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.

Relationship between the controllability grammian and closed-loop eigenvalues: the single input case

The controllability grammian is important in many control applications. Given a set of closed-loop eigenvalues the corresponding controllability grammian can be obtained by computing the controller which assigns the eigenvalues and then by solving the Lyapunov equation that defines the grammian. The relationship between the controllability grammian, resulting from state feedback, and the closed-loop eigenvalues of a single input linear time invariant (LTI) system is obtained. The proposed methodology does not require the computation of the controller that assigns the specified eigenvalues. The closed-loop system matrix is obtained from the knowledge of the open-loop system matrix, control influence matrix and the specified closed-loop eigenvalues. Knowing the closed-loop system matrix, the grammian is then obtained from the solution of the Lyapunov equation that defines it. Finally the proposed idea is extended to find the state covariance matrix for a specified set of closed-loop eigenvalues (without computing the controller), due to impulsive input in the disturbance channel and to solve the eigenvalue assignment problem for the single input case.

Minimum weight design of fiber-reinforced laminated composite structures with maximum stress and Tsai-Wu failure criteria

In this article, a minimum weight design of carbon/epoxy laminates is carried out using genetic algorithms. New failure envelopes have been developed by the combination of two commonly used phenomenological failure criteria, namely Maximum Stress (MS) and Tsai-Wu (TW) are used to obtain the minimum weight of the laminate. These failure envelopes are the most conservative failure envelope (MCFE) and the least conservative failure envelope (LCFE). Uniaxial and biaxial loading conditions are considered for the study and the differences in the optimal weight of the laminate are compared for the MCFE and LCFE. The MCFE can be used for design of critical load-carrying composites, while the LCFE could be used for the design of composite structures where weight reduction is much more important than safety such as unmanned air vehicles.

Novel approach for simultaneous measurement of strain and temperature using a single tapered fiber Bragg grating

A novel approach for simultaneous measurement of strain and temperature with a single tapered fiber Bragg grating is proposed. This method is based on the fact that the reflectivity at central wavelength of FBG reflection changes with chirp (strain gradient). A diode laser is locked to the central wavelength of FBG reflection. Central wavelength of the FBG shifts with temperature. Change in reflectivity & wavelength of the diode laser were used to measure strain and temperature on the FBG respectively.

Simultaneous measurement of strain and temperature with a pair of matched fiber Bragg gratings

A novel approach for simultaneous measurement of static/dynamic strain and temperature with a pair of matched fiber Bragg grating(FBG)s is proposed. When a diode laser locked to the mid reflection frequency of reference FBG is used to illuminate the sensor FBG, reflected intensity changes with strain on sensor FBG. Reference FBG responds with temperature on sensor FBG and is immune to strain, hence, wavelength of the diode laser acts as a signature for temperature measurement. Theoretical sensitivity limit for static strain and temperature are 1.2n epsilon / root Hz and 0.0011 degrees C respectively. Proposed sensor shows a great potential in high sensitive strain measurements with a simplified experimental setup.

Non-linearity in piezo-fiber reinforced composites: an asymptotic approach

An asymptotically correct analysis is developed for Macro Fiber Composite unit cell using Variational Asymptotic Method (VAM). VAM splits the 3D nonlinear problem into two parts: A 1D nonlinear problem along the length of the fiber and a linear 2D cross-sectional problem. Closed form solutions are obtained for the 2D problem which are in terms of 1D parameters.

Simultaneous measurement of multiple parameters using a single fiber Bragg grating

A novel approach for simultaneous measurement of chirp (any parameter that can induce strain gradient on FBG) and temperature using a single FBG is proposed. Change in reflectivity at central wavelength of FBG reflection & Bragg wavelength shifts induced due to temperature were used for chirp & temperature measurements respectively. Theoretical resolution limit for chirp and temperature using an Optical Spectrum Analyzer (OSA) with 1pm wavelength resolution and >58dB dynamic range are 12.8fm and 1/13 degrees C respectively.

Novel signal demodulation technique to estimate the amount of chirp in fiber Bragg gratings

A novel detection technique to estimate the amount of chirp in fiber Bragg gratings (FBGs) is proposed. This method is based on the fact that reflectivity at central wavelength of FBG reflection changes with strain/temperature gradient (linear chirp) applied to the same. Transfer matrix approach was used to vary different grating parameters (length, strength and apodization) to optimize variation of reflectivity with linear chirp. Analysis is done for different sets of `FBG length-refractive index strength' combinations for which reflectivity vary linearly with linear chirp over a decent measurement range. This article acts as a guideline to choose appropriate grating parameters in designing sensing apparatus based on change in reflectivity at central wavelength of FBG reflection.

