Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.

Codes with Locality for Two Erasures

In this paper, we study codes with locality that can recover from two erasures via a sequence of two local, parity-check computations. By a local parity-check computation, we mean recovery via a single parity-check equation associated with small Hamming weight. Earlier approaches considered recovery in parallel; the sequential approach allows us to potentially construct codes with improved minimum distance. These codes, which we refer to as locally 2-reconstructible codes, are a natural generalization along one direction, of codes with all-symbol locality introduced by Gopalan et al, in which recovery from a single erasure is considered. By studying the generalized Hamming weights of the dual code, we derive upper bounds on the minimum distance of locally 2-reconstructible codes and provide constructions for a family of codes based on Turan graphs, that are optimal with respect to this bound. The minimum distance bound derived here is universal in the sense that no code which permits all-symbol local recovery from 2 erasures can have larger minimum distance regardless of approach adopted. Our approach also leads to a new bound on the minimum distance of codes with all-symbol locality for the single-erasure case.

Common-Mode Injection PWM for Parallel Converters

The ac-side terminal voltages of parallel-connected converters are different if the line reactive drops of the individual converters are different. This could result either from differences in per-phase inductances or from differences in the line currents of the converters. In such cases, the modulating signals are different for the converters. Hence, the common-mode (CM) voltages for the converters, injected by conventional space vector pulsewidth modulation (CSVPWM) to increase dc-bus utilization, are different. Consequently, significant low-frequency zero-sequence circulating currents result. This paper proposes a new modulation method for parallel-connected converters with unequal terminal voltages. This method does not cause low-frequency zero-sequence circulating currents and is comparable with CSVPWM in terms of dc-bus utilization and device power loss. Experimental results are presented at a power level of 150 kVA from a circulating-power test setup, where the differences in converter terminal voltages are quite significant.

3-D GPU Based Real Time Diffuse Optical Tomographic System

3-Dimensional Diffuse Optical Tomographic (3-D DOT) image reconstruction algorithm is computationally complex and requires excessive matrix computations and thus hampers reconstruction in real time. In this paper, we present near real time 3D DOT image reconstruction that is based on Broyden approach for updating Jacobian matrix. The Broyden method simplifies the algorithm by avoiding re-computation of the Jacobian matrix in each iteration. We have developed CPU and heterogeneous CPU/GPU code for 3D DOT image reconstruction in C and MatLab programming platform. We have used Compute Unified Device Architecture (CUDA) programming framework and CUDA linear algebra library (CULA) to utilize the massively parallel computational power of GPUs (NVIDIA Tesla K20c). The computation time achieved for C program based implementation for a CPU/GPU system for 3 planes measurement and FEM mesh size of 19172 tetrahedral elements is 806 milliseconds for an iteration.

Effect of Micro-Structured Copper as Cathode Material for P3HT-Based Diode

Here, the effect of micro-structured cathode material on the device performance of indium tin oxide/poly(3hexylethiophene)/copper diode (ITO/P3HT/Cu) is investigated. Two different forms of copper namely bulk metal (Cu{B}) and nanoparticle (Cu{N}) were used as top electrode to probe its effect on device performance. Crystallographic structure and nanoscale morphology of top Cu electrodes were characterized using X-ray diffraction and scanning electronmicroscopy. Electrode formed by evaporation of copper nanoparticle showed enhancement in current density. From capacitance based spectroscopy we observed that density of trap states in ITO/P3HT/copper larger size grain (Cu-LG) are one order greater than that in ITO/P3HT/copper smaller size grain (Cu-SG) device.

A 0.5-2.0 GHz injection locked oscillator cascade for parallel wideband RF spectrum sensing

An area-efficient, wideband RF frequency synthesizer, which simultaneously generates multiple local oscillator (LO) signals, is designed. It is suitable for parallel wideband RF spectrum sensing in cognitive radios. The frequency synthesizer consists of an injection locked oscillator cascade (ILOC) where all the LO signals are derived from a single reference oscillator. The ILOC is implemented in a 130-nm technology with an active area of . It generates 4 uniformly spaced LO carrier frequencies from 500 MHz to 2 GHz. This design is the first known implementation of a CMOS based ILOC for wide-band RF spectrum sensing applications.

