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Application of Numerical Simulations to Extract Protein Folding Parameters from Hydrogen Exchange Mass Spectrometry Experiments under Native Conditions
No full textStudies on the effect of imaging parameters on dynamic mode decomposition of time-resolved schlieren flow images
No full textDynamic modal analysis enables new insights into the spatio-temporal dynamics of complex flow scenarios. Time resolved schlieren imaging provides significant information in compressible flow scenarios on flow structures and their evolution. We conduct a systematic study using synthetic images and experimental schlieren images on the effect of image acquisition parameters on the modal analysis by dynamic mode decomposition (DMD). We consider the effect of two important capture parameters - the capture rate (f(s)) and the exposure time (t(exp)). Analysis is carried out on two sets of synthetic images, SI-I, an unsteady wavy interface created using a linear combination of sinusoids, and SI-II - hypothetical shock oscillations. Finally, a flapping supersonic jet is observed using high-speed schlieren with a nano-pulsed laser light source with three different imaging parameters. We find that among the two parameters the effect of exposure time on modal analysis and its interpretation is more pronounced than capture rate. An exposure time of 5% of maximum exposure produces 8% reduction in mode amplitude, and in case of long exposure the dynamic significance of modes undergoes complete change. If the flow images are instantaneous, then the spatial mode shapes of dominant modes remain the same irrespective of the capture rate. Aliasing has to be considered in sub-Nyquist capture rates, however, the actual frequencies can be suitably resolved
Search for supersymmetry in events with a photon, jets, b-jets, and missing transverse momentum in proton-proton collisions at 13TeV
No full textA search for supersymmetry is presented based on events with at least one photon, jets, and large missing transverse momentum produced in proton-proton collisions at a center-of-mass energy of 13 TeV. The data correspond to an integrated luminosity of 35.9 fb -1 and were recorded at the LHC with the CMS detector in 2016. The analysis characterizes signal-like events by categorizing the data into various signal regions based on the number of jets, the number of b-tagged jets, and the missing transverse momentum. No significant excess of events is observed with respect to the expectations from standard model processes. Limits are placed on the gluino and top squark pair production cross sections using several simplified models of supersymmetric particle production with gauge-mediated supersymmetry breaking. Depending on the model and the mass of the nextto-lightest supersymmetric particle, the production of gluinos with masses as large as 2120 GeV and the production of top squarks with masses as large as 1230 GeV are excluded at 95% confidence level
Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation
No full textDNA Topoisomerase I (TopoI) in eubacteria is the principle DNA relaxase, belonging to Type 1A group. The enzyme from Mycobacterium smegmatis is essential for cell survival and distinct from other eubacteria in having several unusual characteristics. To understand genome-wide TopoI engagements in vivo, functional sites were mapped by employing a poisonous variant of the enzyme and a newly discovered inhibitor, both of which arrest the enzyme activity after the first transestrification reaction, thereby leading to the accumulation of protein-DNA covalent complexes. The cleavage sites are subsets of TopoI binding sites, implying that TopoI recruitment does not necessarily lead to DNA cleavage in vivo. The cleavage protection conferred by nucleoid associated proteins in vitro suggest a similar possibility in vivo. Co-localization of binding and cleavage sites of the enzyme on transcription units, implying that both TopoI recruitment and function are associated with active transcription. Attenuation of the cleavage upon Rifampicin treatment confirms the close connection between transcription and TopoI action. Notably, TopoI is inactive upstream of the Transcription start site (TSS) and activated following transcription initiation. The binding of TopoI at the Ter region, and the DNA cleavage at the Ter indicates TopoI involvement in chromosome segregation, substantiated by its catenation and decatenation activities
Strategy and Methodology in the Synthesis of Multicomponent Molecular Solids: The Quest for Higher Cocrystals
