Improvement of alignment accuracy utilizing sequentially conserved motifs

Background: Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field. Results: We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs. Conclusions: The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at http://caps.ncbs.res.in/FMALIGN/Home.html

Partial-Transfer Absorption Imaging: A versatile technique for optimal imaging of ultracold gases

Partial-transfer absorption imaging is a tool that enables optimal imaging of atomic clouds for a wide range of optical depths. In contrast to standard absorption imaging, the technique can be minimally-destructive and can be used to obtain multiple successive images of the same sample. The technique involves transferring a small fraction of the sample from an initial internal atomic state to an auxiliary state and subsequently imaging that fraction absorptively on a cycling transition. The atoms remaining in the initial state are essentially unaffected. We demonstrate the technique, discuss its applicability, and compare its performance as a minimally-destructive technique to that of phase-contrast imaging.Comment: 10 pages, 5 figures, submitted to Review of Scientific Instrument

Detecting Methane From Leaking Pipelines and as Greenhouse Gas in the Atmosphere

Laser remote sensing measurements of trace gases from orbit can provide unprecedented information about important planetary science and answer critical questions about planetary atmospheres. Methane (CH4) is the second most important anthropogenically produced greenhouse gas. Though its atmospheric abundance is much less than that of CO2 (1.78 ppm vs. 380 ppm), it has much larger greenhouse heating potential. CH4 also contributes to pollution in the lower atmosphere through chemical reactions, leading to ozone production. Atmospheric CH4 concentrations have been increasing as a result of increased fossil fuel production, rice farming, livestock, and landfills. Natural sources of CH4 include wetlands, wild fires, and termites, and perhaps other unknown sources. Important sinks for CH4 include non-saturated soils and oxidation by hydroxyl radicals in the atmosphere. Remotely measuring CH4 and other biogenic molecules (such as ethane and formaldehyde) on Mars also has important implications on the existence of life on Mars. Measuring CH4 at very low (ppb) concentrations from orbit will dramatically improve the sensitivity and spatial resolution in the search for CH4 vents and sub-surface life on other planets. A capability has been developed using lasers and spectroscopic detection techniques for the remote measurements of trace gases in open paths. Detection of CH4, CO2, H2O, and CO in absorption cells and in open paths, both in the mid- IR and near-IR region, has been demonstrated using an Optical Parametric Amplifier laser transmitter developed at GSFC. With this transmitter, it would be possible to develop a remote sensing methane instrument. CH4 detection also has very important commercial applications. Pipeline leak detection from an aircraft or a helicopter can significantly reduce cost, response time, and pinpoint the location. The main advantage is the ability to rapidly detect CH4 leaks remotely. This is extremely important for the petrochemical industry. This capability can be used in manned or unmanned airborne platforms for the detection of leaks in pipelines and other areas of interest where a CH4 leak is suspected

A Ring with a Spin : Superfluidity in a toroidal Bose-Einstein condensate

Superfluidity is a remarkable phenomenon. Superfluidity was initially characterized by flow without friction, first seen in liquid helium in 1938, and has been studied extensively since. Superfluidity is believed to be related to, but not identical to Bose-Einstein condensation, a statistical mechanical phenomena predicted by Albert Einstein in 1924 based on the statistics of Satyendra Nath Bose, where bosonic atoms make a phase transition to form a Bose-Einstein condensate (BEC), a gas which has macroscopic occupation of a single quantum state. Developments in laser cooling of neutral atoms and the subsequent realization of Bose-Einstein condensates in ultracold gases have opened a new window into the study of superfluidity and its relation to Bose-Einstein condensation. In our atomic sodium BEC experiment, we studied superfluidity and dissipationless flow in an all-optical toroidal trap, constructed using the combination of a horizontal ``sheet''-like beam and vertical ``ring''-like beam, which, like a circuit loop, allows flow around the ring. On inducing a single quantum of circulation in the condensate, the smoothness and uniformity of the toroidal BEC enabled the sustaining of a persistent current lasting 40 seconds, limited by the lifetime of the BEC due to background gas pressure. This success set the stage for further experiments studying superfluidity. In a first set of experiments, we studied the stability of the persistent current by inserting a barrier in the flow path of the ring. The superflow stopped abruptly at a barrier strength such that the local flow velocity at the barrier exceeded a critical velocity, which supported decay via the creation of a vortex-antivortex pair. Our precise control in inducing and arresting superflow in the BEC is a first step toward studying other aspects of superfluidity, such as the effect of temperature and dimensionality. This thesis discusses these experiments and also details partial-transfer absorption imaging, an imaging technique developed in the course of this work

