Tuning DNA-amphiphile condensate architecture with strongly binding counterions

Electrostatic self-assembly of colloidal and nanoparticles has attracted a lot of attention in recent years, since it offers the possibility of producing novel crystalline structures that have the potential to be used as advanced materials for photonic and other applications. The stoichiometry of these crystals is not constrained by charge neutrality of the two types of particles due to the presence of counterions, and hence a variety of three-dimensional structures have been observed depending on the relative sizes of the particles and their charge. Here we report structural polymorphism of two-dimensional crystals of oppositely charged linear macroions, namely DNA and self-assembled cylindrical micelles of cationic amphiphiles. Our system differs from those studied earlier in terms of the presence of a strongly binding counterion that competes with DNA to bind to the micelle. The presence of these counterions leads to novel structures of these crystals, such as a square lattice and a root 3 x root 3 superlattice of an underlying hexagonal lattice, determined from a detailed analysis of the small-angle diffraction data. These lower-dimensional equilibrium systems can play an important role in developing a deeper theoretical understanding of the stability of crystals of oppositely charged particles. Further, it should be possible to use the same design principles to fabricate structures on a longer length-scale by an appropriate choice of the two macroions.

On-Chip Memory Architecture Exploration Framework for DSP Processor-Based Embedded System on Chip

Today's SoCs are complex designs with multiple embedded processors, memory subsystems, and application specific peripherals. The memory architecture of embedded SoCs strongly influences the power and performance of the entire system. Further, the memory subsystem constitutes a major part (typically up to 70%) of the silicon area for the current day SoC. In this article, we address the on-chip memory architecture exploration for DSP processors which are organized as multiple memory banks, where banks can be single/dual ported with non-uniform bank sizes. In this paper we propose two different methods for physical memory architecture exploration and identify the strengths and applicability of these methods in a systematic way. Both methods address the memory architecture exploration for a given target application by considering the application's data access characteristics and generates a set of Pareto-optimal design points that are interesting from a power, performance and VLSI area perspective. To the best of our knowledge, this is the first comprehensive work on memory space exploration at physical memory level that integrates data layout and memory exploration to address the system objectives from both hardware design and application software development perspective. Further we propose an automatic framework that explores the design space identifying 100's of Pareto-optimal design points within a few hours of running on a standard desktop configuration.

Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders

DNA is the chemotherapeutic target for treating diseases of genetic origin. Besides well-known double-helical structures (A, B, Z, parallel stranded-DNA etc.), DNA is capable of forming several multi-stranded structures (triplex, tetraplex, i-motif etc.) which have unique biological significance. The G-rich 3'-ends of chromosomes, called telomeres, are synthesized by telomerase, a ribonucleoprotein, and over-expression of telomerase is associated with cancer. The activity of telomerase is suppressed if the G-rich region is folded into the four stranded structures, called G-quadruplexes (G4-DNAs) using small synthetic ligands. Thus design and synthesis of new G4-DNA ligands is an attractive strategy to combat cancer. G4-DNA forming sequences are also prevalent in other genomic regions of biological significance including promoter regions of several oncogenes. Effective gene regulation may be achieved by inducing a G4-DNA structure within the G-rich promoter sequences. To date, several G4-DNA stabilizing ligands are known. DNA groove binders interact with the duplex B-DNA through the grooves (major and minor groove) in a sequence-specific manner. Some of the groove binders are known to stabilize the G4-DNA. However, this is a relatively under explored field of research. In this review, we focus on the recent advances in the understanding of the G4-DNA structures, particularly made from the human telomeric DNA stretches. We summarize the results of various investigations of the interaction of various organic ligands with the G4-DNA while highlighting the importance of groove binder-G4-DNA interactions.

