Constraining East Asian CO2 emissions with GOSAT retrievals: methods and policy implications

NASA Astrophysics Data System (ADS)

Shim, C.; Henze, D. K.; Deng, F.

2017-12-01

The world largest CO2 emissions are from East Asia. However, there are large uncertainties in CO2 emission inventories, mainly because of imperfections in bottom-up statistics and a lack of observations for validating emission fluxes, particularly over China. Here we tried to constrain East Asian CO2 emissions with GOSAT retrievals applying 4-Dvar GEOS-Chem and its adjoint model. We applied the inversion to only the cold season (November - February) in 2009 - 2010 since the summer monsoon and greater transboundary impacts in spring and fall greatly reduced the GOSAT retrievals. In the cold season, the a posteriori CO2 emissions over East Asia generally higher by 5 - 20%, particularly Northeastern China shows intensively higher in a posteriori emissions ( 20%), where the Chinese government is recently focusing on mitigating the air pollutants. In another hand, a posteriori emissions from Southern China are lower 10 - 25%. A posteriori emissions in Korea and Japan are mostly higher by 10 % except over Kyushu region. With our top-down estimates with 4-Dvar CO2 inversion, we will evaluate the current regional CO2 emissions inventories and potential uncertainties in the sectoral emissions. This study will help understand the quantitative information on anthropogenic CO2 emissions over East Asia and will give policy implications for the mitigation targets.

Excited state of protonated benzene and toluene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esteves-López, Natalia; Dedonder-Lardeux, Claude; Jouvet, Christophe, E-mail: Christophe.jouvet@univ-amu.fr

We present photo-fragmentation electronic spectra of the simplest protonated aromatic molecules, protonated benzene and toluene, recorded under medium resolution conditions and compared with the photo-fragmentation spectrum of protonated pyridine. Despite the resolution and cold temperature achieved in the experiment, the electronic spectra of protonated benzene and toluene are structure-less, thus intrinsically broadened. This is in agreement with the large geometrical changes and the fast dynamic toward internal conversion predicted by ab initio calculations for protonated benzene [Rode et al., J. Phys. Chem. A 113, 5865–5873 (2009)].

Investigating Pharmacological Similarity by Charting Chemical Space.

PubMed

Buonfiglio, Rosa; Engkvist, Ola; Várkonyi, Péter; Henz, Astrid; Vikeved, Elisabet; Backlund, Anders; Kogej, Thierry

2015-11-23

In this study, biologically relevant areas of the chemical space were analyzed using ChemGPS-NP. This application enables comparing groups of ligands within a multidimensional space based on principle components derived from physicochemical descriptors. Also, 3D visualization of the ChemGPS-NP global map can be used to conveniently evaluate bioactive compound similarity and visually distinguish between different types or groups of compounds. To further establish ChemGPS-NP as a method to accurately represent the chemical space, a comparison with structure-based fingerprint has been performed. Interesting complementarities between the two descriptions of molecules were observed. It has been shown that the accuracy of describing molecules with physicochemical descriptors like in ChemGPS-NP is similar to the accuracy of structural fingerprints in retrieving bioactive molecules. Lastly, pharmacological similarity of structurally diverse compounds has been investigated in ChemGPS-NP space. These results further strengthen the case of using ChemGPS-NP as a tool to explore and visualize chemical space.

Scrubchem: Building Bioactivity Datasets from Pubchem ...

EPA Pesticide Factsheets

The PubChem Bioassay database is a non-curated public repository with data from 64 sources, including: ChEMBL, BindingDb, DrugBank, EPA Tox21, NIH Molecular Libraries Screening Program, and various other academic, government, and industrial contributors. Methods for extracting this public data into quality datasets, useable for analytical research, presents several big-data challenges for which we have designed manageable solutions. According to our preliminary work, there are approximately 549 million bioactivity values and related meta-data within PubChem that can be mapped to over 10,000 biological targets. However, this data is not ready for use in data-driven research, mainly due to lack of structured annotations.We used a pragmatic approach that provides increasing access to bioactivity values in the PubChem Bioassay database. This included restructuring of individual PubChem Bioassay files into a relational database (ScrubChem). ScrubChem contains all primary PubChem Bioassay data that was: reparsed; error-corrected (when applicable); enriched with additional data links from other NCBI databases; and improved by adding key biological and assay annotations derived from logic-based language processing rules. The utility of ScrubChem and the curation process were illustrated using an example bioactivity dataset for the androgen receptor protein. This initial work serves as a trial ground for establishing the technical framework for accessing, integrating, cu

Porosity effects on crystallization kinetics of Amorphous Solid Water: Implications for cold icy objects in the Outer Solar System

NASA Astrophysics Data System (ADS)

Mitchell, Emily H.; Raut, Ujjwal; Baragiola, Raul A.

2015-11-01

Crystalline ice has been identified on the cold surfaces of most icy satellites and TNOs [1]. This is surprising since accretion of water vapor at temperatures (T < 100 K) should result in the amorphous phase [2]. There are several possible explanations for the unexpected presence of crystalline ice on cold bodies, including cryovolcanism [3] and pulsed heating by micrometeoritic impacts [4].A salient feature of ice films condensed at low T is microporosity, known to increase with deposition angle [5]. Here we investigate the dependence of the crystallization rate on the ice porosity, which could contribute to the observed variation in crystallization time τc reported in the literature [2]. Such dependence is noted in other porous materials such as zeolites and titania [6, 7].Amorphous ice films were deposited on a CsI substrate from a collimated water vapor source at 10 K at incidences varying from 0 to 70°, as well as from an omnidirectional water vapor source. The films were heated to temperatures between 130 and 140 K following deposition. The isothermal transition from amorphous to fully crystalline phase was characterized by analyzing the time-dependent evolution of the OH-stretch absorption band using transmission infrared spectroscopy. Our initial results show that τc decreases with increasing porosity; for instance, a film deposited at 45° was observed to crystallize ~6 times faster than a film deposited at 0°. The preliminary estimate of the porosity of the 45° film is ~50% higher than that of the film deposited at normal incidence. Our findings can explain the reported variation in temperature-dependent τc [2] and contribute to the understanding of crystalline ice on cold bodies in the Outer Solar System.1. Mastrapa, R.M.E. et al. In: Gudipati, M.S. & Castillo-Rogez, J., Eds, The Science of Solar System Ices, Springer, New York, 2013.2. Baragiola, R.A. In: Devlin & Buch, Eds, Water in Confining Geometries, Springer-Verlag, 2003.3. Jewitt, D.C. & Luu, J., Nature 432, 731, 2004.4. Porter, S.B. et al. Icarus 208, 492, 2010.5. Stevenson, K.P., et al. Science 283, 1505, 1999.6. Francis, R.J. & O’Hare, D., J. Chem. Soc., Dalton Trans., 3133, 1998.7. Kirsch, B.L. et al., J. Phys. Chem. B., 108, 12698, 2004.

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

PubMed

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

Molecular Interactions and Properties with Many-Body Methods

DTIC Science & Technology

1990-04-17

AFOSR have been identified in a book by Schaefer , Quantum Chemistry (Oxford, 1984), as being among the 149 most influential papers in the 50-year...Coupled Cluster Investigation of Isomerization Reactions: HCN*HNC, BH3CN-BH 3NC- and HCNBH3 *HNCBH3," J. Am. Chem. Soc. 110, 4926 (1988). 21. M. Rittby...Kucharski, J. Noga and R.J. Bartlett, J. Chem. Phys. 88, 1035 (1988). 49. H. Urban and R.J. Bartlett, J. Am. Chem. Soc. 110, 4926 (1988). 50. G.D

Theory for the solvation of nonpolar solutes in water

NASA Astrophysics Data System (ADS)

Urbic, T.; Vlachy, V.; Kalyuzhnyi, Yu. V.; Dill, K. A.

2007-11-01

We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water.

Theory for the solvation of nonpolar solutes in water.

PubMed

Urbic, T; Vlachy, V; Kalyuzhnyi, Yu V; Dill, K A

2007-11-07

We recently developed an angle-dependent Wertheim integral equation theory (IET) of the Mercedes-Benz (MB) model of pure water [Silverstein et al., J. Am. Chem. Soc. 120, 3166 (1998)]. Our approach treats explicitly the coupled orientational constraints within water molecules. The analytical theory offers the advantage of being less computationally expensive than Monte Carlo simulations by two orders of magnitude. Here we apply the angle-dependent IET to studying the hydrophobic effect, the transfer of a nonpolar solute into MB water. We find that the theory reproduces the Monte Carlo results qualitatively for cold water and quantitatively for hot water.

DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.

PubMed

Soufan, Othman; Ba-Alawi, Wail; Magana-Mora, Arturo; Essack, Magbubah; Bajic, Vladimir B

2018-06-14

High-throughput screening (HTS) performs the experimental testing of a large number of chemical compounds aiming to identify those active in the considered assay. Alternatively, faster and cheaper methods of large-scale virtual screening are performed computationally through quantitative structure-activity relationship (QSAR) models. However, the vast amount of available HTS heterogeneous data and the imbalanced ratio of active to inactive compounds in an assay make this a challenging problem. Although different QSAR models have been proposed, they have certain limitations, e.g., high false positive rates, complicated user interface, and limited utilization options. Therefore, we developed DPubChem, a novel web tool for deriving QSAR models that implement the state-of-the-art machine-learning techniques to enhance the precision of the models and enable efficient analyses of experiments from PubChem BioAssay database. DPubChem also has a simple interface that provides various options to users. DPubChem predicted active compounds for 300 datasets with an average geometric mean and F 1 score of 76.68% and 76.53%, respectively. Furthermore, DPubChem builds interaction networks that highlight novel predicted links between chemical compounds and biological assays. Using such a network, DPubChem successfully suggested a novel drug for the Niemann-Pick type C disease. DPubChem is freely available at www.cbrc.kaust.edu.sa/dpubchem .

An investigation of methods for injecting emissions from boreal wildfires using WRF-Chem during ARCTAS

NASA Astrophysics Data System (ADS)

Sessions, W. R.; Fuelberg, H. E.; Kahn, R. A.; Winker, D. M.

2010-11-01

The Weather Research and Forecasting Model (WRF) is considered a "next generation" mesoscale meteorology model. The inclusion of a chemistry module (WRF-Chem) allows transport simulations of chemical and aerosol species such as those observed during NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) in 2008. The ARCTAS summer deployment phase during June and July coincided with large boreal wildfires in Saskatchewan and Eastern Russia. One of the most important aspects of simulating wildfire plume transport is the height at which emissions are injected. WRF-Chem contains an integrated one-dimensional plume rise model to determine the appropriate injection layer. The plume rise model accounts for thermal buoyancy associated with fires and the local atmospheric stability. This study compares results from the plume model against those of two more traditional injection methods: Injecting within the planetary boundary layer, and in a layer 3-5 km above ground level. Fire locations are satellite derived from the GOES Wildfire Automated Biomass Burning Algorithm (WF_ABBA) and the MODIS thermal hotspot detection. Two methods for preprocessing these fire data are compared: The prep_chem_sources method included with WRF-Chem, and the Naval Research Laboratory's Fire Locating and Monitoring of Burning Emissions (FLAMBE). Results from the simulations are compared with satellite-derived products from the AIRS, MISR and CALIOP sensors. Results show that the FLAMBE pre-processor produces more realistic injection heights than does prep_chem_sources. The plume rise model using FLAMBE provides the best agreement with satellite-observed injection heights. Conversely, when the planetary boundary layer or the 3-5 km AGL layer were filled with emissions, the resulting injection heights exhibit less agreement with observed plume heights. Results indicate that differences in injection heights produce different transport pathways. These differences are especially pronounced in areas of strong vertical wind shear and when the integration period is long.

