exo/Twisted C-endo-C-exo) categories are the most preferred combinations. For Proline rings in proteins, the states C-exo, Twisted C-exo-C-endo and Twisted C-endo-C-exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co-relation to the backbone conformation in which they are observed. It is likely that five-membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations.

Detection limit of etched fiber bragg grating sensors

While Fiber Bragg Grating (FBG) sensors have been extensively used for temperature and strain sensing, clad etched FBGs (EFBGs) have only recently been explored for refractive index sensing. Prior literature in EFBG based refractive index sensing predominantly deals with bulk refractometry only, where the Bragg wavelength shift of the sensor as a function of the bulk refractive index of the sample can be analytically modeled, unlike the situation for adsorption of molecular thin films on the sensor surface. We used a finite element model to calculate the Bragg wavelength change as a function of thickness and refractive index of the adsorbing molecular layer and compared the model with the real-time, in-situ measurement of electrostatic layer-by-layer (LbL) assembly of weak polyelectrolytes on the silica surface of EFBGs. We then used this model to calculate the layer thickness of LbL films and found them to be in agreement with literature. Further, we used this model to arrive at a realistic estimate of the limit of detection of EFBG sensors based on nominal measurement noise levels in current FBG interrogation systems and found that sufficiently thinned EFBGs can provide a competitive platform for real-time measurement of molecular interactions while simultaneously leveraging the high multiplexing capabilities of fiber optics.

Multi-resistance states in the electrical switching behavior of amorphous Si15Te75Ge10 thin films: Possibility of multi-bit storage

Electrical switching studies on amorphous Si15Te75Ge10 thin film devices reveal the existence of two distinct, stable low-resistance, SET states, achieved by varying the electrical input to the device. The multiple resistance levels can be attributed to multi-stage crystallization, as observed from temperature dependant resistance studies. The devices are tested for their ability to be RESET with minimal resistance degradation; further, they exhibit a minimal drift in the SET resistance value even after several months of switching. (c) 2013 Elsevier B.V. All rights reserved.

Photoelectron spectromicroscopy study of metal-insulator transition in NaxWO3

We have investigated the validity of percolation model, which is quite often invoked to explain the metal-insulator transition in sodium tungsten bronzes, NaxWO(3) by photoelectron spectromicroscopy. The spatially resolved direct spectromicroscopic probing on both the insulating and metallic phases of high quality single crystals of NaxWO(3) reveals the absence of any microscopic inhomogeneities embedded in the system within the experimental limit. Neither any metallic domains in the insulating host nor any insulating domains in the metallic host have been found to support the validity of percolation model to explain the metal-insulator transition in NaxWO(3). The possible origin of insulating phase in NaxWO(3) is due to the Anderson localization of all the states near E-F. The localization occurs because of the strong disorder arising from random distribution of Na+ ions in the WO3 lattice.

Information and Efficiency in the Nervous System-A Synthesis

In systems biology, questions concerning the molecular and cellular makeup of an organism are of utmost importance, especially when trying to understand how unreliable components-like genetic circuits, biochemical cascades, and ion channels, among others-enable reliable and adaptive behaviour. The repertoire and speed of biological computations are limited by thermodynamic or metabolic constraints: an example can be found in neurons, where fluctuations in biophysical states limit the information they can encode-with almost 20-60% of the total energy allocated for the brain used for signalling purposes, either via action potentials or by synaptic transmission. Here, we consider the imperatives for neurons to optimise computational and metabolic efficiency, wherein benefits and costs trade-off against each other in the context of self-organised and adaptive behaviour. In particular, we try to link information theoretic (variational) and thermodynamic (Helmholtz) free-energy formulations of neuronal processing and show how they are related in a fundamental way through a complexity minimisation lemma.