Statistical Methods for Accelerated Life Testing with Particular Reference to Resin Impregnated Paper Bushings

Electrical failure of insulation is known to be an extremal random process wherein nominally identical pro-rated specimens of equipment insulation, at constant stress fail at inordinately different times even under laboratory test conditions. In order to be able to estimate the life of power equipment, it is necessary to run long duration ageing experiments under accelerated stresses, to acquire and analyze insulation specific failure data. In the present work, Resin Impregnated Paper (RIP) a relatively new insulation system of choice used in transformer bushings, is taken as an example. The failure data has been processed using proven statistical methods, both graphical and analytical. The physical model governing insulation failure at constant accelerated stress has been assumed to be based on temperature dependent inverse power law model.

HD resolution intra prediction architecture for H.264 decoder

High performance video standards use prediction techniques to achieve high picture quality at low bit rates. The type of prediction decides the bit rates and the image quality. Intra Prediction achieves high video quality with significant reduction in bit rate. This paper presents novel area optimized architecture for Intra prediction of H.264 decoding at HDTV resolution. The architecture has been validated on a Xilinx Virtex-5 FPGA based platform and achieved a frame rate of 64 fps. The architecture is based on multi-level memory hierarchy to reduce latency and ensure optimum resources utilization. It removes redundancy by reusing same functional blocks across different modes. The proposed architecture uses only 13% of the total LUTs available on the Xilinx FPGA XC5VLX50T.

Adaptive power optimization of on-chip SNUCA cache on tiled chip multicore architecture using remap policy

Advances in technology have increased the number of cores and size of caches present on chip multicore platforms(CMPs). As a result, leakage power consumption of on-chip caches has already become a major power consuming component of the memory subsystem. We propose to reduce leakage power consumption in static nonuniform cache architecture(SNUCA) on a tiled CMP by dynamically varying the number of cache slices used and switching off unused cache slices. A cache slice in a tile includes all cache banks present in that tile. Switched-off cache slices are remapped considering the communication costs to reduce cache usage with minimal impact on execution time. This saves leakage power consumption in switched-off L2 cache slices. On an average, there map policy achieves 41% and 49% higher EDP savings compared to static and dynamic NUCA (DNUCA) cache policies on a scalable tiled CMP, respectively.

Power scalable digital baseband architecture for IEEE 802.15.4

We propose a power scalable digital base band for a low-IF receiver for IEEE 802.15.4-2006. The digital section's sampling frequency and bit width are used as knobs to reduce the power under favorable signal and interference scenarios, thus recovering the design margins introduced to handle worst case conditions. We propose tuning of these knobs based on measurements of Signal and the interference levels. We show that in a 0.13u CMOS technology, for an adaptive digital base band section of the receiver designed to meet the 802.15.4 standard specification, power saving can be up to nearly 85% (0.49mW against 3.3mW) in favorable interference and signal conditions.

USHA: unified software and hardware architecture for video decoding

Video decoders used in emerging applications need to be flexible to handle a large variety of video formats and deliver scalable performance to handle wide variations in workloads. In this paper we propose a unified software and hardware architecture for video decoding to achieve scalable performance with flexibility. The light weight processor tiles and the reconfigurable hardware tiles in our architecture enable software and hardware implementations to co-exist, while a programmable interconnect enables dynamic interconnection of the tiles. Our process network oriented compilation flow achieves realization agnostic application partitioning and enables seamless migration across uniprocessor, multi-processor, semi hardware and full hardware implementations of a video decoder. An application quality of service aware scheduler monitors and controls the operation of the entire system. We prove the concept through a prototype of the architecture on an off-the-shelf FPGA. The FPGA prototype shows a scaling in performance from QCIF to 1080p resolutions in four discrete steps. We also demonstrate that the reconfiguration time is short enough to allow migration from one configuration to the other without any frame loss.

Periodic architecture for high performance shock absorbing composites

A novel composite architecture consisting of a periodic arrangement of closely-spaced spheres of a stiff material embedded in a soft matrix is proposed for extremely high damping and shock absorption capacity. Efficacy of this architecture is demonstrated by compression loading a composite, where multiple steel balls were stacked upon each other in a polydimethylsiloxane (PDMS) matrix, at a low strain-rate of 0.05 s(-1) and a very high strain-rate of >2400 s(-1). The balls slide over each other upon loading, and revert to their original position when the load is removed. Because of imposition of additional strains into the matrix via this reversible, constrained movement of the balls, the composite absorbs significantly larger energy and endures much lesser permanent damage than the monolithic PDMS during both quasi-static and impact loadings. During the impact loading, energy absorbed per unit weight for the composite was, 8 times larger than the monolithic PDMS.

