Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA

We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

Asymptotics of the invariant measure in mean field models with jumps

We consider the asymptotics of the invariant measure for the process of spatial distribution of N coupled Markov chains in the limit of a large number of chains. Each chain reflects the stochastic evolution of one particle. The chains are coupled through the dependence of transition rates on the spatial distribution of particles in the various states. Our model is a caricature for medium access interactions in wireless local area networks. Our model is also applicable in the study of spread of epidemics in a network. The limiting process satisfies a deterministic ordinary differential equation called the McKean-Vlasov equation. When this differential equation has a unique globally asymptotically stable equilibrium, the spatial distribution converges weakly to this equilibrium. Using a control-theoretic approach, we examine the question of a large deviation from this equilibrium.

Development of a New Generation of Vectors for Gene Expression, Gene Replacement, and Protein-Protein Interaction Studies in Mycobacteria

Escherichia coli-mycobacterium shuttle vectors are important tools for gene expression and gene replacement in mycobacteria. However, most of the currently available vectors are limited in their use because of the lack of extended multiple cloning sites (MCSs) and convenience of appending an epitope tag(s) to the cloned open reading frames (ORFs). Here we report a new series of vectors that allow for the constitutive and regulatable expression of proteins, appended with peptide tag sequences at their N and C termini, respectively. The applicability of these vectors is demonstrated by the constitutive and induced expression of the Mycobacterium tuberculosis pknK gene, coding for protein kinase K, a serine-threonine protein kinase. Furthermore, a suicide plasmid with expanded MCS for creating gene replacements, a plasmid for chromosomal integrations at the commonly used L5 attB site, and a hypoxia-responsive vector, for expression of a gene(s) under hypoxic conditions that mimic latency, have also been created. Additionally, we have created a vector for the coexpression of two proteins controlled by two independent promoters, with each protein being in fusion with a different tag. The shuttle vectors developed in the present study are excellent tools for the analysis of gene function in mycobacteria and are a valuable addition to the existing repertoire of vectors for mycobacterial research.

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.

Poincare invariant quantum field theories with twisted internal symmetries

Following up the work of 1] on deformed algebras, we present a class of Poincare invariant quantum field theories with particles having deformed internal symmetries. The twisted quantum fields discussed in this work satisfy commutation relations different from the usual bosonic/fermionic commutation relations. Such twisted fields by construction are nonlocal in nature. Despite this nonlocality we show that it is possible to construct interaction Hamiltonians which satisfy cluster decomposition principle and are Lorentz invariant. We further illustrate these ideas by considering global SU(N) symmetries. Specifically we show that twisted internal symmetries can provide a natural-framework for the discussion of the marginal deformations (beta-deformations) of the N = 4 SUSY theories.

Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus

The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.

Surface Instabilities and Generation of Multielectron Bubbles Under Pulsed Electric Fields

We studied the development of surface instabilities leading to the generation of multielectron bubbles (MEBs) in superfluid helium upon the application of a pulsed electric field. We found the statistical distribution of the charge of individual instabilities to be strongly dependent on the duration of the electric field pulse. The rate and probability of generation of these instabilities in relation to the temporal characteristics of the applied field was also investigated.

Power generation using wind energy in northwest Karnataka, India

On the backdrop of climate change scenario, there is emphasis on controlling emission of greenhouse gases such as CO2. Major thrust being seen worldwide as well as in India is for generation of electricity from renewable sources like solar and wind. Chitradurga area of Karnataka is identified as a suitable location for the production of electricity from wind turbines because of high wind-energy resource. The power generated and the performance of 18 wind turbines located in this region are studied based on the actual field data collected over the past seven years. Our study shows a good prospect for expansion of power production using wind turbines.

Identification of prospective locations for generation expansion with least augmentation of network

With ever increasing demand for electric energy, additional generation and associated transmission facilities has to be planned and executed. In order to augment existing transmission facilities, proper planning and selective decisions are to be made whereas keeping in mind the interests of several parties who are directly or indirectly involved. Common trend is to plan optimal generation expansion over the planning period in order to meet the projected demand with minimum cost capacity addition along with a pre-specified reliability margin. Generation expansion at certain locations need new transmission network which involves serious problems such as getting right of way, environmental clearance etc. In this study, an approach to the citing of additional generation facilities in a given system with minimum or no expansion in the transmission facility is attempted using the network connectivity and the concept of electrical distance for projected load demand. The proposed approach is suitable for large interconnected systems with multiple utilities. Sample illustration on real life system is presented in order to show how this approach improves the overall performance on the operation of the system with specified performance parameters.