Entropy of quantum states: Ambiguities

The von Neumann entropy of a generic quantum state is not unique unless the state can be uniquely decomposed as a sum of extremal or pure states. As pointed out to us by Sorkin, this happens if the GNS representation (of the algebra of observables in some quantum state) is reducible, and some representations in the decomposition occur with non-trivial degeneracy. This non-unique entropy can occur at zero temperature. We will argue elsewhere in detail that the degeneracies in the GNS representation can be interpreted as an emergent broken gauge symmetry, and play an important role in the analysis of emergent entropy due to non-Abelian anomalies. Finally, we establish the analogue of an H-theorem for this entropy by showing that its evolution is Markovian, determined by a stochastic matrix.

High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio

Four-dimensional fluorescence microscopy-which records 3D image information as a function of time-provides an unbiased way of tracking dynamic behavior of subcellular components in living samples and capturing key events in complex macromolecular processes. Unfortunately, the combination of phototoxicity and photobleaching can severely limit the density or duration of sampling, thereby limiting the biological information that can be obtained. Although widefield microscopy provides a very light-efficient way of imaging, obtaining high-quality reconstructions requires deconvolution to remove optical aberrations. Unfortunately, most deconvolution methods perform very poorly at low signal-to-noise ratios, thereby requiring moderate photon doses to obtain acceptable resolution. We present a unique deconvolution method that combines an entropy-based regularization function with kernels that can exploit general spatial characteristics of the fluorescence image to push the required dose to extreme low levels, resulting in an enabling technology for high-resolution in vivo biological imaging.

Forming limit investigation of friction stir welded sheets: influence of shoulder diameter and plunge depth

The main aim of the present work is to analyze the influence of shoulder diameter and plunge depth on the formability of friction stir welded sheets. The base material used for welding and forming was AA6061-T6. Formability evaluation was performed through limiting dome height tests. The forming limit curve, FLC (only in the stretching region), thickness distribution, and strain hardening exponent of the weld region were monitored during formability studies. It is found from the work that the forming limit of friction stir welded sheets is better than unwelded sheets. In general, with an increase in shoulder diameter and plunge depth, the forming limit is found to improve considerably. With a decrease in thickness gradient severity and an increase in strain hardening exponent (n) of the weld region, the forming limit is found to increase. The increase in n value of the weld region is believed to occur because of the reduction in dislocation density. The maximum thickness difference is higher in the retreating side, rather than in the advancing side, of the weld. This is due to the differential straining and hardness levels attained by both sides during friction stir welding.

NEW MASS LIMIT OF WHITE DWARFS

Is the Chandrasekhar mass limit for white dwarfs (WDs) set in stone? Not anymore, recent observations of over-luminous, peculiar type Ia supernovae can be explained if significantly super-Chandrasekhar WDs exist as their progenitors, thus barring them to be used as cosmic distance indicators. However, there is no estimate of a mass limit for these super-Chandrasekhar WD candidates yet. Can they be arbitrarily large? In fact, the answer is no! We arrive at this revelation by exploiting the flux freezing theorem in observed, accreting, magnetized WDs, which brings in Landau quantization of the underlying electron degenerate gas. This essay presents the calculations which pave the way for the ultimate (significantly super-Chandrasekhar) mass limit of WDs, heralding a paradigm shift 80 years after Chandrasekhar's discovery.

Performance analysis of boron nitride embedded armchair graphene nanoribbon metal-oxide-semiconductor field effect transistor with Stone Wales defects

We study the performance of a hybrid Graphene-Boron Nitride armchair nanoribbon (a-GNR-BN) n-MOSFET at its ballistic transport limit. We consider three geometric configurations 3p, 3p + 1, and 3p + 2 of a-GNR-BN with BN atoms embedded on either side (2, 4, and 6 BN) on the GNR. Material properties like band gap, effective mass, and density of states of these H-passivated structures are evaluated using the Density Functional Theory. Using these material parameters, self-consistent Poisson-Schrodinger simulations are carried out under the Non Equilibrium Green's Function formalism to calculate the ballistic n-MOSFET device characteristics. For a hybrid nanoribbon of width similar to 5 nm, the simulated ON current is found to be in the range of 265 mu A-280 mu A with an ON/OFF ratio 7.1 x 10(6)-7.4 x 10(6) for a V-DD = 0.68 V corresponding to 10 nm technology node. We further study the impact of randomly distributed Stone Wales (SW) defects in these hybrid structures and only 2.5% degradation of ON current is observed for SW defect density of 3.18%. (C) 2014 AIP Publishing LLC.