Unified Taxonomy for Reference Ontology of Shape Features in Product Model

This paper presents a unified taxonomy of shape features. Such taxonomy is required to construct ontologies to address heterogeneity in product/shape models. Literature provides separate classifications for volumetric, deformation and free-form surface features. The unified taxonomy proposed allows classification, representation and extraction of shape features in a product model. The novelty of the taxonomy is that the classification is based purely on shape entities and therefore it is possible to automatically extract the features from any shape model. This enables the use of this taxonomy to build reference ontology.

e-SURAKSHAK: A Cyber-Physical Healthcare System with Service Oriented Architecture

In this paper we present the design of ``e-SURAKSHAK,'' a novel cyber-physical health care management system of Wireless Embedded Internet Devices (WEIDs) that sense vital health parameters. The system is capable of sensing body temperature, heart rate, oxygen saturation level and also allows noninvasive blood pressure (NIBP) measurement. End to end internet connectivity is provided by using 6LoWPAN based wireless network that uses the 802.15.4 radio. A service oriented architecture (SOA) 1] is implemented to extract meaningful information and present it in an easy-to-understand form to the end-user instead of raw data made available by sensors. A central electronic database and health care management software are developed. Vital health parameters are measured and stored periodically in the database. Further, support for real-time measurement of health parameters is provided through a web based GUI. The system has been implemented completely and demonstrated with multiple users and multiple WEIDs.

DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. CEREVISIAE

Gene expression is the most fundamental biological process, which is essential for phenotypic variation. It is regulated by various external (environment and evolution) and internal (genetic) factors. The level of gene expression depends on promoter architecture, along with other external factors. Presence of sequence motifs, such as transcription factor binding sites (TFBSs) and TATA-box, or DNA methylation in vertebrates has been implicated in the regulation of expression of some genes in eukaryotes, but a large number of genes lack these sequences. On the other hand, several experimental and computational studies have shown that promoter sequences possess some special structural properties, such as low stability, less bendability, low nucleosome occupancy, and more curvature, which are prevalent across all organisms. These structural features may play role in transcription initiation and regulation of gene expression. We have studied the relationship between the structural features of promoter DNA, promoter directionality and gene expression variability in S. cerevisiae. This relationship has been analyzed for seven different measures of gene expression variability, along with two different regulatory effect measures. We find that a few of the variability measures of gene expression are linked to DNA structural properties, nucleosome occupancy, TATA-box presence, and bidirectionality of promoter regions. Interestingly, gene responsiveness is most intimately correlated with DNA structural features and promoter architecture.

Average Modelling of a Voltage Source Inverter with Dead-Time in a Synchronous Reference Frame

Voltage source inverters are an integral part of renewable power sources and smart grid systems. Computationally efficient and fairly accurate models for the voltage source inverter are required to carry out extensive simulation studies on complex power networks. Accuracy requires that the effect of dead-time be incorporated in the inverter model. The dead-time is essentially a short delay introduced between the gating pulses to the complementary switches in an inverter leg for the safety of power devices. As the modern voltage source inverters switch at fairly high frequencies, the dead-time significantly influences the output fundamental voltage. Dead-time also causes low-frequency harmonic distortion and is hence important from a power quality perspective. This paper studies the dead-time effect in a synchronous dq reference frame, since dynamic studies and controller design are typically carried out in this frame of reference. For the sake of computational efficiency, average models are derived, incorporating the dead-time effect, in both RYB and dq reference frames. The average models are shown to consume less computation time than their corresponding switching models, the accuracies of the models being comparable. The proposed average synchronous reference frame model, including effect of dead-time, is validated through experimental results.