Ground and Airborne Methane Measurements Using Optical Parametric Amplifiers

We report on ground and airborne methane measurements with an active sensing instrument using widely tunable, seeded optical parametric generation (OPG). The technique has been used to measure methane, CO2, water vapor, and other trace gases in the near and mid-infrared spectral regions. Methane is a strong greenhouse gas on Earth and it is also a potential biogenic marker on Mars and other planetary bodies. Methane in the Earth's atmosphere survives for a shorter time than CO2 but its impact on climate change can be larger than CO2. Carbon and methane emissions from land are expected to increase as permafrost melts exposing millennial-age carbon stocks to respiration (aerobic-CO2 and anaerobic-CH4) and fires. Methane emissions from c1athrates in the Arctic Ocean and on land are also likely to respond to climate warming. However, there is considerable uncertainty in present Arctic flux levels, as well as how fluxes will change with the changing environment. For Mars, methane measurements are of great interest because of its potential as a strong biogenic marker. A remote sensing instrument that can measure day and night over all seasons and latitudes can localize sources of biogenic gas plumes produced by subsurface chemistry or biology, and aid in the search for extra-terrestrial life. In this paper we report on remote sensing measurements of methane using a high peak power, widely tunable optical parametric generator (OPG) operating at 3.3 micrometers and 1.65 micrometers. We have demonstrated detection of methane at 3.3 micrometers and 1650 nanometers in an open path and compared them to accepted standards. We also report on preliminary airborne demonstration of methane measurements at 1.65 micrometers

Ground and Airborne Methane Measurements with an Optical Parametric Amplifier

Here we report on measurements made with an improved CO2 Sounder lidar during the ASCENDS 2014 and 2016 airborne campaigns. The changes made to the 2011 version of the lidar included incorporating a rapidly wavelength-tunable, step-locked seed laser in the transmittter, using a much more sensitive HgCdTe APD detector andusing an analog digitizer with faster readout time in the receiver. We also improved the lidar's calibration approach and the XCO2 retrieval algorithm. The 2014 and 2016 flights were made over several types of topographic surfaces from3 to 12 km aircraft altitudes in the continental US. The results are compared to the XCO2 values computed from an airborne in situ sensor during spiral-down maneuvers. The 2014 results show significantly better performance and include measurement of horizontal gradients in XCO2 made over the Midwestern US that agree with chemistry transport models. The results from the 2016 airborne lidar retrievals show precisions of 0:7 parts per million (ppm) with 1 s averaging over desert surfaces, which is an improvement of about 8 times compared to similar measurements made in 2011. Measurements in 2016 were also made over fresh snow surfaces that have lower surface reflectance at the laser wavelengths. The results from both campaigns showed that the mean values of XCO2 retrieved from the lidar consistently agreed with those based on the in situ sensor to within 1 ppm. The improved precision and accuracy demonstrated in the 2014 and 2016 flights should benefit future airborne science ampaigns and advance the technique's readiness for a spacebased instrument

Pulsed Lidar Measurements of Atmospheric CO2 Column Absorption in the ASCENDS 2011 Airborne Campaign

We have previously demonstrated an efficient pulsed, wavelength-resolved IPDA lidar technique for measuring the tropospheric CO2 concentrations as a candidate for NASA's ASCENDS mission. Our team participated in the 2010 ASCENDS airborne campaigns we flew airborne version of the CO2 and O2 lidar on the NASA DC-8. The CO2 lidar measures the atmospheric backscatter profiles and shape of the 1572.33 nm absorption line using 250 mW average laser power, 30 wavelength samples per scan and 300 scans per second. Most flights had 5-6 altitude steps to greater than 12 km, and clear CO2 line shapes were observed at all altitudes. Our post-flight analysis estimated the Iidar range and pulse energies at each wavelength every second. We then solved for the best-fit CO2 absorption line shape, and calculated the Differential Optical Depth (DOD) at the line peak. We compared these to CO2 DODs calculated from spectroscopy based on HITRAN 2008 and the conditions from airborne in-situ readings. Analysis of the 2010 measurements over the Pacific Ocean and Lamont OK shows the expected -linear change of the peak DOD with altitude. For measurements at altitudes greater than 6 km the random errors were approximately 0.3 ppm for 80 sec averaging times. After the 2010 flights we improved the airborne lidar's scan uniformity, calibration and receiver sensitivity. Our team participated in the seven ASCENDS science flights during late July and August 2011. These flights were made over a wide variety of surface and cloud conditions near the US, including over the central valley of California, over several mountain ranges, over both broken and solid stratus cloud deck over the Pacific Ocean, snow patches on mountain tops, over thin and broken clouds above the US Southwest and Iowa, and over forests near the WLEF tower in Wisconsin. Analyses show the retrievals of lidar range and CO2 column absorption, as wen as estimates of CO2 mixing ratio worked well when measuring over topography with rapidly changing height and reflectivity, through thin clouds and to stratus cloud tops. For regions where the CO2 concentration was relatively constant, the measured CO2 absorption profile (averaged for 50 sec) matched the predicted profile to better than 1% RMS error for all flight altitudes. For 1 & 10 second averaging, the scatter in the retrievals was limited by signal shot noise (i.e. the sigual photon count). Analysis to date shows the decrease in CO2 due to vegetation when flying easterward over the Great Plains as well as the increase in CO2 concentration in the vicinity ofthe coal-fired power plant in New Mexico. Examples of these and other results will be presented