Three dimensional atom-diatom quantum reactive scattering calculations using absorbing potential: speed up of the propagation scheme.

PubMed

Stoecklin, T

2008-09-01

In this paper a new propagation scheme is proposed for atom-diatom reactive calculations using a negative imaginary potential (NIP) within a time independent approach. It is based on the calculation of a rotationally adiabatic basis set, the neglected coupling terms being re-added in the following step of the propagation. The results of this approach, which we call two steps rotationally adiabatic coupled states calculations (2-RACS), are compared to those obtained using the adiabatic DVR method (J. C. Light and Z. Bazic, J. Chem. Phys., 1987, 87, 4008; C. Leforestier, J. Chem. Phys., 1991, 94, 6388), to the NIP coupled states results of the team of Baer (D. M. Charutz, I. Last and M. Baer, J. Chem. Phys., 1997, 106, 7654) and to the exact results obtained by Zhang (J. Z. H. Zhang and W. H. Miller, J. Chem. Phys., 1989, 91, 1528) for the D + H(2) reaction. The example of implementation of our method of computation of the adiabatic basis will be given here in the coupled states approximation, as this method has proved to be very efficient in many cases and is quite fast.

Modeling the Transport and Radiative Forcing of Taklimakan Dust over the Tibetan Plateau: A case study in the summer of 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Siyu; Huang, J.; Zhao, Chun

2013-01-30

The Weather Research and Forecasting model with chemistry (WRF-Chem) is used to investigate an intense dust storm event during 26 to 30 July 2006 that originated over the Taklimakan Desert (TD) and transported to the northern slope of Tibetan Plateau (TP). The dust storm is initiated by the approach of a strong cold frontal system over the TD. In summer, the meridional transport of TD dust to the TP is favored by the thermal effect of the TP and the weakening of the East Asian westerly winds. During this dust storm, the transport of TD dust over the TP ismore » further enhanced by the passage of the cold front. As a result, TD dust breaks through the planetary boundary layer and extends to the upper troposphere over the northern TP. TD dust flux arrived at the TP with a value of 6.6 Gg/day in this 5 day event but decays quickly during the southward migration over the TP due to dry deposition. The simulations show that TD dust cools the atmosphere near the surface and heats the atmosphere above with a maximum heating rate of 0.11 K day-1 at ~7 km over the TP. The event-averaged net radiative forcings of TD dust over the TP are -3.97, 1.61, and -5.58 Wm-2 at the top of the atmosphere (TOA), in the atmosphere, and at the surface, respectively. The promising performance of WRF-Chem in simulating dust and its radiative forcing provides confidence for use in further investigation of climatic impact of TD dust over the TP.« less

Global analysis of the high temperature infrared emission spectrum of 12CH4 in the dyad (ν2/ν4) region

NASA Astrophysics Data System (ADS)

Amyay, Badr; Louviot, Maud; Pirali, Olivier; Georges, Robert; Vander Auwera, Jean; Boudon, Vincent

2016-01-01

We report new assignments of vibration-rotation line positions of methane (12CH4) in the so-called dyad (ν2/ν4) region (1100-1500 cm-1), and the resulting update of the vibration-rotation effective model of methane, previously reported by Nikitin et al. [Phys. Chem. Chem. Phys. 15, 10071 (2013)], up to and including the tetradecad. High resolution (0.01 cm-1) emission spectra of methane have been recorded up to about 1400 K using the high-enthalpy source developed at Institut de Physique de Rennes associated with the Fourier transform spectrometer of the SOLEIL synchrotron facility (AILES beamline). Analysis of these spectra allowed extending rotational assignments in the well-known cold band (dyad-ground state (GS)) and related hot bands in the pentad-dyad system (3000 cm-1) up to Jmax = 30 and 29, respectively. In addition, 8512 new transitions belonging to the octad-pentad (up to J = 28) and tetradecad-octad (up to J = 21) hot band systems were successfully identified. As a result, the MeCaSDa database of methane was significantly improved. The line positions assigned in this work, together with the information available in the literature, were fitted using 1096 effective parameters with a dimensionless standard deviation σ = 2.09. The root mean square deviations dRMS are 3.60 × 10-3 cm-1 for dyad-GS cold band, 4.47 ×10-3 cm-1 for the pentad-dyad, 5.43 × 10-3 cm-1 for the octad-pentad, and 4.70 × 10-3 cm-1 for the tetradecad-octad hot bands. The resulting new line list will contribute to improve opacity and radiative transfer models for hot atmospheres, such as those of hot-Jupiter type exoplanets.

A practical method to avoid zero-point leak in molecular dynamics calculations: application to the water dimer.

PubMed

Czakó, Gábor; Kaledin, Alexey L; Bowman, Joel M

2010-04-28

We report the implementation of a previously suggested method to constrain a molecular system to have mode-specific vibrational energy greater than or equal to the zero-point energy in quasiclassical trajectory calculations [J. M. Bowman et al., J. Chem. Phys. 91, 2859 (1989); W. H. Miller et al., J. Chem. Phys. 91, 2863 (1989)]. The implementation is made practical by using a technique described recently [G. Czako and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], where a normal-mode analysis is performed during the course of a trajectory and which gives only real-valued frequencies. The method is applied to the water dimer, where its effectiveness is shown by computing mode energies as a function of integration time. Radial distribution functions are also calculated using constrained quasiclassical and standard classical molecular dynamics at low temperature and at 300 K and compared to rigorous quantum path integral calculations.

Precision Spectroscopy in Cold Molecules: The Lowest Rotational Interval of He2 + and Metastable He2

NASA Astrophysics Data System (ADS)

Jansen, Paul; Semeria, Luca; Hofer, Laura Esteban; Scheidegger, Simon; Agner, Josef A.; Schmutz, Hansjürg; Merkt, Frédéric

2015-09-01

Multistage Zeeman deceleration was used to generate a slow, dense beam of translationally cold He2 molecules in the metastable a 3Σu+ state. Precision measurements of the Rydberg spectrum of these molecules at high values of the principal quantum number n have been carried out. The spin-rotational state selectivity of the Zeeman-deceleration process was exploited to reduce the spectral congestion, minimize residual Doppler shifts, resolve the Rydberg series around n =200 and assign their fine structure. The ionization energy of metastable He2 and the lowest rotational interval of the X+ 2Σu+ (ν+=0 ) ground state of 4He2+ have been determined with unprecedented precision and accuracy by Rydberg-series extrapolation. Comparison with ab initio predictions of the rotational energy level structure of 4He2+ [W.-C. Tung, M. Pavanello, and L. Adamowicz, J. Chem. Phys. 136, 104309 (2012)] enabled us to quantify the magnitude of relativistic and quantum-electrodynamics contributions to the fundamental rotational interval of He2+ .

77 FR 57529 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-18

... the fuselage skin along chem- mill steps at certain crown skin and shear wrinkle areas, and repair if... the procedures found in 14 CFR 11.43 and 11.45, by any of the following methods: Federal eRulemaking... to non-chem-mill areas at antenna and door bearstrap installations, and shear wrinkle areas at...

FastChem: A computer program for efficient complex chemical equilibrium calculations in the neutral/ionized gas phase with applications to stellar and planetary atmospheres

NASA Astrophysics Data System (ADS)

Stock, Joachim W.; Kitzmann, Daniel; Patzer, A. Beate C.; Sedlmayr, Erwin

2018-06-01

For the calculation of complex neutral/ionized gas phase chemical equilibria, we present a semi-analytical versatile and efficient computer program, called FastChem. The applied method is based on the solution of a system of coupled nonlinear (and linear) algebraic equations, namely the law of mass action and the element conservation equations including charge balance, in many variables. Specifically, the system of equations is decomposed into a set of coupled nonlinear equations in one variable each, which are solved analytically whenever feasible to reduce computation time. Notably, the electron density is determined by using the method of Nelder and Mead at low temperatures. The program is written in object-oriented C++ which makes it easy to couple the code with other programs, although a stand-alone version is provided. FastChem can be used in parallel or sequentially and is available under the GNU General Public License version 3 at https://github.com/exoclime/FastChem together with several sample applications. The code has been successfully validated against previous studies and its convergence behavior has been tested even for extreme physical parameter ranges down to 100 K and up to 1000 bar. FastChem converges stable and robust in even most demanding chemical situations, which posed sometimes extreme challenges for previous algorithms.

An investigation of methods for injecting emissions from boreal wildfires using WRF-Chem during ARCTAS

NASA Astrophysics Data System (ADS)

Sessions, W. R.; Fuelberg, H. E.; Kahn, R. A.; Winker, D. M.

2011-06-01

The Weather Research and Forecasting Model (WRF) is considered a "next generation" mesoscale meteorology model. The inclusion of a chemistry module (WRF-Chem) allows transport simulations of chemical and aerosol species such as those observed during NASA's Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) in 2008. The ARCTAS summer deployment phase during June and July coincided with large boreal wildfires in Saskatchewan and Eastern Russia. One of the most important aspects of simulating wildfire plume transport is the height at which emissions are injected. WRF-Chem contains an integrated one-dimensional plume rise model to determine the appropriate injection layer. The plume rise model accounts for thermal buoyancy associated with fires and local atmospheric stability. This paper describes a case study of a 10 day period during the Spring phase of ARCTAS. It compares results from the plume model against those of two more traditional injection methods: Injecting within the planetary boundary layer, and in a layer 3-5 km above ground level. Fire locations are satellite derived from the GOES Wildfire Automated Biomass Burning Algorithm (WF_ABBA) and the MODIS thermal hotspot detection. Two methods for preprocessing these fire data are compared: The prep_chem_sources method included with WRF-Chem, and the Naval Research Laboratory's Fire Locating and Monitoring of Burning Emissions (FLAMBE). Results from the simulations are compared with satellite-derived products from the AIRS, MISR and CALIOP sensors. When FLAMBE provides input to the 1-D plume rise model, the resulting injection heights exhibit the best agreement with satellite-observed injection heights. The FLAMBE-derived heights are more realistic than those utilizing prep_chem_sources. Conversely, when the planetary boundary layer or the 3-5 km a.g.l. layer were filled with emissions, the resulting injection heights exhibit less agreement with observed plume heights. Results indicate that differences in injection heights produce different transport pathways. These differences are especially pronounced in area of strong vertical wind shear and when the integration period is long.

Torsional Angle Driver (TorAD) System for HyperChem/Excel

NASA Astrophysics Data System (ADS)

Starkey, Ronald

1999-02-01

The torsional angle driver system for HyperChem/Excel is a package of several Excel spreadsheets and macro programs to be used with HyperChem to obtain and plot information, such as total energy, for the conformations that result from a 360° rotation about a torsional angle system in a molecule. The TorAD system also includes several HyperChem scripts to facilitate its use. TorAD was developed for use in the undergraduate organic chemistry laboratory. The results obtained with TorAD could be obtained manually with HyperChem, but it would take considerable time and would not be instructive to the students. Use of the TorAD system allows students to spend their time on the more important aspect of conformation analysisinterpretation of results. The Excel spreadsheet/macro programs in TorAD include:

· Tor_xl_a and tor_xl obtain and plot the total energy at 5° torsional-angle intervals. The calculation method, the torsional-angle restraint, and the structure to be used at each angle can be set by the user. The advanced version, tor_xl_a, which requires HyperChem 4.5 or later, also allows torsional-angle structures to be saved for later recall as individual structures or, using a HyperChem script, in a movie format. It also provides a rapid scan of the 360° rotation where only single-point calculations, rather than geometry optimizations, are performed. The tor_xl system will perform routine tasks in a manner suitable for most instructional settings. · Tor_Comp performs molecular mechanics optimizations at 5° intervals and obtains and plots four energy parameters (total, torsional, nonbonded, and bond [bend plus stretch] energy) as a function of torsional angle. The calculation method and the restraint can be specified. · TorDipol produces a plot of the total energy and the calculated dipole moment at 5° steps of the torsional angle. The default calculation is the semi-empirical AM1 method, but other methods can be used. The calculation method and the restraint can be specified. · Tor2_180 and Tor2_360 rotate two torsional angles to provide a 3D plot of the resulting total energy surface. Tor2_180 performs a 0 to 180° rotation, in 10° steps, on each of the two torsional angle systems (tor1 and tor2) selected. Tor2_360 will do a -180° to +180° (360° total) rotation of the two torsional angles in 20° steps.

Spectroscopic Manifestation of Vibrationally-Mediated Structure Change in the Isolated Formate Monohydrate

NASA Astrophysics Data System (ADS)

Denton, Joanna K.; Wolke, Conrad T.; Gorlova, Olga; Gerardi, Helen; McCoy, Anne B.; Johnson, Mark

2016-06-01

The breadth of the OH stretching manifold observed in the IR for bulk water is commonly attributed to the thermal population of excited states and the presence of many configurations within the water network. Here, I use carboxylate species as a rigid framework to isolate a single water molecule in the gas phase and cold ion vibrational pre-dissociation spectroscopy to explore excited state contributions to bandwidth. The spectrum of the carboxylate monohydrate exhibits a signature series of peaks in the OH stretching region of this system, providing an archetypal model to study vibrationally adiabatic mode separation. Previous analysis of this behavior accounts for the extensive progression in a Franck-Condon formalism involving displaced vibrationally adiabatic potentials. In this talk I will challenge this prediction by using isotopic substation to systematically change the level structure within these potentials. This picture quantitatively accounts for the diffuse spectrum of this complex at elevated temperature providing a convenient spectroscopic reporter for the temperature of ions in a trap. E. M. Myshakin, K. D. Jordan, E. L. Sibert III, M. A. Johnson J. Chem. Phys. 119, 10138 (2003) W.H. Robertson, et al. J. Phys Chem. 107, 6527 (2003)

Cubic ice and large humidity with respect to ice in cold cirrus clouds

NASA Astrophysics Data System (ADS)

Bogdan, A.; Loerting, T.

2009-04-01

Recently several studies have reported about the possible formation of cubic ice in upper-tropospheric cirrus ice clouds and its role in the observed elevated relative humidity with respect to hexagonal ice, RHi, within the clouds. Since cubic ice is metastable with respect to stable hexagonal ice, its vapour pressure is higher. A key issue in determining the ratio of vapour pressures of cubic ice Pc and hexagonal ice Ph is the enthalpy of transformation from cubic to hexagonal ice Hc→h. By dividing the two integrated forms of the Clausius-Clapeyron equation for cubic ice and hexagonal ice, one obtains the relationship (1): ln Pc-- ln P*c-=--(Hc→h--) Ph P*h R 1T-- 1T* (1) from which the importance of Hc→h is evident. In many literature studies the approximation (2) is used: ln Pc-= Hc-→h. Ph RT (2) Using this approximated form one can predict the ratio of vapour pressures by measuring Hc→h. Unfortunately, the measurement of Hc→h is difficult. First, the enthalpy difference is very small, and the transition takes place over a broad temperature range, e.g., between 230 K and 260 K in some of our calorimetry experiments. Second, cubic ice (by contrast to hexagonal ice) can not be produced as a pure crystal. It always contains hexagonal stacking faults, which are evidenced by the (111)-hexagonal Bragg peak in the powder diffractogram. If the number of hexagonal stacking faults in cubic ice is high, then one could even consider this material as hexagonal ice with cubic stacking faults. Using the largest literature value of the change of enthalpy of transformation from cubic to hexagonal ice, Hc→h ? 160 J/mol, Murphy and Koop (2005) calculated that Pc would be ~10% higher than that of hexagonal ice Phat 180 K - 190 K, which agrees with the measurements obtained later by Shilling et al. (2006). Based on this result Shilling et al. concluded that "the formation of cubic ice at T < 202 K may significantly contribute to the persistent in-cloud water supersaturations" in the upper-tropospheric cold cirrus clouds. Using instead the value of Hc→h ? 50 J/mol (Handa et al., 1986; Mayer and Hallbrucker, 1987) the calculation gives that Pc is only ~3% larger than that of Ph. Recently it has been reported that emulsified water droplets freeze to cubic ice when being cooled at a rate of 10 K/min (Murray and Bertram, 2006,). We prepared emulsified droplets using the same emulsification technique and studied them with a differential scanning calorimeter (DSC) between 278 and 180 K using a scanning rate of 10 K/min. During the warming of the samples we observed a very broad, tiny exothermal peak approximately between 230 and 260 K. Kohl et al. (2000) observed exothermal peak at ~230 K during the warming at 30 K/min of several samples of hyperquenched glassy water (HGW) prepared at temperature between 130 and 190 K. They attributed this peak to the cubic-to-hexagonal ice transition and estimated Hc→h to be between ~33 and 75 J/mol. Johari (2005) used the value of Hc→h ? 37 J/mol. Assuming that in our case the broad peak between 230 and 260 K is also due to the cubic-to-hexagonal ice transition we obtained approximately between 10 and 25 J/mol for Hc→h. This low enthalpy of transformation suggests that cubic ice in the atmosphere contains many hexagonal stacking faults. Using these values of Hc→h for cubic ice as produced at atmospheric cooling rates, the above mentioned formula gives that Pc is larger than that of Ph only by ~1%. We, therefore, suggest that the difference in the water vapor pressures between ice Ic and ice Ih is small and does not play a significant role in the elevation of RHi in cold cirrus clouds. Murphy, D. M., and T. Koop (2005), Q. J. R. Meteorol. Soc. 131, 1539-1565. Shilling, J. E. et al. (2006). Geophys. Res. Lett. 33, L17801, doi:1029/2006GL026671. Handa, P. Y., D. D. Klug, and E. Whalley (1986). J. Chem. Phys. 84, 7009-7010. Mayer, E., and A. Hallbrucker (1987), Nature, 325, 601-602. Murray, B. J. and A. K. Bertram (2006), Phys. Chem. Chem. Phys. 8, 186-192. Kohl, I., E. Mayer, and A. Hallbrucker (2000), Phys. Chem. Chem. Phys. 2, 1579-1586. G. P. Johari, (2005), J. Chem. Phys. 122, 194504.

77 FR 57539 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-18

... cracking of the fuselage skin along chem-mill steps at certain crown skin and shear wrinkle areas, and... comments, using the procedures found in 14 CFR 11.43 and 11.45, by any of the following methods: Federal e... adjacent to non-chem-mill areas at antenna and door bearstrap installations, and shear wrinkle areas at...

Assessment of TD-DFT methods and of various spin scaled CIS(D) and CC2 versions for the treatment of low-lying valence excitations of large organic dyes

NASA Astrophysics Data System (ADS)

Goerigk, Lars; Grimme, Stefan

2010-05-01

We present an extension of our previously published benchmark set for low-lying valence transitions of large organic dyes [L. Goerigk et al., Phys. Chem. Chem. Phys. 11, 4611 (2009)]. The new set comprises in total 12 molecules, including two charged species and one with a clear charge-transfer transition. Our previous study on TD-DFT methods is repeated for the new test set with a larger basis set. Additionally, we want to shed light on different spin-scaled variants of the configuration interaction singles with perturbative doubles correction [CIS(D)] and the approximate coupled cluster singles and doubles method (CC2). Particularly for CIS(D) we want to clarify, which of the proposed versions can be recommended. Our results indicate that an unpublished SCS-CIS(D) variant, which is implemented into the TURBOMOLE program package, shows worse results than the original CIS(D) method, while other modified versions perform better. An SCS-CIS(D) version with a parameterization, that has already been used in an application by us recently [L. Goerigk and S. Grimme, ChemPhysChem 9, 2467 (2008)], yields the best results. Another SCS-CIS(D) version and the SOS-CIS(D) method [Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007)] perform very similar, though. For the electronic transitions considered herein, there is no improvement observed when going from the original CC2 to the SCS-CC2 method but further adjustment of the latter seems to be beneficial. Double-hybrid density functionals belong to best methods tested here. Particularly B2GP-PLYP provides uniformly good results for the complete set and is considered to be close to chemical accuracy within an ab initio theory of color. For conventional hybrid functionals, a Fock-exchange mixing parameter of about 0.4 seems to be optimum in TD-DFT treatments of large chromophores. A range-separated functional such as, e.g., CAM-B3LYP seems also to be promising.

Research and Teaching: Transforming Discussion in General Chemistry with Authentic Experiences for Engineering Students

ERIC Educational Resources Information Center

Crippen, Kent J.; Boyer, Treavor H.; Korolev, Maria; de Torres, Trisha; Brucat, Phil J.; Wu, Chang-Yu

2016-01-01

Undergraduate engineering education in the United States is in need of reform that addresses the recruitment and retention of a diverse population of students. Change Chem is a curriculum reform model that has been created to address this issue for freshman students. This article reports on a mixed method efficacy study of Change Chem, which uses…

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

PubMed Central

Butkiewicz, Mariusz; Lowe, Edward W.; Mueller, Ralf; Mendenhall, Jeffrey L.; Teixeira, Pedro L.; Weaver, C. David; Meiler, Jens

2013-01-01

With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR) models are built using Artificial Neural Networks (ANNs), Support Vector Machines (SVMs), Decision Trees (DTs), and Kohonen networks (KNs). Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS) and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed. PMID:23299552

Magnetic exchange couplings from noncollinear perturbation theory: dinuclear CuII complexes.

