Design issues and caching strategies for CD-ROM based multimedia storage

CD-ROMs have proliferated as a distribution media for desktop machines for a large variety of multimedia applications (targeted for a single-user environment) like encyclopedias, magazines and games. With CD-ROM capacities up to 3 GB being available in the near future, they will form an integral part of Video on Demand (VoD) servers to store full-length movies and multimedia. In the first section of this paper we look at issues related to the single- user desktop environment. Since these multimedia applications are highly interactive in nature, we take a pragmatic approach, and have made a detailed study of the multimedia application behavior in terms of the I/O request patterns generated to the CD-ROM subsystem by tracing these patterns. We discuss prefetch buffer design and seek time characteristics in the context of the analysis of these traces. We also propose an adaptive main-memory hosted cache that receives caching hints from the application to reduce the latency when the user moves from one node of the hyper graph to another. In the second section we look at the use of CD-ROM in a VoD server and discuss the problem of scheduling multiple request streams and buffer management in this scenario. We adapt the C-SCAN (Circular SCAN) algorithm to suit the CD-ROM drive characteristics and prove that it is optimal in terms of buffer size management. We provide computationally inexpensive relations by which this algorithm can be implemented. We then propose an admission control algorithm which admits new request streams without disrupting the continuity of playback of the previous request streams. The algorithm also supports operations such as fast forward and replay. Finally, we discuss the problem of optimal placement of MPEG streams on CD-ROMs in the third section.

Interactions of 3' terminal and 5' terminal regions of physalis mottle virus genomic RNA with its replication complex

Physalis mottle virus (PhMV) belongs to the tymogroup of positive-strand RNA viruses with a genome size of 6 kb. Crude membrane preparations from PhMV-infected Nicotiana glutinosa plants catalyzed the synthesis of PhMV genomic RNA from endogenously bound template. Addition of exogenous genomic RNA enhanced the synthesis which was specifically inhibited by the addition of sense and antisense transcripts corresponding to 3' terminal 242 nucleotides as well as the 5' terminal 458 nucleotides of PhMV genomic RNA while yeast tRNA or ribosomal RNA failed to inhibit the synthesis. This specific inhibition suggested that the 5' and 3' non-coding regions of PhMV RNA might play an important role in viral replication.

Sequential Assembly of an Active RNA Polymerase Molecule at the Air-Water Interface

At the heart of understanding cellular processes lies our ability to explore the specific nature of communication between sequential information carrying biopolymers. However, the data extracted from conventional solution phase studies may not reflect the dynamics of communication between recognized partners as they occur in the crowded cellular milieu. We use the principle of immobilization of histidine-tagged biopolymers at a Ni(II)-encoded Langmuir monolayer to study sequence-specific protein-protein interactions in an artificially crowded environment The advantage of this technique lies in increasing the surface density of one of the interacting partners that allows us to study macromolecular interactions in a controlled crowded environment, but without compromising the speed of the reactions. We have taken advantage of this technique to follow the sequential assembly process of the multiprotein complex Escherichia coil RNA polymerase at the interface and also deciphered the role of one of the proteins, omega (omega), in the assembly pathway. Our reconstitution studies indicate that in the absence of molecular chaperones or other cofactors, omega (omega) plays a decisive role in refolding the largest protein beta prime (beta') and its recruitment into the multimeric assembly to reconstitute an active RNA polymerase. It was also observed that the monolayer had the ability to distinguish between sequence-specific and -nonspecific interactions despite the immobilization of one of the biomacromolecules. The technique provides a universal two-dimensional template for studying protein-ligand interactions while mimicking molecular crowding.

A facile route to synthesize silver nanoparticles in polyelectrolyte capsules

We are reporting a novel green approach to incorporate silver nanoparticles (NPs) selectively in the polyelectrolyte capsule shell for remote opening of polyelectrolyte capsules. This approach involves in situ reduction of silver nitrate to silver NPs using PEG as a reducing agent (polyol reduction method). These nanostructured capsules were prepared via layer by layer (LbL) assembly of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on silica template followed by the synthesis of silver NPs and subsequently the dissolution of the silica core. The size of silver nanoparticles synthesized was 60 +/- 20 nm which increased to 100 +/- 20 nm when the concentration of AgNO3 increased from 25 mM to 50 mM. The incorporated silver NPs induced rupture and deformation of the capsules under laser irradiation. This method has advantages over other conventional methods involving chemical agents that are associated with cytotoxicity in biological applications such as drug delivery and catalysis. (C) 2011 Elsevier B.V. All rights reserved.