High sensitive Static fiber Bragg grating strain sensing using lasers locked to relative frequency reference

A novel high sensitive fiber Bragg grating (FBG) strain sensing technique using lasers locked to relative frequency reference is proposed and analyzed theoretically. Static strain on FBG independent of temperature can be measured by locking frequency of diode laser to the mid reflection frequency of matched reference FBG, which responds to temperature similar to that of the sensor FBG, but is immune to strain applied to the same. Difference between light intensities reflected from the sensor and reference FBGs (proportional to the difference between respective pass band gains at the diode laser frequency) is not only proportional to the relative strain between the sensor and reference FBGs but also independent of servo residual frequency errors. Usage of relative frequency reference avoids all complexities involved in the usage of absolute frequency reference, hence, making the system simple and economical. Theoretical limit for dynamic and static strain sensitivities considering all major noise contributions are of the order of 25 (p epsilon) / root Hz and 1.2 n epsilon / root Hz respectively.

Fiber Bragg Grating Sensors for Real Time Monitoring of Evacuation Process

Fiber bragg grating (FBG) sensors have been widely used for number of sensing applications like temperature, pressure, acousto-ultrasonic, static and dynamic strain, refractive index change measurements and so on. Present work demonstrates the use of FBG sensors in in-situ measurement of vacuum process with simultaneous leak detection capability. Experiments were conducted in a bell jar vacuum chamber facilitated with conventional Pirani gauge for vacuum measurement. Three different experiments have been conducted to validate the performance of FBG sensor in monitoring vacuum creating process and air bleeding. The preliminary results of FBG sensors in vacuum monitoring have been compared with that of commercial Pirani gauge sensor. This novel technique offers a simple alternative to conventional method for real time monitoring of evacuation process. Proposed FBG based vacuum sensor has potential applications in vacuum systems involving hazardous environment such as chemical and gas plants, automobile industries, aeronautical establishments and leak monitoring in process industries, where the electrical or MEMS based sensors are prone to explosion and corrosion.

Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Holographic optical element based single-mode hybrid fiber optic interferometer for realizing zero-order fringe

A holographic optical element (HOE) based single-mode hybrid fiber optic interferometer for realizing the zero-order fringe is described. The HOE proposed and used integrates the actions of a beam combiner and a lens, and endows the interferometer with high tolerance for repositioning errors. The proposed method is simple and offers advantages such as the elimination of in situ processing for the hologram.

Inefficient excision of uracil from loop regions of DNA oligomers by E.coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E.coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable V-max value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased K-m and lowered V-max values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Bloch-Nordsieck thermometers: One-loop exponentiation in finite temperature QED

We study the scattering of hard external particles in a heat bath in a real-time formalism for finite temperature QED. We investigate the distribution of the 4-momentum difference of initial and final hard particles in a fully covariant manner when the scale of the process, Q, is much larger than the temperature, T. Our computations are valid for all T subject to this constraint. We exponentiate the leading infra-red term at one-loop order through a resummation of soft (thermal) photon emissions and absorptions. For T > 0, we find that tensor structures arise which are not present at T = 0. These carry thermal signatures. As a result, external particles can serve as thermometers introduced into the heat bath. We investigate the phase space origin of log (Q/M) and log (Q/T) terms.

Scroll-Wave Dynamics in Human Cardiac Tissue: Lessons from a Mathematical Model with Inhomogeneities and Fiber Architecture

Cardiac arrhythmias, such as ventricular tachycardia (VT) and ventricular fibrillation (VF), are among the leading causes of death in the industrialized world. These are associated with the formation of spiral and scroll waves of electrical activation in cardiac tissue; single spiral and scroll waves are believed to be associated with VT whereas their turbulent analogs are associated with VF. Thus, the study of these waves is an important biophysical problem. We present a systematic study of the combined effects of muscle-fiber rotation and inhomogeneities on scroll-wave dynamics in the TNNP (ten Tusscher Noble Noble Panfilov) model for human cardiac tissue. In particular, we use the three-dimensional TNNP model with fiber rotation and consider both conduction and ionic inhomogeneities. We find that, in addition to displaying a sensitive dependence on the positions, sizes, and types of inhomogeneities, scroll-wave dynamics also depends delicately upon the degree of fiber rotation. We find that the tendency of scroll waves to anchor to cylindrical conduction inhomogeneities increases with the radius of the inhomogeneity. Furthermore, the filament of the scroll wave can exhibit drift or meandering, transmural bending, twisting, and break-up. If the scroll-wave filament exhibits weak meandering, then there is a fine balance between the anchoring of this wave at the inhomogeneity and a disruption of wave-pinning by fiber rotation. If this filament displays strong meandering, then again the anchoring is suppressed by fiber rotation; also, the scroll wave can be eliminated from most of the layers only to be regenerated by a seed wave. Ionic inhomogeneities can also lead to an anchoring of the scroll wave; scroll waves can now enter the region inside an ionic inhomogeneity and can display a coexistence of spatiotemporal chaos and quasi-periodic behavior in different parts of the simulation domain. We discuss the experimental implications of our study.