PubMed

Phillips, Jordan J; Peralta, Juan E

2014-08-07

To benchmark the performance of a new method based on noncollinear coupled-perturbed density functional theory [J. Chem. Phys. 138, 174115 (2013)], we calculate the magnetic exchange couplings in a series of triply bridged ferromagnetic dinuclear Cu(II) complexes that have been recently synthesized [Phys. Chem. Chem. Phys. 15, 1966 (2013)]. We find that for any basis-set the couplings from our noncollinear coupled-perturbed methodology are practically identical to those of spin-projected energy-differences when a hybrid density functional approximation is employed. This demonstrates that our methodology properly recovers a Heisenberg description for these systems, and is robust in its predictive power of magnetic couplings. Furthermore, this indicates that the failure of density functional theory to capture the subtle variation of the exchange couplings in these complexes is not simply an artifact of broken-symmetry methods, but rather a fundamental weakness of current approximate density functionals for the description of magnetic couplings.

Mapped grid methods for long-range molecules and cold collisions

NASA Astrophysics Data System (ADS)

Willner, K.; Dulieu, O.; Masnou-Seeuws, F.

2004-01-01

The paper discusses ways of improving the accuracy of numerical calculations for vibrational levels of diatomic molecules close to the dissociation limit or for ultracold collisions, in the framework of a grid representation. In order to avoid the implementation of very large grids, Kokoouline et al. [J. Chem. Phys. 110, 9865 (1999)] have proposed a mapping procedure through introduction of an adaptive coordinate x subjected to the variation of the local de Broglie wavelength as a function of the internuclear distance R. Some unphysical levels ("ghosts") then appear in the vibrational series computed via a mapped Fourier grid representation. In the present work the choice of the basis set is reexamined, and two alternative expansions are discussed: Sine functions and Hardy functions. It is shown that use of a basis set with fixed nodes at both grid ends is efficient to eliminate "ghost" solutions. It is further shown that the Hamiltonian matrix in the sine basis can be calculated very accurately by using an auxiliary basis of cosine functions, overcoming the problems arising from numerical calculation of the Jacobian J(x) of the R→x coordinate transformation.

Dirac bubble potential for He-He and inadequacies in the continuum: Comparing an analytic model with elastic collision experiments

NASA Astrophysics Data System (ADS)

Chrysos, Michael

2017-01-01

We focus on the long-pending issue of the inadequacy of the Dirac bubble potential model in the description of He-He interactions in the continuum [L. L. Lohr and S. M. Blinder, Int. J. Quantum Chem. 53, 413 (1995)]. We attribute this failure to the lack of a potential wall to mimic the onset of the repulsive interaction at close range separations. This observation offers the explanation to why this excessively simple model proves incapable of quantitatively reproducing previous experimental findings of glory scattering in He-He, although being notorious for its capability of reproducing several distinctive features of the atomic and isotopic helium dimers and trimers [L. L. Lohr and S. M. Blinder, Int. J. Quantum Chem. 90, 419 (2002)]. Here, we show that an infinitely high, energy-dependent potential wall of properly calculated thickness rc(E) taken as a supplement to the Dirac bubble potential suffices for agreement with variable-energy elastic collision cross section experiments for 4He-4He, 3He-4He, and 3He-3He [R. Feltgen et al., J. Chem. Phys. 76, 2360 (1982)]. In the very low energy regime, consistency is found between the Dirac bubble potential (to which our extended model is shown to reduce) and cold collision experiments [J. C. Mester et al., Phys. Rev. Lett. 71, 1343 (1993)]; this consistency, which in this regime lends credence to the Dirac bubble potential, was never noticed by its authors. The revised model being still analytic is of high didactical value while expected to increase in predictive power relative to other appraisals.

Dust modeling over East Asia during the summer of 2010 using the WRF-Chem model

NASA Astrophysics Data System (ADS)

Zhang, B.; Huang, J.; Chen, S.

2017-12-01

An intense summer dust storm over East Asia during June 24-27, 2010, was systematically analyzed using the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) and a variety of in situ measurements and satellite retrievals. The results showed that the WRF-Chem model captured the spatial and temporal distributions of meteorological factors and dust aerosols over East Asia. This summer dust storm was initiated by the approach of a transverse trough in the northwestern Xinjiang. Because of the passage of the cutoff-low, a large amount of cold air was transported southward and further enhanced in the narrow valleys of the Altai and Tianshan Mountains, which resulted in higher wind speeds and huge dust emissions over the Taklimakan Desert (TD). Dust emission fluxes over the TD were as high as 54 μg m-2 s-1 on June 25th. The dust aerosols from the TD then swept across Inner Mongolia, Ningxia and Mongolia, and some were also transported eastward to Beijing, Tianjin, the Hebei region, and even South Korea and Japan. The simulations further showed that summer dust over East Asia exerts an important influence on the radiation budget in the Earth-atmosphere system. Dust heat the atmosphere at a maximum heating rate of 0.14 k day-1, effectively changing the vertical stability of the atmosphere and affecting climate change at regional and even global scales. The dust event-averaged direct radiative forcing induced by dust particles over the TD at all-sky was -6.0, -16.8 and 10.8 W m-2 at the top of the atmosphere, the surface, and in the atmosphere, respectively.

Prognosis and survival analysis of paraquat poisoned patients based on improved HPLC-UV method.

PubMed

Hong, Guangliang; Hu, Lufeng; Tang, Yahui; Zhang, Tao; Kang, Xiaowen; Zhao, Guangju; Lu, Zhongqiu

2016-01-01

Paraquat (PQ) has caused deaths of numerous people around the world. In order to assess the lethal plasma concentration, the patients who acquired acute PQ intoxication were analyzed by plasma concentration monitoring. The plasma PQ concentrations were determined by high performance liquid chromatography (HPLC) which used 5-bromopyrimidine as internal standard and trichloroacetic acid-methanol (1:9) as protein precipitant. The liver, kidney and coagulation function were determined by automatic biochemical analyzer. According to plasma PQ concentration, 90 patients were divided into four groups: trace PQ group (<50ng/mL), low PQ group (<1000ng/mL), medium PQ group (1000-5000ng/mL) and high PQ group (>5000ng/mL). The clinical data from the four groups was statistically analyzed. The results showed the developed HPLC methods exhibited a high degree of accuracy and good linearity within 50-25000ng/mL (R=0.9998). The Spearman's correlation analysis showed PQ concentration had a strong relationship to total bilirubin, direct bilirubin, aspartic transaminase, urea nitrogen, prothrombin time, prothrombin activity, and international normalized ratio (P<0.01). The cured or survival PQ poisoned patients among the trace PQ group, the low PQ group, the medium PQ group, and the high PQ group were 19/19 (100%), 19/21 (90.47%), 11/25 (44.0%), and 0/25 (0%) respectively. The mean hospital days were (10.37±8.04), (18.76±12.06), (16.76±14.44), and (4.04±5.41) days respectively. The Cox regression analysis indicated that plasma PQ concentration was highly related to prognosis (P<0.05). In conclusion, no patient presenting with a PQ concentration over 5000ng/mL survived. The plasma PQ level is related to liver, kidney and coagulation function, which can be used as an important clinical index to judge the prognosis of PQ poisoned patients. Paraquat (PubChem CID: 15938), 5-bromopyrimidine (PubChem CID: 78344), acetonitrile (PubChem CID: 6342), sodium dihydrogen phosphate (PubChem CID: 23672064), sodium heptanesulfonate (PubChem CID: 23672332), methylprednisolone (PubChem CID: 6741), cyclophosphamide (PubChem CID: 2907). Copyright © 2016. Published by Elsevier Inc.

Simulation of vibrational dephasing of I(2) in solid Kr using the semiclassical Liouville method.

PubMed

Riga, Jeanne M; Fredj, Erick; Martens, Craig C

2006-02-14

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

Impact of Asian Aerosols on Precipitation Over California: An Observational and Model Based Approach

NASA Technical Reports Server (NTRS)

Naeger, Aaron R.; Molthan, Andrew L.; Zavodsky, Bradley T.; Creamean, Jessie M.

2015-01-01

Dust and pollution emissions from Asia are often transported across the Pacific Ocean to over the western United States. Therefore, it is essential to fully understand the impact of these aerosols on clouds and precipitation forming over the eastern Pacific and western United States, especially during atmospheric river events that account for up to half of California's annual precipitation and can lead to widespread flooding. In order for numerical modeling simulations to accurately represent the present and future regional climate of the western United States, we must account for the aerosol-cloud-precipitation interactions associated with Asian dust and pollution aerosols. Therefore, we have constructed a detailed study utilizing multi-sensor satellite observations, NOAA-led field campaign measurements, and targeted numerical modeling studies where Asian aerosols interacted with cloud and precipitation processes over the western United States. In particular, we utilize aerosol optical depth retrievals from the NASA Moderate Resolution Imaging Spectroradiometer (MODIS), NOAA Geostationary Operational Environmental Satellite (GOES-11), and Japan Meteorological Agency (JMA) Multi-functional Transport Satellite (MTSAT) to effectively detect and monitor the trans-Pacific transport of Asian dust and pollution. The aerosol optical depth (AOD) retrievals are used in assimilating the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) in order to provide the model with an accurate representation of the aerosol spatial distribution across the Pacific. We conduct WRF-Chem model simulations of several cold-season atmospheric river events that interacted with Asian aerosols and brought significant precipitation over California during February-March 2011 when the NOAA CalWater field campaign was ongoing. The CalWater field campaign consisted of aircraft and surface measurements of aerosol and precipitation processes that help extensively validate our WRF-Chem model simulations. After validating the capability of the WRF-Chem in realistically simulating the aerosol-cloud precipitation interactions, we conduct sensitivity studies where the AOD is doubled to diagnose whether an increasing concentration of Asian aerosols over the western United States will lead to further impacts on the cloud and precipitation processes over California. We also perform sensitivity studies where the aerosols will be partitioned into dust-only and pollution-only in order to separate the impacts of the differing Asian aerosol species. The results of our WRF-Chem model simulations aim to show that the trans-Pacific transport of Asian aerosols influence the precipitation associated with atmospheric river events that can ultimately impact the regional climate of the western United States. 1 University

EarthChem: International Collaboration for Solid Earth Geochemistry in Geoinformatics

NASA Astrophysics Data System (ADS)

Walker, J. D.; Lehnert, K. A.; Hofmann, A. W.; Sarbas, B.; Carlson, R. W.

