Kinetics of interaction of Cotton Leaf Curl Kokhran Virus-Dabawali (CLCuKV-Dab) coat protein and its mutants with ssDNA

Gemini viral assembly and transport of viral DNA into nucleus for replication, ssentially involve DNA-coat protein interactions. The kinetics of interaction of Cotton LeafCtirl Kokhran Virus-Dabawali recombinant coat protein (rCP) with DNA was studied by electrophoretic mobility shift assay (EMSA) and Surface plasmon resonance (SPR). The rCP interacted with ssDNA with a K-A, of 2.6 +/- 0.29 x 10(8) M-1 in a sequence non-specific manner. The CP has a conserved C2H2 type zinc finger motif composed of residues C68, C72, H81 and H85. Mutation of these residues to alanine resulted in reduced binding to DNA probes. The H85A mutant rCP showed the least binding with approximately 756 fold loss in the association rate and a three order magnitude decrease in the binding affinity as compared to rCP. The CP-DNA interactions via the zinc finger motif could play a Crucial role ill Virus assembly and in nuclear transport. (C) 2009 Elsevier Inc.

Unusual effects of anisotropic bonding in Cu(II) and Ni(II) oxides with K2NiF4 structure

Geometric constraints present in A2BO4 compounds with the tetragonal-T structure of K2NiF4 impose a strong pressure on the B---OII---B bonds and a stretching of the A---OI---A bonds in the basal planes if the tolerance factor is t congruent with RAO/√2 RBO < 1, where RAO and RBO are the sums of the A---O and B---O ionic radii. The tetragonal-T phase of La2NiO4 becomes monoclinic for Pr2NiO4, orthorhombic for La2CuO4, and tetragonal-T′ for Pr2CuO4. The atomic displacements in these distorted phases are discussed and rationalized in terms of the chemistry of the various compounds. The strong pressure on the B---OII---B bonds produces itinerant σ*x2−y2 bands and a relative stabilization of localized dz2 orbitals. Magnetic susceptibility and transport data reveal an intersection of the Fermi energy with the d2z2 levels for half the copper ions in La2CuO4; this intersection is responsible for an intrinsic localized moment associated with a configuration fluctuation; below 200 K the localized moment smoothly vanishes with decreasing temperature as the d2z2 level becomes filled. In La2NiO4, the localized moments for half-filled dz2 orbitals induce strong correlations among the σ*x2−y2 electrons above Td reverse similar, equals 200 K; at lower temperatures the σ*x2−y2 electrons appear to contribute nothing to the magnetic susceptibility, which obeys a Curie-Weiss law giving a μeff corresponding to S = 1/2, but shows no magnetic order to lowest temperatures. These surprising results are verified by comparison with the mixed systems La2Ni1−xCuxO4 and La2−2xSr2xNi1−xTixO4. The onset of a charge-density wave below 200 K is proposed for both La2CuO4 and La2NiO4, but the atomic displacements would be short-range cooperative in mixed systems. The semiconductor-metallic transitions observed in several systems are found in many cases to obey the relation Ea reverse similar, equals kTmin, where varrho = varrho0exp(−Ea/kT) and Tmin is the temperature of minimum resistivity varrho. This relation is interpreted in terms of a diffusive charge-carrier mobility with Ea reverse similar, equals ΔHm reverse similar, equals kT at T = Tmin.

Design and analysis of rate aware ad hoc 802.11 networks

802.11 WLANs are characterized by high bit error rate and frequent changes in network topology. The key feature that distinguishes WLANs from wired networks is the multi-rate transmission capability, which helps to accommodate a wide range of channel conditions. This has a significant impact on higher layers such as routing and transport levels. While many WLAN products provide rate control at the hardware level to adapt to the channel conditions, some chipsets like Atheros do not have support for automatic rate control. We first present a design and implementation of an FER-based automatic rate control state machine, which utilizes the statistics available at the device driver to find the optimal rate. The results show that the proposed rate switching mechanism adapts quite fast to the channel conditions. The hop count metric used by current routing protocols has proven itself for single rate networks. But it fails to take into account other important factors in a multi-rate network environment. We propose transmission time as a better path quality metric to guide routing decisions. It incorporates the effects of contention for the channel, the air time to send the data and the asymmetry of links. In this paper, we present a new design for a multi-rate mechanism as well as a new routing metric that is responsive to the rate. We address the issues involved in using transmission time as a metric and presents a comparison of the performance of different metrics for dynamic routing.