No full textCrystal engineering is the art and science of making crystals by design. Crystallization is inherently a purifying phenomenon. Bringing together more than one organic compound into the same crystal always needs deliberate action. Cocrystals are important because they offer a route to the controlled modulation of crystal properties. The route to cocrystal synthesis was opened up with the heterosynthon concept, which considers the complementary recognition of chemical groups from different molecules. Using this concept, binary cocrystals of enormous variety have been generated, even as crystal engineering has evolved into a form of solid-state supramolecular synthesis. Introducing a third component (a component is somewhat arbitrarily defined as an organic substance that is a solid at room temperature, mostly with the idea of excluding solvates) in a stoichiometric manner requires substantially greater effort and a careful balance of intermolecular interactions-their strengths, directional properties, and distance falloff characteristics. The first systematic ternary cocrystal synthesis was reported around 15 years ago. Drawing in a fourth component in stoichiometric amounts is exceedingly difficult, and we reported such syntheses in 2016. To date, a limited number of ternary cocrystals have been realized (around 120 in all, with a half from our group) and an even smaller number of quaternary cocrystals (around 30, all from our group, barring one). It is impressive that our experiments largely yielded the intended higher cocrystal (three- or four-component) with very small traces of contaminating binaries and pure compounds. A fifth or sixth component may be brought into the solid in the manner of a solid solution in that these components are situated at one of the sites of the quaternary cocrystal. To date, five components have not been included stoichiometrically within the same crystal. This is still an open challenge. The merit in synthesizing (higher) cocrystals is that one can systematically engineer property modularity: Each component is associated with a distinct property. This is important in the pharmaceutical industry, where each component can, in principle, confer a different, desirable property-drug action, solubility, or permeability. However, difficult synthetic targets are also addressed in chemistry simply because they are there. The intellectual satisfaction in making something that is very difficult to make renders the enterprise worthwhile in itself, and new chemistry usually gets uncovered in the process. The development of synthetic organic chemistry can undoubtedly be credited to various reliable methods for chemical transformations, and many difficult total syntheses were achieved by employing these methods over two centuries of research. In contrast, supramolecular synthesis (of multicomponent cocrystals and other assemblies) is in no way at a similar level of sophistication because the subject is still relatively young. Our group and others have reported the synthesis of many higher cocrystals with reliable, reproducible, and robust design strategies. There is a general perception that the isolation of some of these cocrystals is a matter of luck! The crux of this Account is that far from being a serendipitous matter, higher cocrystals may only be made with a judicious combination of strategy and methodology-the essence of synthesis
Discovery of a deeply divergent new lineage of vine snake (Colubridae: Ahaetuliinae: Proahaetulla gen. nov.) from the southern Western Ghats of Peninsular India with a revised key for Ahaetuliinae
No full textThe Western Ghats are well known as a biodiversity hotspot, but the full extent of its snake diversity is yet to be uncovered. Here, we describe a new genus and species of vine snake Proahaetulla antiqua gen. et sp. nov., from the Agasthyamalai hills in the southern Western Ghats. It was found to be a member of the Ahaetuliinae clade, which currently comprises the arboreal snake genera Ahaetulla, Dryophiops, Dendrelaphis and Chrysopelea, distributed in South and Southeast Asia. Proahaetulla shows a sister relationship with all currently known taxa belonging to the genus Ahaetulla, and shares ancestry with Dryophiops. In addition to its phylogenetic position and significant genetic divergence, this new taxon is also different in morphology from members of Ahaetuliinae in a combination of characters, having 12-13 partially serrated keels on the dorsal scale rows, 20 maxillary teeth and 3 postocular scales. Divergence dating reveals that the new genus is ancient, dating back to the Mid-Oligocene, and is one of the oldest persisting monotypic lineages of snakes in the Western Ghats. This discovery adds to the growing list of ancient lineages endemic to the Agasthyamalai hills and underscores the biogeographic significance of this isolated massif in the southern Western Ghats
Deciphering Hydrodynamic and Drug-Resistant Behaviors of Metastatic EMT Breast Cancer Cells Moving in a Constricted Microcapillary
No full textEpithelial to mesenchymal transition (EMT) induces cell migration, invasion, and drug resistance, and consequently, contributes to cancer metastasis and disease aggressiveness. This study attempted to address crucial biological parameters to correlate EMT and drug-treated cancer cells traversing through microcapillaries, reminiscent of metastatic conditions. MDA-MB-468 breast cancer cells induced to undergo EMT by treatment with 20 ng/mL of epidermal growth factor (EGF) were initially passed through several blockages and then through a constricted microchannel, mimicking the flow of invasive metastatic cells through constricted blood microcapillaries. EMT cells acquired enhanced migratory properties and retained 50% viability, even after migration through wells 10-15 mu m in size and a constricted passage of 7 mu m and 150 mu m in length at a constant flow rate of 50 mu L/h. The hydrodynamic properties revealed cellular deformation with a deformation index, average transit velocity, and entry time of 2.45, 12.3 mm/s, and 31,000 mu s, respectively for a cell of average diameter 19 mu m