2005-12-01

The current on-line information systems for igneous rock geochemistry - PetDB, GEOROC, and NAVDAT - convincingly demonstrate the value of rigorous scientific data management of geochemical data for research and education. The next generation of hypothesis formulation and testing can be vastly facilitated by enhancing these electronic resources through integration of available datasets, expansion of data coverage in location, time, and tectonic setting, timely updates with new data, and through intuitive and efficient access and data analysis tools for the broader geosciences community. PetDB, GEOROC, and NAVDAT have therefore formed the EarthChem consortium (www.earthchem.org) as a international collaborative effort to address these needs and serve the larger earth science community by facilitating the compilation, communication, serving, and visualization of geochemical data, and their integration with other geological, geochronological, geophysical, and geodetic information to maximize their scientific application. We report on the status of and future plans for EarthChem activities. EarthChem's development plan includes: (1) expanding the functionality of the web portal to become a `one-stop shop for geochemical data' with search capability across databases, standardized and integrated data output, generally applicable tools for data quality assessment, and data analysis/visualization including plotting methods and an information-rich map interface; and (2) expanding data holdings by generating new datasets as identified and prioritized through community outreach, and facilitating data contributions from the community by offering web-based data submission capability and technical assistance for design, implementation, and population of new databases and their integration with all EarthChem data holdings. Such federated databases and datasets will retain their identity within the EarthChem system. We also plan on working with publishers to ease the assimilation of geochemical data into the EarthChem database. As a community resource, EarthChem will address user concerns and respond to broad scientific and educational needs. EarthChem will hold yearly workshops, town hall meetings, and/or exhibits at major meetings. The group has established a two-tier committee structure to help ease the communication and coordination of database and IT issues between existing data management projects, and to receive feedback and support from individuals and groups from the larger geosciences community.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

USGS Publications Warehouse

Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

2017-01-01

Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

Discrete Optimization in Chemical Space Reference Manual

DTIC Science & Technology

2012-10-01

ChemGroup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346 6.3 vanilla -rings.inp...Examples: carbazoles.inp, and vanilla -rings.inp. 4.8.2 Constructor & Destructor Documentation 4.8.2.1 ChemGroup::ChemGroup () 4.8.2.2 ChemGroup::ChemGroup...also: carbazoles.inp and vanilla -rings.inp in the examples section. Read the connector. Read the connector. 4.9.2.6 ChemIdent::ChemIdent (istream & in

The NH3Cl+ Cation

DTIC Science & Technology

2004-05-21

Chem. 1966, 5, 1791; (c) H. W. Roesky, O. Glemser, D. Bormann, Chem. Ber. 1966, 99, 1589; (d) A. V. Pankratov , N. I. Savenkova, Russ. J. Inorg. Chem...J. Am. Chem. Soc. 1991 , 113, 3795. [6] (a) J. K. Ruff, J. Am. Chem. Soc. 1965, 87, 1140; J. K. Ruff, Inorg. Chem. 1966, 5, 1791; (c) A. R. Young, D...unlimited 9 [12] (a) M. Brumm, G. Frenking, W. Koch, Chem. Phys. Lett. 1991 , 182, 310; (b) M. Brumm, G. Frenking, J. Breidung, W. Thiel, Chem. Phys

A theoretical study on hot charge-transfer states and dimensional effects of organic photocells based on an ideal diode model.

PubMed

Shimazaki, Tomomi; Nakajima, Takahito

2017-05-21

This paper discusses an ideal diode model with hot charge-transfer (CT) states to analyze the power conversion efficiency of an organic photocell. A free carrier generation mechanism via sunlight in an organic photocell consists of four microscopic processes: photon absorption, exciton dissociation, CT, and charge separation. The hot CT state effect has been actively investigated to understand the charge separation process. We previously reported a theoretical method to calculate the efficiency of the charge separation process via a hot CT state (T. Shimazaki et al., Phys. Chem. Chem. Phys., 2015, 17, 12538 and J. Chem. Phys., 2016, 144, 234906). In this paper, we integrate the simulation method into the ideal photocell diode model and calculate several properties such as short circuit current, open circuit voltage, and power conversion efficiency. Our results highlight that utilizing the dimensional (entropy) effect together with the hot CT state can play an essential role in developing more efficient organic photocell devices.

Potential Energy Surfaces and Dynamics for Energetic Ionic Liquids

DTIC Science & Technology

2012-04-09

advantage of such architectures12. Very recently, we have implemented the FMO method on the BG/ P system at Argonne National Laboratory, demonstrating that...Molecular Orbital Method”, J. Comp. Theoret. Chem., 6, 1 (2010). 4. T. Nagata, D . Fedorov, K. Kitaura, and M.S. Gordon, “A Combined Effective Fragment...Chem., 3, 177 (2007). 6. T. Nagata, D . Fedorov, K. Kitaura, and M.S. Gordon, “A Combined Effective Fragment Potential - Fragment Molecular Orbital

Martian fluvial conglomerates at Gale crater.

PubMed

Williams, R M E; Grotzinger, J P; Dietrich, W E; Gupta, S; Sumner, D Y; Wiens, R C; Mangold, N; Malin, M C; Edgett, K S; Maurice, S; Forni, O; Gasnault, O; Ollila, A; Newsom, H E; Dromart, G; Palucis, M C; Yingst, R A; Anderson, R B; Herkenhoff, K E; Le Mouélic, S; Goetz, W; Madsen, M B; Koefoed, A; Jensen, J K; Bridges, J C; Schwenzer, S P; Lewis, K W; Stack, K M; Rubin, D; Kah, L C; Bell, J F; Farmer, J D; Sullivan, R; Van Beek, T; Blaney, D L; Pariser, O; Deen, R G

2013-05-31

Observations by the Mars Science Laboratory Mast Camera (Mastcam) in Gale crater reveal isolated outcrops of cemented pebbles (2 to 40 millimeters in diameter) and sand grains with textures typical of fluvial sedimentary conglomerates. Rounded pebbles in the conglomerates indicate substantial fluvial abrasion. ChemCam emission spectra at one outcrop show a predominantly feldspathic composition, consistent with minimal aqueous alteration of sediments. Sediment was mobilized in ancient water flows that likely exceeded the threshold conditions (depth 0.03 to 0.9 meter, average velocity 0.20 to 0.75 meter per second) required to transport the pebbles. Climate conditions at the time sediment was transported must have differed substantially from the cold, hyper-arid modern environment to permit aqueous flows across several kilometers.

Martian fluvial conglomerates at Gale Crater

USGS Publications Warehouse

Williams, Rebecca M.E.; Grotzinger, J.P.; Dietrich, W.E.; Gupta, S.; Sumner, D.Y.; Wiens, R.C.; Mangold, N.; Malin, M.C.; Edgett, K.S.; Maurice, S.; Forni, O.; Gasnault, O.; Ollila, A.; Newsom, Horton E.; Dromart, G.; Palucis, M.C.; Yingst, R.A.; Anderson, Ryan B.; Herkenhoff, K. E.; Le Mouélic, S.; Goetz, W.; Madsen, M.B.; Koefoed, A.; Jensen, J.K.; Bridges, J.C.; Schwenzer, S.P.; Lewis, K.W.; Stack, K.M.; Rubin, D.; Kah, L.C.; Bell, J.F.; Farmer, J.D.; Sullivan, R.; Van Beek, T.; Blaney, D.L.; Pariser, O.; Deen, R.G.

2013-01-01

Observations by the Mars Science Laboratory Mast Camera (Mastcam) in Gale crater reveal isolated outcrops of cemented pebbles (2 to 40 millimeters in diameter) and sand grains with textures typical of fluvial sedimentary conglomerates. Rounded pebbles in the conglomerates indicate substantial fluvial abrasion. ChemCam emission spectra at one outcrop show a predominantly feldspathic composition, consistent with minimal aqueous alteration of sediments. Sediment was mobilized in ancient water flows that likely exceeded the threshold conditions (depth 0.03 to 0.9 meter, average velocity 0.20 to 0.75 meter per second) required to transport the pebbles. Climate conditions at the time sediment was transported must have differed substantially from the cold, hyper-arid modern environment to permit aqueous flows across several kilometers.

Regional modelling of polycyclic aromatic hydrocarbons: WRF-Chem-PAH model development and East Asia case studies

NASA Astrophysics Data System (ADS)

Mu, Qing; Lammel, Gerhard; Gencarelli, Christian N.; Hedgecock, Ian M.; Chen, Ying; Přibylová, Petra; Teich, Monique; Zhang, Yuxuan; Zheng, Guangjie; van Pinxteren, Dominik; Zhang, Qiang; Herrmann, Hartmut; Shiraiwa, Manabu; Spichtinger, Peter; Su, Hang; Pöschl, Ulrich; Cheng, Yafang

2017-10-01

Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants, with increasing emissions in pace with economic development in East Asia, but their distribution and fate in the atmosphere are not yet well understood. We extended the regional atmospheric chemistry model WRF-Chem (Weather Research Forecast model with Chemistry module) to comprehensively study the atmospheric distribution and the fate of low-concentration, slowly degrading semivolatile compounds. The WRF-Chem-PAH model reflects the state-of-the-art understanding of current PAHs studies with several new or updated features. It was applied for PAHs covering a wide range of volatility and hydrophobicity, i.e. phenanthrene, chrysene and benzo[a]pyrene, in East Asia. Temporally highly resolved PAH concentrations and particulate mass fractions were evaluated against observations. The WRF-Chem-PAH model is able to reasonably well simulate the concentration levels and particulate mass fractions of PAHs near the sources and at a remote outflow region of East Asia, in high spatial and temporal resolutions. Sensitivity study shows that the heterogeneous reaction with ozone and the homogeneous reaction with the nitrate radical significantly influence the fate and distributions of PAHs. The methods to implement new species and to correct the transport problems can be applied to other newly implemented species in WRF-Chem.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

DOE PAGES

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens; ...

2016-12-15

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

Biophenols: Enzymes (β-secretase, Cholinesterases, histone deacetylase and tyrosinase) inhibitors from olive (Olea europaea L.).

