800 research outputs found
Single-molecule fluorescence analysis of opening and closing of the RNA polymerase clamp
No full textCrystal structures of RNA polymerase (RNAP) indicate that the RNAP β’ pincer (“clamp”) can exist in conformational states, ranging from a fully open conformation that permits entry and exit of DNA, to a fully closed conformation that prevents entry and exit of DNA. It has been hypothesized that the clamp also adopts multiple conformational states in solution and conformational changes in the clamp are important for function. In this work, a single-molecule fluorescence resonance energy transfer (smFRET) approach was developed that enables determination of RNAPclamp conformation in solution. smFRET was measured between a probe at the tip of the RNAP clamp and a probe at a fixed reference point in RNAP. A computational framework was then employed to interpret measured FRET efficiencies in terms of structural changes. Using this approach, RNAP clamp conformation was defined in each step of 70-dependent transcription initiation and elongation and in each step in σ54-dependent transcription initiation. Additionally, effects of four RNAP inhibitors, myxopyronin, corallopyronin, ripostatin and Gp2 on RNAP clamp conformation were assessed. It was observed that the clamp is predominantly open in free RNAP and in all steps leading up to the formation of a catalytically-competent-transcription-initiation complex. Upon formation of a catalytically-competent-transcription-initiation complex, the clamp closes, and continues to remain closed during transcription elongation. It was further observed that myxopyronin, corallopyronin, ripostatin and Gp2, prevent opening of the RNAP clamp. The results lead to the proposal that, the open clamp state is important for entry of DNA into, and unwinding of DNA in, the RNAP active center cleft during formation of a catalytically-competent-transcription initiation complex. The results lead to the proposal that, after entry of DNA into the RNAP active-center cleft upon formation of the catalytically competent transcription initiation complex, electrostatic interactions between the negatively charged DNA and the positively charged inner facet of the clamp, induce and/or stabilize clamp closure. The results are in agreement with the proposal that, clamp closure is important for stability of the catalytically competent transcription initiation complex and for stability and processivity of the transcription elongation complex.Ph. D.Includes bibliographical referencesby Anirban Chakrabort
Quantitative analysis of hidden particles diffusing behind a scattering layer using speckle correlation
No full textInternational audienceSpeckle-correlation imaging is a family of methods that makes use of the “memory effect” to image objects hidden behind visually opaque layers. Here, we show that a correlation analysis can be applied to quantitative imaging of an ensemble of dynamic fluorescent beads diffusing on a 2D surface. We use an epi-fluorescence microscope where both the illumination and detection light patterns are speckled, due to light scattering by a thin disordered layer. The spatio-temporal cross-correlation of the detection speckle pattern is calculated as a function of lag time and spatial shift and is used to determine the diffusion constant and number of fluorescent particles in the sample without requiring any phase retrieval procedure. It is worth to note that the “memory effect” range is not required to extend beyond a distance of few speckle grains, thus making our method potentially useful for nearly arbitrary values of the thickness of the scattering layer
Visualizing WSPDs and Their Applications (Media Exposition)
No full textIntroduced by Callahan and Kosaraju back in 1995, the concept of well-separated pair decomposition (WSPD) has occupied a special significance in computational geometry when it comes to solving distance problems in d-space. We present an in-browser tool that can be used to visualize WSPDs and several of their applications in 2-space. Apart from research, it can also be used by instructors for introducing WSPDs in a classroom setting. The tool will be permanently maintained by the third author at https://wisno33.github.io/VisualizingWSPDsAndTheirApplications/