Entropy and dynamics of water in hydration layers of a bilayer

We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (T Delta S) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules. (C) 2010 American Institute of Physics. doi:10.1063/1.3494115]

Memory Bandwidth and Power Reduction Using Lossy Reference Frame Compression in Video Encoding

Large external memory bandwidth requirement leads to increased system power dissipation and cost in video coding application. Majority of the external memory traffic in video encoder is due to reference data accesses. We describe a lossy reference frame compression technique that can be used in video coding with minimal impact on quality while significantly reducing power and bandwidth requirement. The low cost transformless compression technique uses lossy reference for motion estimation to reduce memory traffic, and lossless reference for motion compensation (MC) to avoid drift. Thus, it is compatible with all existing video standards. We calculate the quantization error bound and show that by storing quantization error separately, bandwidth overhead due to MC can be reduced significantly. The technique meets key requirements specific to the video encode application. 24-39% reduction in peak bandwidth and 23-31% reduction in total average power consumption are observed for IBBP sequences.

Surface resistance and residual losses of Ag?doped YBa2Cu3O7?? thin films on sapphire

High?quality Ag?doped YBa2Cu3O7?? thin films have been grown by laser ablation on R?plane ?1102? sapphire without any buffer layer. Thin films have been found to be highly c?axis oriented with Tc=90 K, transition width ?T?1 K, and transport Jc=1.2×106 A?cm?2 at 77 K in self?field conditions. The microwave surface resistance of these films measured on patterned microstrip resonators has been found to be 530 ?? at 10 GHz at 77 K which is the lowest reported on unbuffered sapphire. Improved in?plane epitaxy and reduced reaction rate between the substrate and the film caused due to Ag in the film are believed to be responsible for this greatly improved microwave surface resistance. © 1995 American Institute of Physics.

Influence of the ferromagnetic layer on the pair breaking and low alternating current field magnetic response in superconductor/ferromagnet bilayer

We investigate the influence of the ferromagnetic layer on the magnetic and transport properties of YBa2Cu3O7-delta in YBa2Cu3O7-delta (YBCO)/La0.7Sr0.3MnO3 (LSMO) bilayers. The temperature dependent dc magnetization study reveals the presence of magnetic anisotropy in YBCO/LSMO bilayer as compared to the pure YBCO layer. The ac susceptibility study on YBCO/LSMO bilayers reveals stronger pinning and the temperature dependent critical current is found to be less prone to temperature. Besides, the current (I) dependent electrical transport studies on YBCO/LSMO exhibit a significant reduction in the superconducting T-c with increase in I and it follows I-2/3 dependence in accord with the pair breaking effect. The higher reduction of superconducting T-c in YBCO/LSMO is believed to be due to the enhanced pair-breaking induced by the spin polarized carriers being injected into the superconductor. (C) 2011 American Institute of Physics. doi: 10.1063/1.3560029]

Synthesis and properties of nanodispersed granular materials

Nanometric granular materials represent a new class of materials with significant promise. We shall discuss in this paper two phase granular materials where one of the phases having nanometric dimension is embedded in a matrix of larger dimension. These materials show many interesting properties which include structural, magnetic and transport properties, The phase transformation of the embedded particles shows distinctive behavior and yields new insight. We shall first highlight the strategy of synthesis of these materials through rapid solidification. This will be followed by three examples where the nanoscale dimension of the embedded particles play a unique role. These are melting and solidification of the nanodispersed embedded particles and the superconducting transition. (C) 1997 Elsevier Science S.A.

Synthesis and metallic probe induced conductance of Au tipped ultranarrow PbS rods

Au tipped ultranarrow PbS nanorods are synthesized. DFT electronic structure calculations and transport studies show that Au probes modify the nature and energies of PbS nanorod orbitals creating efficient electron conduction channels for enhanced conductance even at low applied bias.

A numerical model of a liquid-feed solid polymer electrolyte DMFC and its experimental validation

A one-dimensional, biphasic, multicomponent steady-state model based on phenomenological transport equations for the catalyst layer, diffusion layer, and polymeric electrolyte membrane has been developed for a liquid-feed solid polymer electrolyte direct methanol fuel cell (SPE- DMFC). The model employs three important requisites: (i) implementation of analytical treatment of nonlinear terms to obtain a faster numerical solution as also to render the iterative scheme easier to converge, (ii) an appropriate description of two-phase transport phenomena in the diffusive region of the cell to account for flooding and water condensation/evaporation effects, and (iii) treatment of polarization effects due to methanol crossover. An improved numerical solution has been achieved by coupling analytical integration of kinetics and transport equations in the reaction layer, which explicitly include the effect of concentration and pressure gradient on cell polarization within the bulk catalyst layer. In particular, the integrated kinetic treatment explicitly accounts for the nonhomogeneous porous structure of the catalyst layer and the diffusion of reactants within and between the pores in the cathode. At the anode, the analytical integration of electrode kinetics has been obtained within the assumption of macrohomogeneous electrode porous structure, because methanol transport in a liquid-feed SPE- DMFC is essentially a single-phase process because of the high miscibility of methanol with water and its higher concentration in relation to gaseous reactants. A simple empirical model accounts for the effect of capillary forces on liquid-phase saturation in the diffusion layer. Consequently, diffusive and convective flow equations, comprising Nernst-Plank relation for solutes, Darcy law for liquid water, and Stefan-Maxwell equation for gaseous species, have been modified to include the capillary flow contribution to transport. To understand fully the role of model parameters in simulating the performance of the DMCF, we have carried out its parametric study. An experimental validation of model has also been carried out. (C) 2003 The Electrochemical Society.

Distributed Source Coding for Sensor Data Model and Estimation of Cluster Head Errors Using Bayesian and K-Near Neighborhood Classifiers in Deployment of Dense Wireless Sensor Networks

The lifetime calculation of large dense sensor networks with fixed energy resources and the remaining residual energy have shown that for a constant energy resource in a sensor network the fault rate at the cluster head is network size invariant when using the network layer with no MAC losses.Even after increasing the battery capacities in the nodes the total lifetime does not increase after a max limit of 8 times. As this is a serious limitation lots of research has been done at the MAC layer which allows to adapt to the specific connectivity, traffic and channel polling needs for sensor networks. There have been lots of MAC protocols which allow to control the channel polling of new radios which are available to sensor nodes to communicate. This further reduces the communication overhead by idling and sleep scheduling thus extending the lifetime of the monitoring application. We address the two issues which effects the distributed characteristics and performance of connected MAC nodes. (1) To determine the theoretical minimum rate based on joint coding for a correlated data source at the singlehop, (2a) to estimate cluster head errors using Bayesian rule for routing using persistence clustering when node densities are the same and stored using prior probability at the network layer, (2b) to estimate the upper bound of routing errors when using passive clustering were the node densities at the multi-hop MACS are unknown and not stored at the multi-hop nodes a priori. In this paper we evaluate many MAC based sensor network protocols and study the effects on sensor network lifetime. A renewable energy MAC routing protocol is designed when the probabilities of active nodes are not known a priori. From theoretical derivations we show that for a Bayesian rule with known class densities of omega1, omega2 with expected error P* is bounded by max error rate of P=2P* for single-hop. We study the effects of energy losses using cross-layer simulation of - large sensor network MACS setup, the error rate which effect finding sufficient node densities to have reliable multi-hop communications due to unknown node densities. The simulation results show that even though the lifetime is comparable the expected Bayesian posterior probability error bound is close or higher than Pges2P*.

Microstructure, shape, stability and melting inembeddednanoparticles

The present article reviews some of the current work on a new class of materials which are nanoscale granular materials. We shall discuss in this paper two phase granular materials where one of the phases having nanometric dimension is embedded in a matrix of larger dimension. Known as nanoembedded materials, nanocomposites or ultrafine granular materials, this class of materials has attracted attention because of the opportunity of basic studies on the effect of size and embedding matrix on transformation behaviors as well as some novel properties, which include structural, magnetic and transport properties. These are in addition to the tremendous interests in what is known as quantum structures(embedded particles size less than 5 nm) for the case of semiconductors, which will not be discussed here. We shall primarily review the work done on metallic systems where the dispersed phases have low melting points and borrow extensively from the work done in our group. The phase transformations of the embedded particles show distinctive behavior and yield new insights. We shall first highlight briefly the strategy of synthesis of these materials by non-equilibrium processing techniques, which will be followed by examples where the effect of length scales on phase transformation behaviors like melting and solidification are discussed.

Traffic Profiling for Efficient Network Resource Utilization.

Traffic Engineering has been the prime concern for Internet Service Providers (ISPs), with the main focus being minimization of over-utilization of network capacity even though additional capacity is available which is under-utilized, Furthermore, requirements of timely delivery of digitized audiovisual information raises a new challenge of finding a path meeting these requirements. This paper addresses the issue of (a) distributing load to achieve global efficiency in resource utilization. (b) Finding a path satisfying the real time requirements of, delay and bandwidth requested by the applications. In this paper we do a critical study of the link utilization that varies over time and determine the time interval during which the link occupancy remains constant across days. This information helps in pre-determining link utilization that is useful in balancing load in the network Finally, we run simulations that use a dynamic time interval for profiling traffic and show improvement in terms number of calls admitted/blocked.

Anomalous low-temperature magnetic and magnetotransport properties in Ru-deficient SrRuO3

SrRuO3 is a well-known itinerant ferromagnet with many intriguing characteristics. The Ru deficiency in this system is believed to play a pivotal role in influencing many of its magnetic and transport properties. The present study involves the magnetic and transport properties of the Ru-deficient SrRu0.93O3 sample to gain more insight into the unusual low-temperature behavior. The ac susceptibility study reveals a sharp ferromagnetic transition at 150 K followed by a hump at T-h similar to 50 K, which has anomalous frequency dependence. Besides, the T-h shifts to lower temperatures with an increase in the superposed dc-biasing field and adheres to H-2 dependence, in accordance with the Gabay and Toulouse line for the Heisenberg spin glass systems. We also observe a pronounced memory effect toward the low-temperature side, signifying the characteristic of glassy behavior. The temperature-dependent magnetoresistance indicates the signature of an additional ordering toward the low-temperature side. All of the interesting findings combined unveil the existence of low-temperature cryptic magnetic phase in SrRu0.93O3. (C) 2012 American Institute of Physics. doi:10.1063/1.3673427]

An Exported Heat Shock Protein 40 Associates with Pathogenesis-Related Knobs in Plasmodium falciparum Infected Erythrocytes

Cell surface structures termed knobs are one of the most important pathogenesis related protein complexes deployed by the malaria parasite Plasmodium falciparum at the surface of the infected erythrocyte. Despite their relevance to the disease, their structure, mechanisms of traffic and their process of assembly remain poorly understood. In this study, we have explored the possible role of a parasite-encoded Hsp40 class of chaperone, namely PFB0090c/PF3D7_0201800 (KAHsp40) in protein trafficking in the infected erythrocyte. We found the gene coding for PF3D7_0201800 to be located in a chromosomal cluster together with knob components KAHRP and PfEMP3. Like the knob components, KAHsp40 too showed the presence of PEXEL motif required for transport to the erythrocyte compartment. Indeed, sub-cellular fractionation and immunofluorescence analysis (IFA) showed KAHsp40 to be exported in the erythrocyte cytoplasm in a stage dependent manner localizing as punctuate spots in the erythrocyte periphery, distinctly from Maurer's cleft, in structures which could be the reminiscent of knobs. Double IFA analysis revealed co-localization of PF3D7_0201800 with the markers of knobs (KAHRP, PfEMP1 and PfEMP3) and components of the PEXEL translocon (Hsp101, PTEX150). KAHsp40 was also found to be in a complex with KAHRP, PfEMP3 and Hsp101 as confirmed by co-immunoprecipitation assay. Our results suggest potential involvement of a parasite encoded Hsp40 in chaperoning knob assembly in the erythrocyte compartment.