PubMed

Omar, Syed Haris; Scott, Christopher J; Hamlin, Adam S; Obied, Hassan K

2018-07-01

The focus of this study was on inhibition of enzymes involved in the pathogenesis Alzheimer's disease (AD) including prime amyloid beta (Aβ) producing enzyme (β-secretase: BACE-1) and disease progression enzymes including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), histone deacetylase (HDAC), and tyrosinase along with the catecholamine L-DOPA, by using olive biophenols. Here we report the strongest inhibition of BACE-1 from rutin (IC 50 : 3.8 nM) followed by verbascoside (IC 50 : 6.3 nM) and olive fruit extract (IC 50 : 18 ng), respectively. Olive biophenol, quercetin exhibited strongest enzyme inhibitory activity against tyrosinase (IC 50 : 10.73 μM), BChE (IC 50 : 19.08 μM), AChE (IC 50 : 55.44 μM), and HDAC (IC 50 : 105.1 μM) enzymes. Furthermore, olive biophenol verbascoside (IC 50 : 188.6 μM), and hydroxytyrosol extreme extract (IC 50 : 66.22 μg) were showed the highest levels of inhibition against the HDAC enzyme. Neuroprotective capacity against levodopa-induced toxicity in neuroblastoma (SH-SY5Y) cells of olive biophenols were assessed, where rutin indicated the highest neuroprotection (74%), followed by caffeic acid (73%), and extract hydroxytyrosol extreme (97%), respectively. To the best of our knowledge, this is the first in vitro report on the enzymes inhibitory activity of olive biophenols. Taken together, our in vitro results data suggest that olive biophenols could be a promising natural inhibitor, which may reduce the enzyme-induced toxicity associated with the oxidative stress involved in the progression of AD. Acetylthiocholine iodide (PubChem CID: 74629); S-Butyrylthiocholine chloride (PubChem CID: 3015121); Caffeic acid (PubChem CID: 689043); Dimethyl sulfoxide (DMSO) (PubChem: 679); L-3,4-Dihydroxyphenylalanine (L-DOPA) (PubChem CID: 6047); 5,5'-Dithiobis (2-nitrobenzoic acid) (DTNB) (PubChem CID: 6254); Epigallocatechin gallate (EGCG) (PubChem CID: 65064); Ethylenediamine tetraacetic acid (EDTA) (PubChem CID: 6049); Galantamine hydrobromide (PubChem CID: 121587); l-Glutamine (PubChem CID: 5961); Hydroxytyrosol (PubChem CID: 82755); Kojic acid (PubChem CID: 3840); Luteolin (PubChem CID: 5280445); Oleuropein (PubChem CID: 5281544); Penicillin-streptomycin (PubChem CID: 131715954); Quercetin (PubChem CID: 5280343); Rutin (PubChem CID: 5280805); Tris-HCl buffer (PubChem: 93573); Trypan blue (PubChem: 9562061). Copyright © 2018 Elsevier B.V. All rights reserved.

Atmospheric Ammonia Over China: Emission Estimates And Impact On Air Quality

NASA Astrophysics Data System (ADS)

Zhang, L.; Chen, Y.; Zhao, Y.; Henze, D. K.

2016-12-01

Ammonia (NH3) in the atmosphere is an important precursor of aerosols, and its deposition through wet and dry processes can cause adverse effects on ecosystems. The ammonia emissions over China are particularly large due to intensive agricultural activities, yet our current estimates of Chinese ammonia emissions and associated consequences on air quality are subject to large errors. We use the GEOS-Chem chemical transport model and its adjoint model to better quantify this issue. The TES satellite observations of ammonia concentrations and surface measurements of wet deposition fluxes are assimilated into the model to constrain the ammonia emissions over China. Optimized emissions show a strong seasonal variability with emissions in summer a factor of 3 higher than winter. This is consistent with an improved bottom-up estimate of Chinese ammonia emissions from fertilizer use by using more practical fertilizer application rates for different crop types. We further use the GEOS-Chem adjoint at 0.25x0.3125 degree resolution to examine the sources contributing to the PM2.5 air pollution over North China. We show that wintertime PM2.5 over Beijing is largely contributed by residential and industrial sources, and ammonia emissions from agriculture activities. PM2.5 concentrations over North China are particularly sensitive to emissions of ammonia and nitrogen oxides, reflecting strong formation of aerosol nitrate in the cold seasons.

An experimental/theoretical method to measure the capacitive compactness of an aqueous electrolyte surrounding a spherical charged colloid

NASA Astrophysics Data System (ADS)

Moraila-Martínez, Carmen Lucía; Guerrero-García, Guillermo Iván; Chávez-Páez, Martín; González-Tovar, Enrique

2018-04-01

The capacitive compactness has been introduced very recently [G. I. Guerrero-García et al., Phys. Chem. Chem. Phys. 20, 262-275 (2018)] as a robust and accurate measure to quantify the thickness, or spatial extension, of the electrical double layer next to either an infinite charged electrode or a spherical macroion. We propose here an experimental/theoretical scheme to determine the capacitive compactness of a spherical electrical double layer that relies on the calculation of the electrokinetic charge and the associated mean electrostatic potential at the macroparticle's surface. This is achieved by numerically solving the non-linear Poisson-Boltzmann equation of point ions around a colloidal sphere and matching the corresponding theoretical mobility, predicted by the O'Brien and White theory [J. Chem. Soc., Faraday Trans. 2 74, 1607-1626 (1978)], with experimental measurements of the electrophoretic mobility under the same conditions. This novel method is used to calculate the capacitive compactness of NaCl and CaCl2 electrolytes surrounding a negatively charged polystyrene particle as a function of the salt concentration.

Ring-polymer instanton theory of electron transfer in the nonadiabatic limit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, Jeremy O., E-mail: jeremy.richardson@fau.de

We take the golden-rule instanton method derived in the previous paper [J. O. Richardson, R. Bauer, and M. Thoss, J. Chem. Phys. 143, 134115 (2015)] and reformulate it using a ring-polymer instanton approach. This gives equations which can be used to compute the rates of electron-transfer reactions in the nonadiabatic (golden-rule) limit numerically within a semiclassical approximation. The multidimensional ring-polymer instanton trajectories are obtained efficiently by minimization of the action. In this form, comparison with Wolynes’ quantum instanton method [P. G. Wolynes, J. Chem. Phys. 87, 6559 (1987)] is possible and we show that our semiclassical approach is the steepest-descentmore » limit of this method. We discuss advantages and disadvantages of both methods and give examples of where the new approach is more accurate.« less

Comment on `A novel experimental method: Electrochemical detection of phase transition in ferroelectric single crystals', Chem. Phys. Lett. 384 (2004) 262 by K. Gatner and R. Jakubas

NASA Astrophysics Data System (ADS)

Ćwikiel, K.; Matlak, M.

2006-03-01

We comment the Letter 'A novel experimental method: electrochemical detection of phase transition in ferroelectric single crystals', Chem. Phys. Lett. 384 (2004) 262 by K. Gatner and R. Jakubas. We indicate that the method used in this Letter is not 'A novel method' but the application of the method described in Refs. [M. Matlak, M. Pietruszka, E. Rówiński, Phys. Rev. B 63 (2001) 52101; M. Matlak, M. Pietruszka, E. Rówiński, Phys. Stat. Sol. A 184 (2001) 335; W. Gaweł, E. Zaleska, Z. Sztuba, Met. Sci. Eng. A 324 (2002) 255], well known to Gatner, but not cited in the commented Letter. Additionally Gatner, cooperating with us, has used our TGS samples and published the results in the commented Letter without our knowledge and permission.

Effect of chemically and biologically synthesized Ag nanoparticles on the algae growth inhibition

NASA Astrophysics Data System (ADS)

Anna, Mražiková; Oksana, Velgosová; Jana, Kavuličová

2017-12-01

Over the past few years green methods for preparation of silver nanoparticles has become necessary due to its friendly influence on ecosystem. In the present work antimicrobial properties of biologically synthesized silver nanoparticles (Bio-AgNPs) using green algae extract and chemically synthesized silver nanoparticles (Chem-AgNPs) using sodium citrate against algae Parachlorella kessleri is investigated. Both used Bio-AgNPs and Chem-AgNPs exhibit long-term stability as demonstrated by UV-vis spectroscopy measurements. The results revealed stronger toxic effects of Bio-AgNPs on agar plates what was confirmed clear inhibition zone around wells impregnated with Bio-AgNPs. On the other hand Bio-AgNPs were confirmed to be less toxic in aquatic environments for the growths of green algae P. kessleri comparing to Chem-AgNPs.

Dust modeling over East Asia during the summer of 2010 using the WRF-Chem model

NASA Astrophysics Data System (ADS)

Chen, Siyu; Yuan, Tiangang; Zhang, Xiaorui; Zhang, Guolong; Feng, Taichen; Zhao, Dan; Zang, Zhou; Liao, Shujie; Ma, Xiaojun; Jiang, Nanxuan; Zhang, Jie; Yang, Fan; Lu, Hui

2018-07-01

An intense summer dust storm over East Asia during June 24-27, 2010, was systematically analyzed based on the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) and a variety of in situ measurements and satellite retrievals. The results showed that the WRF-Chem model captures the spatial and temporal distributions of meteorological factors and dust aerosol in summer over East Asia well. This summer dust storm is initiated by the approach of a transverse trough in the northwestern Xinjiang. Because of the passage of the cutoff-low, a large amount of cold air is transported southward and further enhanced by the narrow valleys of the Altai and Tianshan Mountains, which results in higher wind speeds and huge dust emissions over the Taklimakan Desert (TD). Dust emission fluxes over the TD areas are high as 54 μg m-2 s-1 on June 25. The dust aerosol from the TD then sweeps across Inner Mongolia, Ningxia and Mongolia, and some are also transported eastward to Beijing, Tianjin, Hebei, and even South Korea and Japan. The simulations further show that summer dust over East Asia exerts an important influence on the radiation budget in the Earth-atmosphere system. Dust heats the atmosphere at a maximum heating rate of 0.14 K day-1, effectively changing the vertical stability of the atmosphere and affecting climate change at regional and even global scales. The average direct radiative forcing induced by dust particles over the TD at all-sky is -6.0, -16.8 and 10.8 W m-2 at the top of the atmosphere, the surface, and in the atmosphere, respectively. The discussion about radiative forcing induced by summer dust provides confidence for future investigation of summer dust impact on cloud properties and precipitation efficiency in the eastern China.

Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition.

PubMed

Didziapetris, Remigijus; Dapkunas, Justas; Sazonovas, Andrius; Japertas, Pranas

2010-11-01

A new structure-activity relationship model predicting the probability for a compound to inhibit human cytochrome P450 3A4 has been developed using data for >800 compounds from various literature sources and tested on PubChem screening data. Novel GALAS (Global, Adjusted Locally According to Similarity) modeling methodology has been used, which is a combination of baseline global QSAR model and local similarity based corrections. GALAS modeling method allows forecasting the reliability of prediction thus defining the model applicability domain. For compounds within this domain the statistical results of the final model approach the data consistency between experimental data from literature and PubChem datasets with the overall accuracy of 89%. However, the original model is applicable only for less than a half of PubChem database. Since the similarity correction procedure of GALAS modeling method allows straightforward model training, the possibility to expand the applicability domain has been investigated. Experimental data from PubChem dataset served as an example of in-house high-throughput screening data. The model successfully adapted itself to both data classified using the same and different IC₅₀ threshold compared with the training set. In addition, adjustment of the CYP3A4 inhibition model to compounds with a novel chemical scaffold has been demonstrated. The reported GALAS model is proposed as a useful tool for virtual screening of compounds for possible drug-drug interactions even prior to the actual synthesis.

Oxygen surface exchange kinetics measurement by simultaneous optical transmission relaxation and impedance spectroscopy: Sr(Ti,Fe)O3-x thin film case study.