Prediction of Queue Waiting Times for Metascheduling on Parallel Batch Systems

Prediction of queue waiting times of jobs submitted to production parallel batch systems is important to provide overall estimates to users and can also help meta-schedulers make scheduling decisions. In this work, we have developed a framework for predicting ranges of queue waiting times for jobs by employing multi-class classification of similar jobs in history. Our hierarchical prediction strategy first predicts the point wait time of a job using dynamic k-Nearest Neighbor (kNN) method. It then performs a multi-class classification using Support Vector Machines (SVMs) among all the classes of the jobs. The probabilities given by the SVM for the class predicted using k-NN and its neighboring classes are used to provide a set of ranges of predicted wait times with probabilities. We have used these predictions and probabilities in a meta-scheduling strategy that distributes jobs to different queues/sites in a multi-queue/grid environment for minimizing wait times of the jobs. Experiments with different production supercomputer job traces show that our prediction strategies can give correct predictions for about 77-87% of the jobs, and also result in about 12% improved accuracy when compared to the next best existing method. Experiments with our meta-scheduling strategy using different production and synthetic job traces for various system sizes, partitioning schemes and different workloads, show that the meta-scheduling strategy gives much improved performance when compared to existing scheduling policies by reducing the overall average queue waiting times of the jobs by about 47%.

Structured illumination microscopy

Illumination plays an important role in optical microscopy. Kohler illumination, introduced more than a century ago, has been the backbone of optical microscopes. The last few decades have seen the evolution of new illumination techniques meant to improve certain imaging capabilities of the microscope. Most of them are, however, not amenable for wide-field observation and hence have restricted use in microscopy applications such as cell biology and microscale profile measurements. The method of structured illumination microscopy has been developed as a wide-field technique for achieving higher performance. Additionally, it is also compatible with existing microscopes. This method consists of modifying the illumination by superposing a well-defined pattern on either the sample itself or its image. Computational techniques are applied on the resultant images to remove the effect of the structure and to obtain the desired performance enhancement. This method has evolved over the last two decades and has emerged as a key illumination technique for optical sectioning, super-resolution imaging, surface profiling, and quantitative phase imaging of microscale objects in cell biology and engineering. In this review, we describe various structured illumination methods in optical microscopy and explain the principles and technologies involved therein. (C) 2015 Optical Society of America

An Optimizing Code Generator for a Class of Lattice-Boltzmann Computations

The Lattice-Boltzmann method (LBM), a promising new particle-based simulation technique for complex and multiscale fluid flows, has seen tremendous adoption in recent years in computational fluid dynamics. Even with a state-of-the-art LBM solver such as Palabos, a user has to still manually write the program using library-supplied primitives. We propose an automated code generator for a class of LBM computations with the objective to achieve high performance on modern architectures. Few studies have looked at time tiling for LBM codes. We exploit a key similarity between stencils and LBM to enable polyhedral optimizations and in turn time tiling for LBM. We also characterize the performance of LBM with the Roofline performance model. Experimental results for standard LBM simulations like Lid Driven Cavity, Flow Past Cylinder, and Poiseuille Flow show that our scheme consistently outperforms Palabos-on average by up to 3x while running on 16 cores of an Intel Xeon (Sandybridge). We also obtain an improvement of 2.47x on the SPEC LBM benchmark.

Three-degree-of-freedom Parallel Manipulator to Track the Sun for Concentrated Solar Power Systems

In concentrated solar power(CSP) generating stations, incident solar energy is reflected from a large number of mirrors or heliostats to a faraway receiver. In typical CSP installations, the mirror needs to be moved about two axes independently using two actuators in series with the mirror effectively mounted at a single point. A three degree-of-freedom parallel manipulator, namely the 3-RPS parallel manipulator, is proposed to track the sun. The proposed 3-RPS parallel manipulator supports the load of the mirror, structure and wind loading at three points resulting in less deflection, and thus a much larger mirror can be moved with the required tracking accuracy and without increasing the weight of the support structure. The kinematics equations to determine motion of the actuated prismatic joints in the 3-RPS parallel manipulator such that the sun's rays are reflected on to a stationary receiver are developed. Using finite element analysis, it is shown that for same sized mirror, wind loading and maximum deflection requirement, the weight of the support structure is between 15% and 60% less with the 3-RPS parallel manipulator when compared to azimuth-elevation or the target-aligned configurations.

An efficient design of serial and parallel memory using Quantum dot cellular automata

Quantum cellular automata (QCA) is a new technology in the nanometer scale and has been considered as one of the alternative to CMOS technology. In this paper, we describe the design and layout of a serial memory and parallel memory, showing the layout of individual memory cells. Assuming that we can fabricate cells which are separated by 10nm, memory capacities of over 1.6 Gbit/cm2 can be achieved. Simulations on the proposed memories were carried out using QCADesigner, a layout and simulation tool for QCA. During the design, we have tried to reduce the number of cells as well as to reduce the area which is found to be 86.16sq mm and 0.12 nm2 area with the QCA based memory cell. We have also achieved an increase in efficiency by 40%.These circuits are the building block of nano processors and provide us to understand the nano devices of the future.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel -sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac(12)c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac(12)c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C-,C--dialkylated residue Ac(12)c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel -sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac(12)c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel -sheet in crystals, twisted or helical -sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted -sheet assembly in crystals. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd.