Direct regulation of topoisomerase activity by a nucleoid-associated protein

The topological homeostasis of bacterial chromosomes is maintained by the balance between compaction and the topological organization of genomes. Two classes of proteins play major roles in chromosome organization: the nucleoid-associated proteins (NAPs) and topoisomerases. The NAPs bind DNA to compact the chromosome, whereas topoisomerases catalytically remove or introduce supercoils into the genome. We demonstrate that HU, a major NAP of Mycobacterium tuberculosis specifically stimulates the DNA relaxation ability of mycobacterial topoisomerase I (TopoI) at lower concentrations but interferes at higher concentrations. A direct physical interaction between M. tuberculosis HU (MtHU) and TopoI is necessary for enhancing enzyme activity both in vitro and in vivo. The interaction is between the amino terminal domain of MtHU and the carboxyl terminal domain of TopoI. Binding of MtHU did not affect the two catalytic trans-esterification steps but enhanced the DNA strand passage, requisite for the completion of DNA relaxation, a new mechanism for the regulation of topoisomerase activity. An interaction-deficient mutant of MtHU was compromised in enhancing the strand passage activity. The species-specific physical and functional cooperation between MtHU and TopoI may be the key to achieve the DNA relaxation levels needed to maintain the optimal superhelical density of mycobacterial genomes.

Direct correlation between non-random distribution of cations and ion transport mechanism in soda-lime silicate glasses

We report a direct correlation between dissimilar ion pair formation and alkali ion transport in soda-lime silicate glasses established via broad band conductivity spectroscopy and local structural probe techniques. The combined Raman and Nuclear Magnetic Resonance (NMR) spectroscopy techniques on these glasses reveal the coexistence of different anionic species and the prevalence of Na+-Ca2+ dissimilar pairs as well as their distributions. The spectroscopic results further confirm the formation of dissimilar pairs atomistically, where it increases with increasing alkaline-earth oxide content These results, are the manifestation of local structural changes in the silicate network with composition which give rise to different environments into which the alkali ions hop. The Na+ ion mobility varies inversely with dissimilar pair formation, i.e. it decreases with increase of non-random formation of dissimilar pairs. Remarkably, we found that increased degree of non-randomness leads to temperature dependent variation in number density of sodium ions. Furthermore, the present study provides the strong link between the dynamics of the alkali ions and different sites associated with it in soda-lime silicate glasses. (C) 2014 Elsevier B.V. All rights reserved.

Image-Segmentation Technique to Analyze Deformation Profiles in Different Direct Shear Tests

Results from interface shear tests on sand-geosynthetic interfaces are examined in light of surface roughness of the interacting geosynthetic material. Three different types of interface shear tests carried out in the frame of direct shear-test setup are compared to understand the effect of parameters like box fixity and symmetry on the interface shear characteristics. Formation of shear bands close to the interface is visualized in the tests and the bands are analyzed using image-segmentation techniques in MATLAB. A woven geotextile with moderate roughness and a geomembrane with minimal roughness are used in the tests. The effect of surface roughness of the geosynthetic material on the formation of shear bands, movement of sand particles, and interface shear parameters are studied and compared through visual observations, image analyses, and image-segmentation techniques.

A comparative study of a direct discretization and an operator-splitting solver for population balance systems

A direct discretization approach and an operator-splitting scheme are applied for the numerical simulation of a population balance system which models the synthesis of urea with a uni-variate population. The problem is formulated in axisymmetric form and the setup is chosen such that a steady state is reached. Both solvers are assessed with respect to the accuracy of the results, where experimental data are used for comparison, and the efficiency of the simulations. Depending on the goal of simulations, to track the evolution of the process accurately or to reach the steady state fast, recommendations for the choice of the solver are given. (C) 2015 Elsevier Ltd. All rights reserved.

Direct measurements of growing amorphous order and non-monotonic dynamic correlations in a colloidal glass-former

The transformation of flowing liquids into rigid glasses is thought to involve increasingly cooperative relaxation dynamics as the temperature approaches that of the glass transition. However, the precise nature of this motion is unclear, and a complete understanding of vitrification thus remains elusive. Of the numerous theoretical perspectives(1-4) devised to explain the process, random first-order theory (RFOT; refs 2,5) is a well-developed thermodynamic approach, which predicts a change in the shape of relaxing regions as the temperature is lowered. However, the existence of an underlying `ideal' glass transition predicted by RFOT remains debatable, largely because the key microscopic predictions concerning the growth of amorphous order and the nature of dynamic correlations lack experimental verification. Here, using holographic optical tweezers, we freeze a wall of particles in a two-dimensional colloidal glass-forming liquid and provide direct evidence for growing amorphous order in the form of a static point-to-set length. We uncover the non-monotonic dependence of dynamic correlations on area fraction and show that this non-monotonicity follows directly from the change in morphology and internal structure of cooperatively rearranging regions(6,7). Our findings support RFOT and thereby constitute a crucial step in distinguishing between competing theories of glass formation.

Ultrasound-modulated optical tomography: direct recovery of elasticity distribution from experimentally measured intensity autocorrelation

Based on an ultrasound-modulated optical tomography experiment, a direct, quantitative recovery of Young's modulus (E) is achieved from the modulation depth (M) in the intensity autocorrelation. The number of detector locations is limited to two in orthogonal directions, reducing the complexity of the data gathering step whilst ensuring against an impoverishment of the measurement, by employing ultrasound frequency as a parameter to vary during data collection. The M and E are related via two partial differential equations. The first one connects M to the amplitude of vibration of the scattering centers in the focal volume and the other, this amplitude to E. A (composite) sensitivity matrix is arrived at mapping the variation of M with that of E and used in a (barely regularized) Gauss-Newton algorithm to iteratively recover E. The reconstruction results showing the variation of E are presented. (C) 2015 Optical Society of America

Copper-Catalyzed Direct Transformation of Secondary Allylic and Benzylic Alcohols into Azides and Amides: An Efficient Utility of Azide as a Nitrogen Source

A mild and convenient method for the synthesis of amides has been explored by using secondary alcohols, Cu(ClO4)(2)6H(2)O as a catalyst, and trimethylsilyl azide (TMSN3) as a nitrogen source in the presence of 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) at ambient temperature. This method has been successfully adapted to the preparation of azides directly from their corresponding alcohols and offers excellent chemoselectivity in the formation of -halo azides and the azidation of allylic alcohols in the presence of a benzyl alcohol moiety. In addition, this strategy provides an opportunity to synthesize azides that can serve as precursors to -amino acids.

Direct Link-Aware Optimal Relay Selection and a Low Feedback Variant for Underlay CR

Cooperative relaying combined with selection has been extensively studied in the literature to improve the performance of interference-constrained secondary users in underlay cognitive radio (CR). We present a novel symbol error probability (SEP)-optimal amplify-and-forward relay selection rule for an average interference-constrained underlay CR system. A fundamental principle, which is unique to average interference-constrained underlay CR, that the proposed rule brings out is that the choice of the optimal relay is affected not just by the source-to-relay, relay-to-destination, and relay-to-primary receiver links, which are local to the relay, but also by the direct source-to-destination (SD) link, even though it is not local to any relay. We also propose a simpler, practically amenable variant of the optimal rule called the 1-bit rule, which requires just one bit of feedback about the SD link gain to the relays, and incurs a marginal performance loss relative to the optimal rule. We analyze its SEP and develop an insightful asymptotic SEP analysis. The proposed rules markedly outperform several ad hoc SD link-unaware rules proposed in the literature. They also generalize the interference-unconstrained and SD link-unaware optimal rules considered in the literature.

Direct Measurement of Three-Dimensional Forces in Atomic Force Microscopy

Direct measurement of three-dimensional (3-D) forces between an atomic force microscope (AFM) probe and the sample benefits diverse applications of AFM, including force spectroscopy, nanometrology, and manipulation. This paper presents the design and evaluation of a measurement system, wherein the deflection of the AFM probe is obtained at two points to enable direct measurement of all the three components of 3-D tip-sample forces in real time. The optimal locations for measurement of deflection on the probe are derived for a conventional AFM probe. Further, a new optimal geometry is proposed for the probe that enables measurement of 3-D forces with identical sensitivity and nearly identical resolution along all three axes. Subsequently, the designed measurement system and the optimized AFM probe are both fabricated and evaluated. The evaluation demonstrates accurate measurement of tip-sample forces with minimal cross-sensitivities. Finally, the real-time measurement system is employed as part of a feedback control system to regulate the normal component of the interaction force, and to perform force-controlled scribing of a groove on the surface of polymethyl methacrylate.

Direct Observation of Thermal Equilibrium of Excited Triplet States of 9,10-Phenanthrenequinone. A Time-Resolved Resonance Raman Study

The photochemistry of aromatic ketones plays a key role in various physicochemical and biological processes, and solvent polarity can be used to tune their triplet state properties. Therefore, a comprehensive analysis of the conformational structure and the solvent polarity induced energy level reordering of the two lowest triplet states of 9,10-phenanthrenequinone (PQ) was carried out using nanosecond-time-resolved absorption (ns-TRA), time-resolved resonance Raman (TR3) spectroscopy, and time dependent-density functional theory (TD-DFT) studies. The ns-TRA of PQ in acetonitrile displays two bands in the visible range, and these two bands decay with similar lifetime at least at longer time scales (mu s). Interestingly, TR3 spectra of these two bands indicate that the kinetics are different at shorter time scales (ns), while at longer time scales they followed the kinetics of ns-TRA spectra. Therefore, we report a real-time observation of the thermal equilibrium between the two lowest triplet excited states of PQ assigned to n pi* and pi pi* of which the pi pi* triplet state is formed first through intersystem crossing. Despite the fact that these two states are energetically close and have a similar conformational structure supported by TD-DFT studies, the slow internal conversion (similar to 2 ns) between the T-2(1(3)n pi*) and T-1(1(3)pi pi*) triplet states indicates a barrier. Insights from the singlet excited states of PQ in protic solvents J. Chem. Phys. 2015, 142, 24305] suggest that the lowest n pi* and pi pi* triplet states should undergo hydrogen bond weakening and strengthening, respectively, relative to the ground state, and these mechanisms are substantiated by TD-DFT calculations. We also hypothesize that the different hydrogen bonding mechanisms exhibited by the two lowest singlet and triplet excited states of PQ could influence its ISC mechanism.

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations

New molecular beam scattering experiments have been performed to measure the total ( elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as `hydrogen bonded'.

Status of the MSSM Higgs sector using global analysis and direct search bounds, and future prospects at the High Luminosity LHC

In this paper, we search for the regions of the phenomenological minimal supersymmetric standard model (pMSSM) parameter space where one can expect to have moderate Higgs mixing angle (alpha) with relatively light (up to 600 GeV) additional Higgses after satisfying the current LHC data. We perform a global fit analysis using most updated data (till December 2014) from the LHC and Tevatron experiments. The constraints coming from the precision measurements of the rare b-decays B-s -> mu(+)mu(-) and b -> s gamma are also considered. We find that low M-A(less than or similar to 350) and high tan beta(greater than or similar to 25) regions are disfavored by the combined effect of the global analysis and flavor data. However, regions with Higgs mixing angle alpha similar to 0.1-0.8 are still allowed by the current data. We then study the existing direct search bounds on the heavy scalar/pseudoscalar (H/A) and charged Higgs boson (H-+/-) masses and branchings at the LHC. It has been found that regions with low to moderate values of tan beta with light additional Higgses (mass <= 600 GeV) are unconstrained by the data, while the regions with tan beta > 20 are excluded considering the direct search bounds by the LHC-8 data. The possibility to probe the region with tan beta <= 20 at the high luminosity run of LHC are also discussed, giving special attention to the H -> hh, H/A -> t (t) over bar and H/A -> tau(+)tau(-) decay modes.

Direct Link-Aware Relay Selection for Average Interference-Constrained Underlay Cognitive Radio

Cooperative relaying combined with selection exploits spatial diversity to significantly improve the performance of interference-constrained secondary users in an underlay cognitive radio network. We present a novel and optimal relay selection (RS) rule that minimizes the symbol error probability (SEP) of an average interference-constrained underlay secondary system that uses amplify-and-forward relays. A key point that the rule highlights for the first time is that, for the average interference constraint, the signal-to-interference-plus-noise-ratio (SINR) of the direct source-to-destination (SI)) link affects the choice of the optimal relay. Furthermore, as the SINR increases, the odds that no relay transmits increase. We also propose a simpler, more practical, and near-optimal variant of the optimal rule that requires just one bit of feedback about the state of the SD link to the relays. Compared to the SD-unaware ad hoc RS rules proposed in the literature, the proposed rules markedly reduce the SEP by up to two orders of magnitude.

DESIGN REQUIREMENTS FOR DIRECT SUPERCRITICAL CARBON DIOXIDE RECEIVER DEVELOPMENT AND TESTING

This paper establishes the design requirements for the development and testing of direct supercritical carbon dioxide (sCO2) solar receivers. Current design considerations are based on the ASME Boiler and Pressure Vessel Code (BPVC). Section I (BPVC) considers typical boilers/superheaters (i.e. fired pressure vessels) which work under a constant low heat flux. Section VIII (BPVC) considers pressure vessels with operating pressures above 15 psig 2 bar] (i.e. unfired pressure vessels). Section III, Division I - Subsection NH (BPVC) considers a more detailed stress calculation, compared to Section I and Section VIII, and requires a creep-fatigue analysis. The main drawback from using the BPVC exclusively is the large safety requirements developed for nuclear power applications. As a result, a new set of requirements is needed to perform detailed thermal-structural analyses of solar thermal receivers subjected to a spatially-varying, high-intensity heat flux. The last design requirements document of this kind was an interim Sandia report developed in 1979 (SAND79-8183), but it only addresses some of the technical challenges in early-stage steam and molten-salt solar receivers but not the use of sCO2 receivers. This paper presents a combination of the ASME BPVC and ASME B31.1 Code modified appropriately to achieve the reliability requirements in sCO(2) solar power systems. There are five main categories in this requirements document: Operation and Safety, Materials and Manufacturing, Instrumentation, Maintenance and Environmental, and General requirements. This paper also includes the modeling guidelines and input parameters required in computational fluid dynamics and structural analyses utilizing ANSYS Fluent, ANSYS Mechanical, and nCode Design Life. The main purpose of this document is to serve as a reference and guideline for design and testing requirements, as well as to address the technical challenges and provide initial parameters for the computational models that will be employed for the development of sCO(2) receivers.