PubMed

Perry, Nicola H; Kim, Jae Jin; Tuller, Harry L

2018-01-01

We compare approaches to measure oxygen surface exchange kinetics, by simultaneous optical transmission relaxation (OTR) and AC-impedance spectroscopy (AC-IS), on the same mixed conducting SrTi 0.65 Fe 0.35 O 3-x film. Surface exchange coefficients were evaluated as a function of oxygen activity in the film, controlled by gas partial pressure and/or DC bias applied across the ionically conducting yttria-stabilized zirconia substrate. Changes in measured light transmission through the film over time (relaxations) resulted from optical absorption changes in the film corresponding to changes in its oxygen and oxidized Fe (~Fe 4+ ) concentrations; such relaxation profiles were successfully described by the equation for surface exchange-limited kinetics appropriate for the film geometry. The k chem values obtained by OTR were significantly lower than the AC-IS derived k chem values and k q values multiplied by the thermodynamic factor (bulk or thin film), suggesting a possible enhancement in k by the metal current collectors (Pt, Au). Long-term degradation in k chem and k q values obtained by AC-IS was also attributed to deterioration of the porous Pt current collector, while no significant degradation was observed in the optically derived k chem values. The results suggest that, while the current collector might influence measurements by AC-IS, the OTR method offers a continuous, in situ , and contact-free method to measure oxygen exchange kinetics at the native surfaces of thin films.

Bound state potential energy surface construction: ab initio zero-point energies and vibrationally averaged rotational constants.

PubMed

Bettens, Ryan P A

2003-01-15

Collins' method of interpolating a potential energy surface (PES) from quantum chemical calculations for reactive systems (Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816) has been applied to a bound state problem. The interpolation method has been combined for the first time with quantum diffusion Monte Carlo calculations to obtain an accurate ground state zero-point energy, the vibrationally average rotational constants, and the vibrationally averaged internal coordinates. In particular, the system studied was fluoromethane using a composite method approximating the QCISD(T)/6-311++G(2df,2p) level of theory. The approach adopted in this work (a) is fully automated, (b) is fully ab initio, (c) includes all nine nuclear degrees of freedom, (d) requires no assumption of the functional form of the PES, (e) possesses the full symmetry of the system, (f) does not involve fitting any parameters of any kind, and (g) is generally applicable to any system amenable to quantum chemical calculations and Collins' interpolation method. The calculated zero-point energy agrees to within 0.2% of its current best estimate. A0 and B0 are within 0.9 and 0.3%, respectively, of experiment.

The EnVision++ system: a new immunohistochemical method for diagnostics and research. Critical comparison with the APAAP, ChemMate, CSA, LABC, and SABC techniques.

PubMed Central

Sabattini, E; Bisgaard, K; Ascani, S; Poggi, S; Piccioli, M; Ceccarelli, C; Pieri, F; Fraternali-Orcioni, G; Pileri, S A

1998-01-01

AIM: To assess a newly developed immunohistochemical detection system, the EnVision++. METHODS: A large series of differently processed normal and pathological samples and 53 relevant monoclonal antibodies were chosen. A chessboard titration assay was used to compare the results provided by the EnVision++ system with those of the APAAP, CSA, LSAB, SABC, and ChemMate methods, when applied either manually or in a TechMate 500 immunostainer. RESULTS: With the vast majority of the antibodies, EnVision++ allowed two- to fivefold higher dilutions than the APAAP, LSAB, SABC, and ChemMate techniques, the staining intensity and percentage of expected positive cells being the same. With some critical antibodies (such as the anti-CD5), it turned out to be superior in that it achieved consistently reproducible results with differently fixed or overfixed samples. Only the CSA method, which includes tyramide based enhancement, allowed the same dilutions as the EnVision++ system, and in one instance (with the anti-cyclin D1 antibody) represented the gold standard. CONCLUSIONS: The EnVision++ is an easy to use system, which avoids the possibility of disturbing endogenous biotin and lowers the cost per test by increasing the dilutions of the primary antibodies. Being a two step procedure, it reduces both the assay time and the workload. Images PMID:9797726

Effects on Student Achievement in General Chemistry Following Participation in an Online Preparatory Course. ChemPrep, a Voluntary, Self-Paced, Online Introduction to Chemistry

NASA Astrophysics Data System (ADS)

Botch, Beatrice; Day, Roberta; Vining, William; Stewart, Barbara; Rath, Kenneth; Peterfreund, Alan; Hart, David

2007-03-01

ChemPrep was developed to be a stand-alone preparatory short-course to help students succeed in general chemistry. It is Web-based and delivered using the OWL system. Students reported that the ChemPrep materials (short information pages, parameterized questions with detailed feedback, tutorials, and answers to questions through the OWL message system) permitted them to work independently without the need for textbook or lecture. On average, students who completed ChemPrep had higher grades in the subsequent GenChem, Nursing, and Honors chemistry courses, with a greater percentage achieving a grade of C- or higher. Participation in ChemPrep was voluntary, and more women than men responded. Students in the Honors course enrolled in ChemPrep in higher percentages than students in GenChem and Nursing. SAT and departmental math placement exam scores were used as proxy measures of prior achievement and ability. Based on these, Honors chemistry ChemPrep users were on par with their peers but performed better in the course than non-users. In GenChem and Nursing chemistry courses, ChemPrep helped students of high prior achievement and ability perform better than their achievement scores would predict. Weaker or less motivated students did not respond to the voluntary offerings of ChemPrep in the same numbers as stronger or more motivated students, and we are seeking alternate ways to reach this population.

Getting the Most out of PubChem for Virtual Screening

PubMed Central

Kim, Sunghwan

2016-01-01

Introduction With the emergence of the “big data” era, the biomedical research community has great interest in exploiting publicly available chemical information for drug discovery. PubChem is an example of public databases that provide a large amount of chemical information free of charge. Areas covered This article provides an overview of how PubChem’s data, tools, and services can be used for virtual screening and reviews recent publications that discuss important aspects of exploiting PubChem for drug discovery. Expert opinion PubChem offers comprehensive chemical information useful for drug discovery. It also provides multiple programmatic access routes, which are essential to build automated virtual screening pipelines that exploit PubChem data. In addition, PubChemRDF allows users to download PubChem data and load them into a local computing facility, facilitating data integration between PubChem and other resources. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering polypharmacologic (multi-target) ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). These studies demonstrate the usefulness of PubChem as a key resource for computer-aided drug discovery and related area. PMID:27454129

Non-adiabatic molecular dynamics with complex quantum trajectories. I. The diabatic representation.

PubMed

Zamstein, Noa; Tannor, David J

2012-12-14

We extend a recently developed quantum trajectory method [Y. Goldfarb, I. Degani, and D. J. Tannor, J. Chem. Phys. 125, 231103 (2006)] to treat non-adiabatic transitions. Each trajectory evolves on a single surface according to Newton's laws with complex positions and momenta. The transfer of amplitude between surfaces stems naturally from the equations of motion, without the need for surface hopping. In this paper we derive the equations of motion and show results in the diabatic representation, which is rarely used in trajectory methods for calculating non-adiabatic dynamics. We apply our method to the first two benchmark models introduced by Tully [J. Chem. Phys. 93, 1061 (1990)]. Besides giving the probability branching ratios between the surfaces, the method also allows the reconstruction of the time-dependent wavepacket. Our results are in quantitative agreement with converged quantum mechanical calculations.

A New Direct Coupled Regional-scale Meteorology and Chemistry Model

NASA Astrophysics Data System (ADS)

Li, J.; Hsu, S.; Liu, T.; Chiang, C.; Chang, J.

2007-12-01

WRF/Chem was first developed in the US and generously made available to the international research community a short time ago. Starting from this, many groups have contributed new components and subroutines to this model. Based on WRF/Chem, a new online integrated model system named WRF/ChemT was established in Taiwan. It is significantly different from WRF/Chem in the following important aspects. For an online model, all chemical species emission must be direct coupled to WRF meteorology. All publicly available versions of WRF/Chem do not have this fundamental coupling. For these WRF/Chem models all emission data must first be preprocessed by SMOKE or other emission models driven by MM5 or WRF meteorologies in offline manner. WRF/ChemT has a self-consistent online emission process. We replaced the old emission driver with NCU driver, the plume rise of point sources and biogenic VOCs emission are calculated online. So that meteorology model, emission model and chemistry transport model are coupled directly in WRF/ChemT. Cloud impact on actinic flux should be consistent with WRF cloud-aerosol submodel used, not just moisture parameterization. Photolysis rates in WRF/ChemT are self consistent in every sub modules. New dry deposition routines were developed including addition of a vertical mixing scheme named the Asymmetrical Convective Model (ACM) which is used in CMAQ. The advantage of using ACM submodel had been demonstrated in earlier studies. Computational inefficiency has been a lingering problem for WRF/Chem. We have worked on this aspect of WRF/Chem development and by using a new chemical solver and also reorganizing the operator splitting computational algorithm we have made significant computational speed gain. WRF/chemT is about a factor of 4 faster in the chemistry solver and a factor of 2 faster in chemical species transport. When added together it is about a factor of 2 faster than WRF/Chem(version 2.1.2), i. e. gas-phase chemistry and meteorology are now equally fast. WRF/ChemT was evaluated and applied in regional air quality research in Taiwan. The comparison with WRF/Chem and selected current applications will be discussed in this report.

Analysis of photon count data from single-molecule fluorescence experiments

NASA Astrophysics Data System (ADS)

Burzykowski, T.; Szubiakowski, J.; Rydén, T.

2003-03-01

We consider single-molecule fluorescence experiments with data in the form of counts of photons registered over multiple time-intervals. Based on the observation schemes, linking back to works by Dehmelt [Bull. Am. Phys. Soc. 20 (1975) 60] and Cook and Kimble [Phys. Rev. Lett. 54 (1985) 1023], we propose an analytical approach to the data based on the theory of Markov-modulated Poisson processes (MMPP). In particular, we consider maximum-likelihood estimation. The method is illustrated using a real-life dataset. Additionally, the properties of the proposed method are investigated through simulations and compared to two other approaches developed by Yip et al. [J. Phys. Chem. A 102 (1998) 7564] and Molski [Chem. Phys. Lett. 324 (2000) 301].

Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

NASA Astrophysics Data System (ADS)

Kristyán, Sándor

1997-11-01

In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

Literature information in PubChem: associations between PubChem records and scientific articles.

PubMed

Kim, Sunghwan; Thiessen, Paul A; Cheng, Tiejun; Yu, Bo; Shoemaker, Benjamin A; Wang, Jiyao; Bolton, Evan E; Wang, Yanli; Bryant, Stephen H

2016-01-01

PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results. Graphical abstractLiterature information for PubChem records is derived from various sources.