Role of spacer chain length in dimeric micellar organization. Small angle neutron scattering and fluorescence studies

Micelles of different dimeric amphiphiles Br-, n-C(16)H(33)NMe(2)(+) -(CH)(m)-N(+)Me(2)-n-C16H33, Br- (where m = 3, 4, 5, 6, 8, 10, and 12) adapt different morphologies and internal packing arrangements in aqueous media depending on their spacer chain length (m). Detailed measurements of small angle neutron scattering (SANS) cross sections from different bis-cationic, dimeric surfactant micelles in aqueous media (D2O) are reported. The data have been analyzed using the Hayter and Penfold model for macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric micelles. The SANS analysis clearly indicated that the extent of aggregate growth and the variations of shapes of the dimeric micelles depend primarily on the spacer chain length. With spacer chain length, m less than or equal to 4, the propensity of micellar growth was particularly pronounced. The effects of the variation of the concentration of dimeric surfactants with m = 5 and 10 on the SANS spectra and the effects of the temperature variation for the micellar system with m = 10 were also examined. The critical micelle concentrations (cmc) and their microenvironmental feature, namely, the microviscosities that the dimeric micellar aggregates offer to a solubilized, extrinsic fluorescence probe, 1,6-diphenyl-1,3,5-hexatriene, were also determined. The changes of cmcs and microviscosities as a function of spacer chain length have been explained in terms of conformational variations and progressive looping of the spacer in micellar core upon increasing m values.

Preparation and characterization of multiwall carbon nanotube/polypyrrole coaxial fibrils

Multiwall carbon nanotube (MWNT)/polypyrrole (PPy) fibrils were fabricated by template-free in situ electrochemical deposition of PPy over MWNTs, and characterized by electron microscopy and electrical measurements. Scanning and transmission electron microscopy studies reveal that PPy coating on the surface of nanotube is quite uniform throughout the length, with the possibility of forming unique Y-junctions. Current (I)-voltage (V) characteristics at various temperatures show nonlinearity due to tunneling and hopping contributions to transport across the barriers. AC conductivity measurements (300-4.2 K) show that the onset frequency scales with temperature, and the nanoscale connectivity in MWNT/PPy fibrils decreases with the lowering of temperature. (C) 2011 Elsevier B.V. All rights reserved.

Synthesis and structural characterization of perovskite 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3) nanotubes

We report the synthesis and structural characterization of 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3) (PMN-PT) nanotubes prepared by a novel sal-gel template method. X-ray diffraction (XRD) and selected-area electron diffraction (SAED) investigations demonstrated that the postannealed (650 degrees C for 1 h) PMN-PT nanotubes were polycrystalline with perovskite crystal structure. The field emission scanning electron microscope (FE-SEM) shows that as prepared PMN-PT nanotubes were hollow with diameter to be about 200 nm. High resolution transmission electron microscope (HRTEM) analysis confirmed that the obtained PMN-PT nanotubes made up of nanoparticles (10-20 nm) which were randomly aligned in the nanotubes. Energy-dispersive X-ray spectroscopy (EDX) analysis confirmed the stoichiometric 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3). The possible formation mechanism of PMN-PT nanotubes was proposed at the end. (C) 2011 Elsevier B.V. All rights reserved.

Nanoporous alloy aggregates: synthesis and electrocatalytic activity

Nanoporous structures are widely used for many applications and hence there have been several efforts directed towards their synthesis. While several template-based and template-less approaches are available for monometallic systems, there is no general method for the synthesis of nanoporous multicomponent systems/alloys. We present a general template-less strategy for the synthesis of nanoporous alloy aggregates by controlled aggregation of nanoparticles in the solution phase with excellent control over morphology and composition as illustrated using AuPt, AuPd, PdPt and PtRu systems as examples. The Pt-based nanoporous clusters exhibit excellent activity for methanol oxidation with good long-term stability and CO tolerance. We show that the method can be extended to produce ternary catalysts and hence we expect our method to be widely used for the synthesis of multifunctional nanoporous structures for catalysis, sensor and drug-delivery applications.

An Efficient Robust Algorithm for the Surface-Potential Calculation of Independent DG MOSFET

Although the recently proposed single-implicit-equation-based input voltage equations (IVEs) for the independent double-gate (IDG) MOSFET promise faster computation time than the earlier proposed coupled-equations-based IVEs, it is not clear how those equations could be solved inside a circuit simulator as the conventional Newton-Raphson (NR)-based root finding method will not always converge due to the presence of discontinuity at the G-zero point (GZP) and nonremovable singularities in the trigonometric IVE. In this paper, we propose a unique algorithm to solve those IVEs, which combines the Ridders algorithm with the NR-based technique in order to provide assured convergence for any bias conditions. Studying the IDG MOSFET operation carefully, we apply an optimized initial guess to the NR component and a minimized solution space to the Ridders component in order to achieve rapid convergence, which is very important for circuit simulation. To reduce the computation budget further, we propose a new closed-form solution of the IVEs in the near vicinity of the GZP. The proposed algorithm is tested with different device parameters in the extended range of bias conditions and successfully implemented in a commercial circuit simulator through its Verilog-A interface.