A GIS (geographical information system)-based spatial data mining approach for optimal location and capacity planning of distributed biomass power generation facilities: A case study of Tumkur district, India

This paper primarily intends to develop a GIS (geographical information system)-based data mining approach for optimally selecting the locations and determining installed capacities for setting up distributed biomass power generation systems in the context of decentralized energy planning for rural regions. The optimal locations within a cluster of villages are obtained by matching the installed capacity needed with the demand for power, minimizing the cost of transportation of biomass from dispersed sources to power generation system, and cost of distribution of electricity from the power generation system to demand centers or villages. The methodology was validated by using it for developing an optimal plan for implementing distributed biomass-based power systems for meeting the rural electricity needs of Tumkur district in India consisting of 2700 villages. The approach uses a k-medoid clustering algorithm to divide the total region into clusters of villages and locate biomass power generation systems at the medoids. The optimal value of k is determined iteratively by running the algorithm for the entire search space for different values of k along with demand-supply matching constraints. The optimal value of the k is chosen such that it minimizes the total cost of system installation, costs of transportation of biomass, and transmission and distribution. A smaller region, consisting of 293 villages was selected to study the sensitivity of the results to varying demand and supply parameters. The results of clustering are represented on a GIS map for the region.

Multilevel octadecagonal space vector generation for induction motor drives by cascading asymmetric three level inverters

Multilevel inverters with hexagonal and dodecagonal voltage space vector structures have improved harmonic profile compared to two level inverters. Further improvement in the quality of the waveform is possible using multilevel octadecagonal (18 sided polygon) voltage space vectors. This paper proposes an inverter circuit topology capable of generating multilevel octadecagonal voltage space vectors, by cascading two asymmetric three level inverters. By proper selection of DC link voltages and the resultant switching states for the inverters, voltage space vectors, whose tips lie on three concentric octadecagons, are obtained. The advantages of octadecagonal voltage space vector based PWM techniques are the complete elimination of fifth, seventh, eleventh and thirteenth harmonics in phase voltages and the extension of linear modulation range. In this paper, a simple PWM timing calculation method is also proposed. Matlab simulation results and experimental results have been presented in this paper to validate the proposed concept.

Identification of fault location in power distribution system with distributed generation using support vector machines

This paper presents a multi-class support vector machine (SVMs) approach for locating and diagnosing faults in electric power distribution feeders with the penetration of Distributed Generations (DGs). The proposed approach is based on the three phase voltage and current measurements which are available at all the sources i.e. substation and at the connection points of DG. To illustrate the proposed methodology, a practical distribution feeder emanating from 132/11kV-grid substation in India with loads and suitable number of DGs at different locations is considered. To show the effectiveness of the proposed methodology, practical situations in distribution systems (DS) such as all types of faults with a wide range of varying fault locations, source short circuit (SSC) levels and fault impedances are considered for studies. The proposed fault location scheme is capable of accurately identify the fault type, location of faulted feeder section and the fault impedance. The results demonstrate the feasibility of applying the proposed method in practical in smart grid distribution automation (DA) for fault diagnosis.

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

Generation of Ligand Specificity and Modes of Oligomerization in beta-Prism I Fold Lectins

beta-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.

Effect of hinged leaflets on vortex pair generation

We experimentally study the effect of having hinged leaflets at the jet exit on the formation of a two-dimensional counter-rotating vortex pair. A piston-cylinder mechanism is used to generate a starting jet from a high-aspect-ratio channel into a quiescent medium. For a rigid exit, with no leaflets at the channel exit, the measurements at a central plane show that the trailing jet in the present case is never detached from the vortex pair, and keeps feeding into the latter, unlike in the axisymmetric case. Passive flexibility is introduced in the form of rigid leaflets or flaps that are hinged at the exit of the channel, with the flaps initially parallel to the channel walls. The experimental arrangement closely approximates the limiting case of a free-to-rotate rigid flap with negligible structural stiffness, damping and flap inertia, as these limiting structural properties permit the largest flap openings. Using this arrangement, we start the flow and measure the flap kinematics and the vorticity fields for different flap lengths and piston velocity programs. The typical motion of the flaps involves a rapid opening and a subsequent more gradual return to its initial position, both of which occur when the piston is still moving. The initial opening of the flaps can be attributed to an excess pressure that develops in the channel when the flow starts, due to the acceleration that has to be imparted to the fluid slug between the flaps. In the case with flaps, two additional pairs of vortices are formed because of the motion of the flaps, leading to the ejection of a total of up to three vortex pairs from the hinged exit. The flaps' length (L-f) is found to significantly affect flap motions when plotted using the conventional time scale L/d, where L is the piston stroke and d is the channel width. However, with a newly defined time scale based on the flap length (L/L-f), we find a good collapse of all the measured flap motions irrespective of flap length and piston velocity for an impulsively started piston motion. The maximum opening angle in all these impulsive velocity program cases, irrespective of the flap length, is found to be close to 15 degrees. Even though the flap kinematics collapses well with L/L-f, there are differences in the distribution of the ejected vorticity even for the same L/L-f. Such a redistribution of vorticity can lead to important changes in the overall properties of the flow, and it gives us a better understanding of the importance of exit flexibility in such flows.