The genetics of Mycobacterium tuberculosis

Gene manipulation in Mycobacterium tuberculosis has been slow in coming of age owing to the inherent difficulties associated with working on this aerosol-transmitted pathogen, in addition to the paucity of molecular tools such as plasmids and transposons. One of the early approaches to overcome these difficulties was the development of phasmids, which combined the properties of phages and plasmids and allowed introduction of recombinant genes into mycobacteria. The lone plasmid pAL5000 of mycobacteria has been exploited to its fullest potential in the construction of a plethora of vectors. Above all, the single most important achievement has been the development of elegant and innovative approaches to overcome the problem of illegitimate recombination which threatened the success of allelic-exchange mutagenesis in the slow-growing pathogenic mycobacterial species. In this review I discuss the current status of conditionally replicating plasmid and transposon vectors and their application in generating targeted mutations in mycobacteria.

Structural phase transitions in Bi2V1-xGexO5.5-x/2 (x=0.2, 0.4, and 0.6) single crystals: X-ray crystallographic study

Single crystals of Bi2V1-xGexO5.5-x/2 (x = 0.2, 0.4, and 0.6) were grown by slow cooling of melts. Bismuth vanadate transforms from an orthorhombic to a tetragonal structure and subsequently to an orthorhombic system when the Ge4+ concentration was varied from x = 0.2 to x = 0.6. All of these compositions crystallized in polar space groups (Aba2, F4mm, and Fmm2 for x = 0.2, 0.4, and 0.6, respectively). The structures were fully determined by single crystal X-ray diffraction studies, (C) 1999 Elsevier Science Ltd.

Non-resonant perturbation formula for interaction impedance measurement for a folded-waveguide SWS

The non-resonant perturbation formula for the measurement of interaction impedance of a folded-waveguide slow-wave structure was derived for the relevant electromagnetic field configuration at the axis of the beam-hole of the structure. Efficacy of the theory was benchmarked through virtual measurement using 3D electromagnetic modeling in CST-studio.

Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Polarization switching studies in ferroelectric glycine phosphite single crystals

Glycine Phosphite [NH3CH2COOH3PO3], abbreviated as GPI, undergoes a para-ferroelectric phase transition from the monoclinic symmetry P2(1)/a to P2(1) at 224.7 K. We report here a systematic study of the polarization switching process in this crystal. Growth of these crystals from aqueous solution has been undertaken employing both solvent evaporation and slow cooling methods. Hysteresis loop measurements along the polar b-axis yielded a spontaneous polarization value of 0.5 muC/cm(2) and a coercive field of 2.5 kV/cm. Conventional Merz technique was employed for polarization switching studies, wherein bipolar square pulses were applied to the sample to induce domain reversal. The transient switching pulse that flows through the sample on application of the field was recorded. The maximum switching time required for domain switching was measured both as a function of electric field and temperature. The experimentally observed switching curves were fitted with the model based on the Pulvari-Kuebler theory of nucleation and growth of domains. From the experimental data, the values of mobility and activation field were obtained. It was observed that switching process in this crystal is predominantly governed by the forward growth of domain walls in the high field region. However, switching process in GPI crystal was found to be slower than that found in other glycine based ferroelectric crystals.

Effect of orientational motion of mobile chromophores on the dynamics of Forster energy transfer in polymers

Brownian dynamics (BD) simulations have been carried out to explore the effects of the orientational motion of the donor-acceptor (D-A) chromophore pair on the Forster energy transfer between the D-A pair embedded in a polymer chain in solution. It is found that the usually employed orientational averaging (that is, replacing the orientational factor, kappa, by kappa (2) = 2/3) may lead to an error in the estimation of the rate of the reaction by about 20%. In the limit of slow orientational relaxation, the preaveraging of the orientational factor leads to an overestimation of the rate, while in the opposite limit of very fast orientational relaxation, the usual scheme underestimates the rate. The latter results from an interesting interplay between reaction and diffusion. On the other hand, when one of the chromophores is fixed, the preaveraged rate is found to be fairly reliable if the rotational relaxation of the chromophore is sufficiently fast. The present study also reveals a power law dependence of the FRET rate on the chain length (rate proportional to N- alpha, with alpha approximate to 2.6).

Growth and characterization of ferroelectric glycine phosphite single crystals

Single crystals of a recent ferroelectric material, glycine phosphite were grown from aqueous solution employing the techniques of slow cooling and controlled evaporation. Powder X-ray diffraction studies as well as thermal analysis were carried out on the grown crystals. The morphology of the crystal has been determined using contact and optical goniometry. The mechanical hardness of the crystal was evaluated by Vickers indentation method. Thickness dependence of the dielectric properties has been investigated and the results can be interpreted in terms of a surface layer of lower dielectric constant.

Equilibrium and relaxation in turbulent wakes

In order to study the memory of the larger eddies in turbulent shear flow, experiments have been conducted on plane turbulent wakes undergoing transition from an initial (carefully prepared) equilibrium state to a different final one, as a result of a nearly impulsive pressure gradient. It is shown that under the conditions of the experiments the equations of motion possess self-preserving solutions in the sense of Townsend (1956), but the observed behaviour of the wake is appreciably different when the pressure gradient is not very small, as the flow goes through a slow relaxation process before reaching final equilibrium. Measurements of the Reynolds stresse show that the approach to a new equilibrium state is exponential, with a relaxation length of the order of 103 momentum thicknesses. It is suggested that a flow satisfying the conditions required by a self-preservation analysis will exhibit equilibrium only if the relaxation length is small compared with a characteristic streamwise length scale of the flow.

Albedo enhancement of marine clouds to counteract global warming: impacts on the hydrological cycle

Recent studies have shown that changes in solar radiation affect the hydrological cycle more strongly than equivalent CO(2) changes for the same change in global mean surface temperature. Thus, solar radiation management ``geoengineering'' proposals to completely offset global mean temperature increases by reducing the amount of absorbed sunlight might be expected to slow the global water cycle and reduce runoff over land. However, proposed countering of global warming by increasing the albedo of marine clouds would reduce surface solar radiation only over the oceans. Here, for an idealized scenario, we analyze the response of temperature and the hydrological cycle to increased reflection by clouds over the ocean using an atmospheric general circulation model coupled to a mixed layer ocean model. When cloud droplets are reduced in size over all oceans uniformly to offset the temperature increase from a doubling of atmospheric CO(2), the global-mean precipitation and evaporation decreases by about 1.3% but runoff over land increases by 7.5% primarily due to increases over tropical land. In the model, more reflective marine clouds cool the atmospheric column over ocean. The result is a sinking motion over oceans and upward motion over land. We attribute the increased runoff over land to this increased upward motion over land when marine clouds are made more reflective. Our results suggest that, in contrast to other proposals to increase planetary albedo, offsetting mean global warming by reducing marine cloud droplet size does not necessarily lead to a drying, on average, of the continents. However, we note that the changes in precipitation, evaporation and P-E are dominated by small but significant areas, and given the highly idealized nature of this study, a more thorough and broader assessment would be required for proposals of altering marine cloud properties on a large scale.

Multi-hop Cooperative Wireless Networks: Diversity Multiplexing Tradeoff and Optimal Code Design

We consider single-source single-sink (ss-ss) multi-hop relay networks, with slow-fading links and single-antenna half-duplex relay nodes. While two-hop cooperative relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this paper, we identify two families of networks that are multi-hop generalizations of the two-hop network: K-Parallel-Path (KPP)networks and layered networks.KPP networks, can be viewed as the union of K node-disjoint parallel relaying paths, each of length greater than one. KPP networks are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the DMT of these families of networks completely for K > 3. Layered networks are networks comprising of layers of relays with edges existing only between adjacent layers, with more than one relay in each layer. We prove that a linear DMT between the maximum diversity dmax and the maximum multiplexing gain of 1 is achievable for single-antenna fully-connected layered networks. This is shown to be equal to the optimal DMT if the number of relaying layers is less than 4.For multiple-antenna KPP and layered networks, we provide an achievable DMT, which is significantly better than known lower bounds for half duplex networks.For arbitrary multi-terminal wireless networks with multiple source-sink pairs, the maximum achievable diversity is shown to be equal to the min-cut between the corresponding source and the sink, irrespective of whether the network has half-duplex or full-duplex relays. For arbitrary ss-ss single-antenna directed acyclic networks with full-duplex relays, we prove that a linear tradeoff between maximum diversity and maximum multiplexing gain is achievable.Along the way, we derive the optimal DMT of a generalized parallel channel and derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. We also give alternative and often simpler proofs of several existing results and show that codes achieving full diversity on a MIMO Rayleigh fading channel achieve full diversity on arbitrary fading channels. All protocols in this paper are explicit and use only amplify-and-forward (AF) relaying. We also construct codes with short block-lengths based on cyclic division algebras that achieve the optimal DMT for all the proposed schemes.Two key implications of the results in the paper are that the half-duplex constraint does not entail any rate loss for a large class of cooperative networks and that simple AF protocols are often sufficient to attain the optimal DMT

Stream-Close: Fast mining of Closed Frequent Itemsets in high speed data streams

With the emergence of large-volume and high-speed streaming data, the recent techniques for stream mining of CFIpsilas (closed frequent itemsets) will become inefficient. When concept drift occurs at a slow rate in high speed data streams, the rate of change of information across different sliding windows will be negligible. So, the user wonpsilat be devoid of change in information if we slide window by multiple transactions at a time. Therefore, we propose a novel approach for mining CFIpsilas cumulatively by making sliding width(ges1) over high speed data streams. However, it is nontrivial to mine CFIpsilas cumulatively over stream, because such growth may lead to the generation of exponential number of candidates for closure checking. In this study, we develop an efficient algorithm, stream-close, for mining CFIpsilas over stream by exploring some interesting properties. Our performance study reveals that stream-close achieves good scalability and has promising results.

Model track studies on fouled ballast using ground penetrating radar and multichannel analysis of surface wave

Ballast fouling is created by the breakdown of aggregates or outside contamination by coal dust from coal trains, or from soil intrusion beneath rail track. Due to ballast fouling, the conditions of rail track can be deteriorated considerably depending on the type of fouling material and the degree of fouling. So far there is no comprehensive guideline available to identify the critical degree of fouling for different types of fouling materials. This paper presents the identification of degree of fouling and types of fouling using non-destructive testing, namely seismic surface-wave and ground penetrating radar (GPR) survey. To understand this, a model rail track with different degree of fouling has been constructed in Civil engineering laboratory, University of Wollongong, Australia. Shear wave velocity obtained from seismic survey has been employed to identify the degree of fouling and types of fouling material. It is found that shear wave velocity of fouled ballast increases initially, reaches optimum fouling point (OFP), and decreases when the fouling increases. The degree of fouling corresponding after which the shear wave velocity of fouled ballast will be smaller than that of clean ballast is called the critical fouling point (CFP). Ground penetrating radar with four different ground coupled antennas (500 MHz, 800 MHz, 1.6 GHz and 2.3 GHz) was also used to identify the ballast fouling condition. It is found that the 800 MHz ground coupled antenna gives a better signal in assessing the ballast fouling condition. Seismic survey is relatively slow when compared to GPR survey however it gives quantifiable results. In contrast, GPR survey is faster and better in estimating the depth of fouling. (C) 2011 Elsevier B.V. All rights reserved.

Energy-Efficient Decentralized Routing with Localized Cooperation Suitable for Fast Fading

Wireless networks transmit information from a source to a destination via multiple hops in order to save energy and, thus, increase the lifetime of battery-operated nodes. The energy savings can be especially significant in cooperative transmission schemes, where several nodes cooperate during one hop to forward the information to the next node along a route to the destination. Finding the best multi-hop transmission policy in such a network which determines nodes that are involved in each hop, is a very important problem, but also a very difficult one especially when the physical wireless channel behavior is to be accounted for and exploited. We model the above optimization problem for randomly fading channels as a decentralized control problem – the channel observations available at each node define the information structure, while the control policy is defined by the power and phase of the signal transmitted by each node.In particular, we consider the problem of computing an energy-optimal cooperative transmission scheme in a wireless network for two different channel fading models: (i) slow fading channels, where the channel gains of the links remain the same for a large number of transmissions, and (ii) fast fading channels,where the channel gains of the links change quickly from one transmission to another. For slow fading, we consider a factored class of policies (corresponding to local cooperation between nodes), and show that the computation of an optimal policy in this class is equivalent to a shortest path computation on an induced graph, whose edge costs can be computed in a decentralized manner using only locally available channel state information(CSI). For fast fading, both CSI acquisition and data transmission consume energy. Hence, we need to jointly optimize over both these; we cast this optimization problem as a large stochastic optimization problem. We then jointly optimize over a set of CSI functions of the local channel states, and a corresponding factored class of control policies corresponding to local cooperation between nodes with a local outage constraint. The resulting optimal scheme in this class can again be computed efficiently in a decentralized manner. We demonstrate significant energy savings for both slow and fast fading channels through numerical simulations of randomly distributed networks.

An Efficient MPI_Allgather for Grids

Allgather is an important MPI collective communication. Most of the algorithms for allgather have been designed for homogeneous and tightly coupled systems. The existing algorithms for allgather on Gridsystems do not efficiently utilize the bandwidths available on slow wide-area links of the grid. In this paper, we present an algorithm for allgather on grids that efficiently utilizes wide-area bandwidths and is also wide-area optimal. Our algorithm is also adaptive to gridload dynamics since it considers transient network characteristics for dividing the nodes into clusters. Our experiments on a real-grid setup consisting of 3 sites show that our algorithm gives an average performance improvement of 52% over existing strategies.

Giant photoinduced optical bleaching at room and liquid helium temperatures in Sb/As(2)S(3) multilayered films

We report the observation of giant photo induced optical bleaching in Sb/As(2)S(3) multilayered film at room and liquid He temperatures, when irradiated with 532 nm laser at moderate intensities. The experimental results show a dramatic increase in transmittance near the band gap regime at both the temperatures; however the rates at which transmission change occurs are rather slow at low temperature. The huge change in transmission is due to the photo induced intermixing of As(2)S(3) layer with Sb. Our XPS measurements show that photo induced intermixing occurs through the wrong homopolar bonds, which under actinic light illumination are converted into energetically favored hetropolar bonds. (C) 2011 Elsevier B.V. All rights reserved.