Zirconia nanotubes

Hollow nanotubes of zirconia as well as of yttria-stabilized zirconia are successfully prepared by first coating the carbon nanotubes appropriately with the oxidic material and then burning off the carbon of the template.

Synthesis, spectral characterization and in vitro microbiological evaluation of novel glyoxal, biacetyl and benzil bis-hydrazone macrocyclic Schiff bases and their Co(II), Ni(II) and Cu(II) complexes

A series of binuclear Co(II), Ni(II) and Cu(II) complexes were synthesized by the template condensation of glyoxal, biacetyl or benzil bis-hydrazide, 2,6-diformyl-4-methylphenol and Co(11), Ni(II) or Cu(II) chloride in a 2:2:2 M ratio in ethanol. These 22-membered macrocyclic complexes were characterized by elemental analyses, magnetic, molar conductance, spectral, thermal and fluorescence studies. Elemental analyses suggest the complexes have a 2:1 stoichiometry of the type (M2LX2]center dot nH(2)O and Ni(2)LX(2)2H(2)O]center dot nH(2)O (where M = Co(II) and Cu(II); L = H2L1, H2L2 and H2L3; X = Cl; n = 2). From the spectroscopic and magnetic studies, it has been concluded that the Co(11) and Cu(11) complexes display a five coordinated square pyramidal geometry and the Ni(II) complexes have a six coordinated octahedral geometry. The Schiff bases and their metal complexes have also been screened for their antibacterial and antifungal activities by the MIC method. (C) 2011 Elsevier Ltd. All rights reserved.

Characterization of RNA polymerase III transcription factor TFIIIC from the mulberry silkworm, Bombyx mori

Fractionation of nuclear extracts from posterior silk glands of mulberry silkworm Bombyx mori. resolved the transcription factor TFIIIC into two components (designated here as TFIIIC and TFIIIC1) as in HeLa cell nuclear extracts. The reconstituted transcription of tRNA genes required the presence of both components. The affinity purified TFIIIC is a heteromeric complex comprising of five subunits ranging from 44 to 240 kDa. Of these, the 51-kDa subunit could be specifically crosslinked to the B box of tRNA(1)(Gly). Purified swTFIIIC binds to the B box sequences with an affinity in the same range as of yTFIIIC or hTFIIIC2. Although an histone acetyl transferase (HAT) activity was associated with the TFIIIC fractions during the initial stages of purification. the HAT activity, unlike the human TFIIIC preparations, was separated at the final DNA affinity step. The tRNA transcription from DNA template was independent of HAT activity but the repressed transcription from chromatin template could be partially restored by external supplementation of the dissociated HAT activity. This is the first report on the purification and characterization of TFIIIC from insect systems.

An Optimized SDE Model for Slotted Aloha

We consider a stochastic differential equation (SDE) model of slotted Aloha with the retransmission probability as the associated parameter. We formulate the problem in both (a) the finite horizon and (b) the infinite horizon average cost settings. We apply the algorithm of 3] for the first setting, while for the second, we adapt a related algorithm from 2] that was originally developed in the simulation optimization framework. In the first setting, we obtain an optimal parameter trajectory that prescribes the parameter to use at any given instant while in the second setting, we obtain an optimal time-invariant parameter. Our algorithms are seen to exhibit good performance.

Discovery of Application Workloads from Network File Traces

An understanding of application I/O access patterns is useful in several situations. First, gaining insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enable it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.

A Transcript Cleavage Factor of Mycobacterium tuberculosis Important for Its Survival

After initiation of transcription, a number of proteins participate during elongation and termination modifying the properties of the RNA polymerase (RNAP). Gre factors are one such group conserved across bacteria. They regulate transcription by projecting their N-terminal coiled-coil domain into the active center of RNAP through the secondary channel and stimulating hydrolysis of the newly synthesized RNA in backtracked elongation complexes. Rv1080c is a putative gre factor (MtbGre) in the genome of Mycobacterium tuberculosis. The protein enhanced the efficiency of promoter clearance by lowering abortive transcription and also rescued arrested and paused elongation complexes on the GC rich mycobacterial template. Although MtbGre is similar in domain organization and shares key residues for catalysis and RNAP interaction with the Gre factors of Escherichia coli, it could not complement an E. coli gre deficient strain. Moreover, MtbGre failed to rescue E. coli RNAP stalled elongation complexes, indicating the importance of specific protein-protein interactions for transcript cleavage. Decrease in the level of MtbGre reduced the bacterial survival by several fold indicating its essential role in mycobacteria. Another Gre homolog, Rv3788 was not functional in transcript cleavage activity indicating that a single Gre is sufficient for efficient transcription of the M. tuberculosis genome.