110th Anniversary: Near-Total Epoxidation Selectivity and Hydrogen Peroxide Utilization with Nb-EISA Catalysts for Propylene Epoxidation

The Nb-EISA catalyst with relatively low Nb loadings (∼2 wt %) shows exceptional propylene epoxidation performance with H2O2 as oxidant at 30–40 °C, 5–9 bar propylene pressure with nearly total propylene oxide (PO) selectivity (>99%), H2O2 utilization (>99%) toward PO formation, high productivity (∼3200 mg/h/g), and mild Nb leaching (3–6%). The predominantly Lewis acidic nature of the Nb-EISA catalysts favors epoxidation while their relatively low Brønsted acidity inhibits H2O2 decomposition and Nb leaching. At higher Nb loadings (8–17 wt %), the catalytic performance deteriorates. However, significant performance improvements were achieved when the Nb-EISA materials are calcined in N2 (instead of air) during synthesis, depositing a carbon layer in the pores. The resulting pore hydrophobicity not only inhibits epoxide ring opening but also increases propylene concentration inside the pores resulting in higher EO productivity and lower H2O2 decomposition. The carbonized Nb-EISA materials also show improved stability to leaching

Towards highly selective ethylene epoxidation catalysts using hydrogen peroxide and tungsten- or niobium-incorporated mesoporous silicate (KIT-6)

This is the published version. Copyright 2014 Royal Society of ChemistrySignificant ethylene epoxidation activity was observed over Nb- and W-incorporated KIT-6 materials with aqueous hydrogen peroxide (H2O2) as the oxidant and methanol as solvent under mild operating conditions (35 °C and 50 bar) where CO2 formation is avoided. The Nb-KIT-6 materials generally show greater epoxidation activity compared to the W-KIT-6 materials. Further, the ethylene oxide (EO) productivity observed with these materials [30–800 mg EO h−1 (g metal)−1] is of the same order of magnitude as that of the conventional silver (Ag)-based gas phase ethylene epoxidation process. Our results reveal that the framework-incorporated metal species, rather than the extra-framework metal oxide species, are mainly responsible for the observed epoxidation activity. However, the tetrahedrally coordinated framework metal species also introduce Lewis acidity that promotes their solvolysis (which in turn results in their gradual leaching) as well as H2O2 decomposition. These results and mechanistic insights provide rational guidance for developing catalysts with improved leaching resistance and minimal H2O2 decomposition

Fenton-like degradation of Bisphenol A catalyzed by mesoporous Cu/TUD-1

A family of copper oxide catalysts with loadings spanning 1–5 wt% were dispersed on a three dimensional, mesoporous TUD-1 silica through a hydrothermal, surfactant-free route employing tetraethylene glycol as a structure-directing agent. Their bulk and surface properties were characterized by N2 physisorption, XRD, DRUVS, EPR, TEM and Raman spectroscopy, confirming the expected mesoporous wormhole/foam support morphology and presence of well-dispersed CuO nanoparticles (∼5–20 nm). The catalytic performance of Cu/TUD-1 was evaluated as heterogeneous Fenton-like catalysts for Bisphenol A (BPA) oxidative degradation in the presence of H2O2 as a function of [H2O2], and CuO loading. Up to 90.4% of 100 ppm BPA removal was achieved over 2.5 wt% Cu/TUD-1 within 180 min, with negligible Cu leaching into the treated water