Tailoring superconducting states in superconductor-ferromagnet hybrids
No full textWe present results of a comprehensive investigation of two phenomena arising in superconductor(S)/ferromagnet(F) heterostructures of Nb on FePd with a lateral magnetic domain pattern: domain-superconductivity and spin-triplet Cooper pair generation. Resistivity measurements in a magnetic field applied out-of-plane to a Nb/FePd (S/F) sample with high magnetocrystalline anisotropy give evidence of stray field generated domain-wall- and reverse-domain-superconductivity. A corresponding bilayer comprising low magnetocrystalline anisotropy exhibits spin-triplet Cooper pair generation and a notable high variation of the S critical temperature due to spin-triplet generation (ΔTc) of 100 mK in an in-plane applied field. Using reference samples we can clearly distinguish stray field from proximity effects. The relevance of the characteristic S and F length scales related to the observed proximity effects is discussed
Magnetic Field-Assisted Chemical Vapor Deposition of Iron Oxide Thin Films: Influence of Field–Matter Interactions on Phase Composition and Morphology
No full textMagnetic field-assisted CVD offers a direct pathway to manipulate the evolution of microstructure, phase composition, and magnetic properties of the as-prepared film. We report on the role of applied magnetic fields (0.5 T) during a cold-wall CVD deposition of iron oxide from [FeIII(OtBu)3]2 leading to higher crystallinity, larger particulates, and better out-of-plane magnetic anisotropy, if compared with zero-field depositions. Whereas selective formation of homogeneous magnetite films was observed for the field-assisted process, coexistence of hematite and amorphous iron(III) oxide was confirmed under zero-field conditions. Comparison of the coercive field (11 vs 60 mT) indicated lower defect concentration for the field-assisted process with nearly superparamagnetic behavior. X-ray photoemission electron microscopy (X-PEEM) in absorption mode at the O-K and Fe-L3,2 edges confirmed the selective formation of magnetite (field-assisted) and hematite (zero-field) with coexisting amorphous phases, respectively, emphasizing the importance of field–matter interactions in the phase-selective synthesis of magnetic thin films
Hyperaeschra innotata
No full textHyperaeschra innotata (Hampson, 1896) Phalera innotata * Hampson, 1896; 4: 455. Hyperaeschra innotata; Schintlmeister, 2013; 11: 222. TL: Khasis [Meghalaya, India]; TD: unknown type depository. Distribution: India: Meghalaya. Note: Endemic to NE India. *Hampson mentioned “Swinh. MS.” against the species in volume 4 of Fauna of British India, Moths. Since the species was described there for the first time, the credit as the main author is given to Hampson.Published as part of Chandra, Kailash, Mazumder, Arna, Sanyal, Abesh Kumar, Ash, Anirban, Bandyopadhyay, Uttaran, Mallick, Kaushik & Raha, Angshuman, 2018, Catalogue of Indian Notodontidae Stephens, 1829 (Lepidoptera: Noctuoidea), pp. 1-84 in Zootaxa 4505 (1) on page 37, DOI: 10.11646/zootaxa.4505.1.1, http://zenodo.org/record/260670
Data Publication: Sensitivity of the Polyakov loop and related observables to chiral symmetry restoration
No full textClarke D, Kaczmarek O, Karsch F, Lahiri A, Sarkar M. Data Publication: Sensitivity of the Polyakov loop and related observables to chiral symmetry restoration. Bielefeld University; 2021.Data publication for "Sensitivity of the Polyakov loop and related observables to chiral symmetry restoration", [arXiv:2008.11678](https://arxiv.org/abs/2008.11678), [DOI: 10.1103/PhysRevD.103.L011501](https://link.aps.org/doi/10.1103/PhysRevD.103.L011501). Contains all data necessary to generate the figures of that publication
An Interactive Tool for Experimenting with Bounded-Degree Plane Geometric Spanners (Media Exposition)
No full textThe construction of bounded-degree plane geometric spanners has been a focus of interest in the field of geometric spanners for a long time. To date, several algorithms have been designed with various trade-offs in degree and stretch factor. Using JSXGraph, a state-of-the-art JavaScript library for geometry, we have implemented seven of these sophisticated algorithms so that they can be used for further research and teaching computational geometry. We believe that our interactive tool can be used by researchers from related fields to understand and apply the algorithms in their research. Our tool can be run in any modern browser. The tool will be permanently maintained by the second author at https://ghoshanirban.github.io/bounded-degree-plane-spanners/index.htm