Upper bound solution for pullout capacity of vertical anchors in sand using finite elements and limit analysis

The horizontal pullout capacity of vertical anchors embedded in sand has been determined by using an upper bound theorem of the limit analysis in combination with finite elements. The numerical results are presented in nondimensional form to determine the pullout resistance for various combinations of embedment ratio of the anchor (H/B), internal friction angle (ϕ) of sand, and the anchor-soil interface friction angle (δ). The pullout resistance increases with increases in the values of embedment ratio, friction angle of sand and anchor-soil interface friction angle. As compared to earlier reported solutions in literature, the present solution provides a better upper bound on the ultimate collapse load.

Observation of localized states in atomically thin MoS2 field effect transistor

We present electrical transport arid low frequency (1/f) noise measurements on mechanically exfoliated single, In and triLayer MoS2-based FPI devices on Si/SiO2 substrate. We find that tie electronic states hi MoS2 are localized at low temperatures (T) and conduction happens through variable range hopping (VRH). A steep increase of 1/f noise with decreasing T, typical for localized regime was observed in all of our devices. From gate voltage dependence of noise, we find that the noise power is inversely proportional to square of the number density (proportional to 1/n(2)) for a wide range of T, indicating number density fluctuations to be the dominant source of 1/f noise in these MoS2 FETs.

Revisiting some physics issues related to the new mass limit for magnetized white dwarfs

We clarify important physics issues related to the recently established new mass limit for magnetized white dwarfs which is significantly super-Chandrasekhar. The issues include, justification of high magnetic field and the corresponding formation of stable white dwarfs, contribution of the magnetic field to the total density and pressure, flux freezing, variation of magnetic field and related currents therein. We also attempt to address the observational connection of such highly magnetized white dwarfs.

REDUCING COMPUTATIONAL EFFORT IN SOLVING GEOMECHANICS PROBLEMS WITH UPPER BOUND FINITE ELEMENTS LIMIT ANALYSIS AND LINEAR OPTIMIZATION

This paper presents a simple technique for reducing the computational effort while solving any geotechnical stability problem by using the upper bound finite element limit analysis and linear optimization. In the proposed method, the problem domain is discretized into a number of different regions in which a particular order (number of sides) of the polygon is chosen to linearize the Mohr-Coulomb yield criterion. A greater order of the polygon needs to be selected only in that region wherein the rate of the plastic strains becomes higher. The computational effort required to solve the problem with this implementation reduces considerably. By using the proposed method, the bearing capacity has been computed for smooth and rough strip footings and the results are found to be quite satisfactory.

Calibration Curve with Improved Limit of Detection for Cadmium in Soil: An Approach to Minimize the Matrix Effect in Laser-Induced Breakdown Spectroscopic Analysis

The present article describes a working or combined calibration curve in laser-induced breakdown spectroscopic analysis, which is the cumulative result of the calibration curves obtained from neutral and singly ionized atomic emission spectral lines. This working calibration curve reduces the effect of change in matrix between different zone soils and certified soil samples because it includes both the species' (neutral and singly ionized) concentration of the element of interest. The limit of detection using a working calibration curve is found better as compared to its constituent calibration curves (i.e., individual calibration curves). The quantitative results obtained using the working calibration curve is in better agreement with the result of inductively coupled plasma-atomic emission spectroscopy as compared to the result obtained using its constituent calibration curves.