passing through one of the 7 mu m constricted sections. Interestingly, cells collected at the channel outlet regained epithelial character, undergoing reverse transition (mesenchymal to epithelial transition, MET) in the absence of EGF. Remarkably, real-time polymerase chain reaction (PCR) analysis confirmed increases of 2- and 2.7-fold in the vimentin and fibronectin expression in EMT cells, respectively; however, their expression reduced to basal level in the MET cells. A scratch assay revealed the pronounced migratory nature of EMT cells compared with MET cells. Furthermore, the number of colonies formed from EMT cells and paclitaxel-treated EMT cells after passing through a constriction were found to be 95 +/- 10 and 79 +/- 4, respectively, confirming that the EMT cells were more drug resistant with a concomitant two-fold higher expression of the multi-drug resistance (MDR1) gene. Our results highlight the hydrodynamic and drug-evading properties of cells that have undergone an EMT, when passed through a constricted microcapillary that mimics their journey in blood circulation
Recovery from an eavesdropping attack on a qubit of a graph state
No full textGraph states are multipartite entangled pure states that can describe distributed quantum information in a formal setting via the notion of nodes and edges. One qubit is present at each node, and the entangling interactions are represented via the edges. We investigate eavesdropping on one of the qubits of the graph state. The eavesdropper uses an ancilla qubit to unitarily interact with one of the qubits followed by a measurement on the ancilla qubit. We study the effect of eavesdropping on the graph state and its connections to the graph topology. We propose the use of a modified graph state by performing certain controlled unitary operations on the existing graph state. This improves the error correcting ability of the graph state, and the modified graph state can correct any error on one qubit
Anomalous electron transport in epitaxial NdNiO3 films
No full textThe origin of simultaneous electronic, structural, and magnetic transitions in bulk rare-earth nickelates (RENiO3) remains puzzling with multiple conflicting reports on the nature of these entangled phase transitions. Heterostructure engineering of these materials offers unique opportunity to decouple the metal-insulator transition (MIT) from the magnetic transition. However, the evolution of underlying electronic properties across these decoupled transitions remains largely unexplored. In order to address this, we have measured Hall effect on a series of epitaxial NdNiO3 films, spanning a variety of electronic and magnetic phases. We find that the MIT results in only a partially gapped Fermi surface, whereas the full insulating phase forms below the magnetic transition. In addition, we also find a systematic reduction of the Hall coefficient R-H in the metallic phase of these films with epitaxial strain and also a surprising transition to a negative value at large compressive strain. The partially gapped, weakly insulating, paramagnetic phase is reminiscence of pseudogap behavior of high-T-c cuprates. The precursor metallic phase, which undergoes transition to the insulating phase, is a non-Fermi liquid with a temperature exponent n of resistivity of 1, whereas the exponent increases to 4/3 in the noninsulating samples. Such a nickelate phase diagram with sign reversal of R-H, a pseudogap phase, and non-Fermi-liquid behavior is intriguingly similar to high-T-c cuprates, giving important guidelines to engineer unconventional superconductivity in oxide heterostructures
Simulations of black carbon over the Indian region: improvements and implications of diurnality in emissions
No full textWith a view to improving the performance of WRF-Chem over the Indian region in simulating BC (black carbon) mass concentrations as well as its short-term variations, especially on a diurnal scale, a region-specific diurnal variation scheme has been introduced in the model emissions and the performance of the modified simulations has been evaluated against high-resolution measurements carried out over eight ARFI (Aerosol Radiative Forcing over India) network observatories spread across India for distinct seasons: pre-monsoon (represented by May), post-monsoon (represented by October) and winter (represented by December). In addition to an overall improvement in the simulated concentrations and their temporal variations, we have also found that the effects of prescribing diurnally varying emissions on the simulated near-surface concentrations largely depend on the boundary layer turbulence. The effects are perceived quickly (within about 2-3 h) during the evening-early morning hours when the atmospheric boundary layer is shallow and convective mixing is weak, while they are delayed, taking as much as about 5-6 h, during periods when the boundary layer is deep and convective mixing is strong. This information would also serve as an important input for agencies concerned with urban planning and pollution mitigation. Despite these improvements in the near-surface concentrations, the simulated columnar aerosol optical depth (AOD) still remains largely underestimated vis-a-vis the satellite-retrieved products. These modifications will serve as a guideline for further model-improvement initiatives at a regional scale