Synthesis of Bioinspired Dioxygen Reduction Catalysts Involving Mono and Polynuclear Late Transition Metal Complexes and Spectroscopic Trapping of Reactive Intermediates
No full textDie selektive Funktionalisierung nicht aktivierter C−H-Bindungen und die Disauerstoffreduktionsreaktion (ORR) sind extrem wichtig bei der Beschäftigung mit verschiedenen technologischen Problemstellungen wie der Energiekrise, der Synthese kommerziell relevanter organischer Verbindungen usw. Die Nutzung molekularen Sauerstoffs als reichlich vorhandenes und umweltverträgliches Oxidationsmittel ist von großem Interesse in der Entwicklung bioinspirierter synthetischer Oxidationskatalysatoren. Die katalytische Vier-Elektronen-Reduktion von Disauerstoff zu Wasser erlangte auch immer größere Aufmerksamkeit wegen ihrer Bedeutung in der Brennstoffzellentechnologie. Natürlich vorkommende Metalloenzyme aktivieren Disauerstoff durch die Nutzung günstiger Übergangsmetalle (z.B. Eisen, Nickel, Mangan und Kupfer) und weisen diverse oxidative Reaktivitäten auf. Des Weiteren werden solche Reaktionen unter Umgebungsbedingungen mit hoher Effizienz und Stereoselektivität durchgeführt. Deshalb kann die Isolierung und Charakterisierung hochvalenter Metall-Disauerstoff-Intermediate (wie Metall-Superoxo-, Metall-Peroxo-, Metall-Hydroperoxo- und Metall-Oxo-Verbindungen) eine Menge nützlicher Informationen über die Reaktionsmechanismen liefern und daher hilfreich für die zukünftige Entwicklung effizienterer Katalysatoren sein. Diese Arbeit hat die Chemie verschiedener Metall-Disauerstoff-Intermediate von end-on-1,2-Peroxo-dicobalt(III)-Spezies bis zu Superoxo-nickel(II)-Kernen erforscht. Detaillierte spektroskopische Untersuchungen sowie Reaktivitätsstudien der Intermediate wurden durchgeführt, um den Zusammenhang zwischen ihrer elektronischen Struktur und ihren Reaktivitätsmustern aufzuklären. In meiner Arbeit untersuchte ich den Effekt der ‚Struktur-Aktivität-Beziehung‘ verschiedener Metall-Disauerstoff-Intermediate gegenüber exogener Substrate. Diese Arbeit zeigte auch den Einfluss des Designs geeigneter Liganden auf das Verhalten eines gegebenen reaktiven Metall-Disauerstoff-Systems.Selective functionalization of unactivated C−H bonds and dioxygen reduction reaction (ORR) are extremely important in the context of addressing various technological issues such as energy-crisis, synthesis of commercially important organic compounds, etc. The utilization of molecular oxygen as an abundant and environmentally benign oxidant is of great interest in the design of bioinspired synthetic oxidation catalysts. The catalytic four-electron reduction of dioxygen to water has also merited increasing attention because of its relevance to fuel cell technology. Naturally occurring metalloenzymes activate dioxygen by employing cheap transition metals (e.g. iron, nickel, manganese, and copper) and exhibit diverse oxidative reactivities. Moreover, such reactions are carried out under ambient conditions with high efficiency and stereospecificity. Therefore, the isolation and characterization of the high-valent metal-dioxygen intermediates (such as metal-superoxo, -peroxo, -hydroperoxo, and -oxo can provide a lot of useful information about the reaction mechanisms and is therefore helpful for the future design of more efficient catalysts.
This thesis has explored the chemistry of different metal-dioxygen intermediates ranging from bridging end-on μ-1,2-peroxo-dicobalt(III) species to nickel(II)-superoxo cores. Detailed spectroscopic and reactivity studies of the intermediates have been performed to reveal the correlations between their electronic structures and reactivity patterns. In my present thesis, I investigated the effect of the ‘structure-activity relationship’ of different metal-dioxygen intermediates towards exogenous substrates. This thesis also demonstrated the impact of suitable ligand design on the behaviour of a given metal-dioxygen reactive system
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