Optimal control of open quantum systems: A combined surrogate Hamiltonian optimal control theory approach applied to photochemistry on surfaces

NASA Astrophysics Data System (ADS)

Asplund, Erik; Klüner, Thorsten

2012-03-01

In this paper, control of open quantum systems with emphasis on the control of surface photochemical reactions is presented. A quantum system in a condensed phase undergoes strong dissipative processes. From a theoretical viewpoint, it is important to model such processes in a rigorous way. In this work, the description of open quantum systems is realized within the surrogate Hamiltonian approach [R. Baer and R. Kosloff, J. Chem. Phys. 106, 8862 (1997)], 10.1063/1.473950. An efficient and accurate method to find control fields is optimal control theory (OCT) [W. Zhu, J. Botina, and H. Rabitz, J. Chem. Phys. 108, 1953 (1998), 10.1063/1.475576; Y. Ohtsuki, G. Turinici, and H. Rabitz, J. Chem. Phys. 120, 5509 (2004)], 10.1063/1.1650297. To gain control of open quantum systems, the surrogate Hamiltonian approach and OCT, with time-dependent targets, are combined. Three open quantum systems are investigated by the combined method, a harmonic oscillator immersed in an ohmic bath, CO adsorbed on a platinum surface, and NO adsorbed on a nickel oxide surface. Throughout this paper, atomic units, i.e., ℏ = me = e = a0 = 1, have been used unless otherwise stated.

Exploring the free energy surface using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-01

Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

Application of distance correction to ChemCam laser-induced breakdown spectroscopy measurements

DOE PAGES

Mezzacappa, A.; Melikechi, N.; Cousin, A.; ...

2016-04-04

Laser-induced breakdown spectroscopy (LIBS) provides chemical information from atomic, ionic, and molecular emissions from which geochemical composition can be deciphered. Analysis of LIBS spectra in cases where targets are observed at different distances, as is the case for the ChemCam instrument on the Mars rover Curiosity, which performs analyses at distances between 2 and 7.4 m is not a simple task. Previously, we showed that spectral distance correction based on a proxy spectroscopic standard created from first-shot dust observations on Mars targets ameliorates the distance bias in multivariate-based elemental-composition predictions of laboratory data. In this work, we correct an expandedmore » set of neutral and ionic spectral emissions for distance bias in the ChemCam data set. By using and testing different selection criteria to generate multiple proxy standards, we find a correction that minimizes the difference in spectral intensity measured at two different distances and increases spectral reproducibility. When the quantitative performance of distance correction is assessed, there is improvement for SiO 2, Al 2O 3, CaO, FeOT, Na 2O, K 2O, that is, for most of the major rock forming elements, and for the total major-element weight percent predicted. But, for MgO the method does not provide improvements while for TiO 2, it yields inconsistent results. Additionally, we observed that many emission lines do not behave consistently with distance, evidenced from laboratory analogue measurements and ChemCam data. This limits the effectiveness of the method.« less

Decadal application of WRF/Chem for regional air quality and climate modeling over the U.S. under the representative concentration pathways scenarios. Part 1: Model evaluation and impact of downscaling

NASA Astrophysics Data System (ADS)

Yahya, Khairunnisa; Wang, Kai; Campbell, Patrick; Chen, Ying; Glotfelty, Timothy; He, Jian; Pirhalla, Michael; Zhang, Yang

2017-03-01

An advanced online-coupled meteorology-chemistry model, i.e., the Weather Research and Forecasting Model with Chemistry (WRF/Chem), is applied for current (2001-2010) and future (2046-2055) decades under the representative concentration pathways (RCP) 4.5 and 8.5 scenarios to examine changes in future climate, air quality, and their interactions. In this Part I paper, a comprehensive model evaluation is carried out for current decade to assess the performance of WRF/Chem and WRF under both scenarios and the benefits of downscaling the North Carolina State University's (NCSU) version of the Community Earth System Model (CESM_NCSU) using WRF/Chem. The evaluation of WRF/Chem shows an overall good performance for most meteorological and chemical variables on a decadal scale. Temperature at 2-m is overpredicted by WRF (by ∼0.2-0.3 °C) but underpredicted by WRF/Chem (by ∼0.3-0.4 °C), due to higher radiation from WRF. Both WRF and WRF/Chem show large overpredictions for precipitation, indicating limitations in their microphysics or convective parameterizations. WRF/Chem with prognostic chemical concentrations, however, performs much better than WRF with prescribed chemical concentrations for radiation variables, illustrating the benefit of predicting gases and aerosols and representing their feedbacks into meteorology in WRF/Chem. WRF/Chem performs much better than CESM_NCSU for most surface meteorological variables and O3 hourly mixing ratios. In addition, WRF/Chem better captures observed temporal and spatial variations than CESM_NCSU. CESM_NCSU performance for radiation variables is comparable to or better than WRF/Chem performance because of the model tuning in CESM_NCSU that is routinely made in global models.

Comparison of wildfire smoke estimation methods and associations with cardiopulmonary-related hospital admissions.

PubMed

Gan, Ryan W; Ford, Bonne; Lassman, William; Pfister, Gabriele; Vaidyanathan, Ambarish; Fischer, Emily; Volckens, John; Pierce, Jeffrey R; Magzamen, Sheryl

2017-03-01

Climate forecasts predict an increase in frequency and intensity of wildfires. Associations between health outcomes and population exposure to smoke from Washington 2012 wildfires were compared using surface monitors, chemical-weather models, and a novel method blending three exposure information sources. The association between smoke particulate matter ≤2.5 μm in diameter (PM 2.5 ) and cardiopulmonary hospital admissions occurring in Washington from 1 July to 31 October 2012 was evaluated using a time-stratified case-crossover design. Hospital admissions aggregated by ZIP code were linked with population-weighted daily average concentrations of smoke PM 2.5 estimated using three distinct methods: a simulation with the Weather Research and Forecasting with Chemistry (WRF-Chem) model, a kriged interpolation of PM 2.5 measurements from surface monitors, and a geographically weighted ridge regression (GWR) that blended inputs from WRF-Chem, satellite observations of aerosol optical depth, and kriged PM 2.5 . A 10 μg/m 3 increase in GWR smoke PM 2.5 was associated with an 8% increased risk in asthma-related hospital admissions (odds ratio (OR): 1.076, 95% confidence interval (CI): 1.019-1.136); other smoke estimation methods yielded similar results. However, point estimates for chronic obstructive pulmonary disease (COPD) differed by smoke PM 2.5 exposure method: a 10 μg/m 3 increase using GWR was significantly associated with increased risk of COPD (OR: 1.084, 95%CI: 1.026-1.145) and not significant using WRF-Chem (OR: 0.986, 95%CI: 0.931-1.045). The magnitude (OR) and uncertainty (95%CI) of associations between smoke PM 2.5 and hospital admissions were dependent on estimation method used and outcome evaluated. Choice of smoke exposure estimation method used can impact the overall conclusion of the study.

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions.

PubMed

Ruvinsky, Anatoly M

2007-06-01

We present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein-ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein-ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock scoring function, by 2-25% with G-Score, by 7-41% with D-Score, by 0-8% with LigScore, by 1-6% with PLP, by 0-12% with LUDI, by 2-8% with F-Score, by 7-29% with ChemScore, by 0-9% with X-Score, by 2-19% with PMF, and by 1-7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering-RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering-RMSD for 11 scoring functions.

Continuous spectra of atomic hydrogen in a strong magnetic field

NASA Astrophysics Data System (ADS)

Zhao, L. B.; Zatsarinny, O.; Bartschat, K.

2016-09-01

We describe a theoretical method, developed in the coupled-channel formalism, to study photoionization of H atoms in a strong magnetic field of a size that is typical for magnetic white dwarfs. The coupled Schrödinger equations are solved numerically using the renormalized Numerov method proposed by Johnson [B. R. Johnson, J. Chem. Phys. 67, 4086 (1977), 10.1063/1.435384; B. R. Johnson, J. Chem. Phys. 69, 4678 (1978), 10.1063/1.436421]. The distinct advantage of this method is the fact that no overflow problems are encountered in the classically forbidden region, and hence the method exhibits excellent numerical stability. Photoionization cross sections are presented for magnetized H atoms in the ground and 2 p excited states. The calculated results are compared with those obtained by other theories. The present method is particularly useful for explaining the complex features of continuous spectra in a strong magnetic field and hence provides an efficient tool for modeling photoionization spectra observed in the atmosphere of magnetic white dwarfs.

The EnVision++ system: a new immunohistochemical method for diagnostics and research. Critical comparison with the APAAP, ChemMate, CSA, LABC, and SABC techniques.

PubMed

Sabattini, E; Bisgaard, K; Ascani, S; Poggi, S; Piccioli, M; Ceccarelli, C; Pieri, F; Fraternali-Orcioni, G; Pileri, S A

1998-07-01

To assess a newly developed immunohistochemical detection system, the EnVision++. A large series of differently processed normal and pathological samples and 53 relevant monoclonal antibodies were chosen. A chessboard titration assay was used to compare the results provided by the EnVision++ system with those of the APAAP, CSA, LSAB, SABC, and ChemMate methods, when applied either manually or in a TechMate 500 immunostainer. With the vast majority of the antibodies, EnVision++ allowed two- to fivefold higher dilutions than the APAAP, LSAB, SABC, and ChemMate techniques, the staining intensity and percentage of expected positive cells being the same. With some critical antibodies (such as the anti-CD5), it turned out to be superior in that it achieved consistently reproducible results with differently fixed or overfixed samples. Only the CSA method, which includes tyramide based enhancement, allowed the same dilutions as the EnVision++ system, and in one instance (with the anti-cyclin D1 antibody) represented the gold standard. The EnVision++ is an easy to use system, which avoids the possibility of disturbing endogenous biotin and lowers the cost per test by increasing the dilutions of the primary antibodies. Being a two step procedure, it reduces both the assay time and the workload.

Chemically grafted fibronectin for use in QCM-D cell studies

PubMed Central

Sobolewski, Peter; Tomczyk, Nancy; Composto, Russell J.; Eckmann, David M.

2014-01-01

Traditionally, fibronectin has been used as a physisorbed surface coating (physFN) in cell culture experiments due to its critical role in cell adhesion. However, because the resulting layer is thick, unstable, and of unpredictable uniformity, this method of fibronectin deposition is unsuitable for some types of research, including quartz crystal microbalance (QCM) experiments involving cells. Here, we present a new method for chemical immobilization of fibronectin onto silicon oxide surfaces, including QCM crystals pre-coated with silicon oxide. We characterize these chemically coated fibronectin surfaces (chemFN) as well as physFN ones using surface ellipsometry (SE), Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM), and contact angle measurements. A cell culture model demonstrates that cells on chemFN and physFN surfaces exhibit similar viability, structure, adhesion and metabolism. Finally, we perform QCM experiments using cells on both surfaces which demonstrate the superior suitability of chemFN coatings for QCM research, and provide real-time QCM-D data from cells subjected to an actin depolymerizing agent. Overall, our method of chemical immobilization of fibronectin yields great potential for furthering cellular experiments in which thin, stable and uniform coatings are desirable. As QCM research with cells has been rather limited in success thus far, we anticipate that this new technique will particularly benefit this experimental system by availing it to the much broader field of cell mechanics. PMID:24657645

High Energy Density Materials

DTIC Science & Technology

2004-03-23

Phys. Chem. 1995, 99, 187. [11] G. Schatte, H. Willner, Z. Naturforsch. 1991 , 46b, 483. [12] G. Rasul, G. K. S. Prakash, G. A. Olah, J. Am. Chem. Soc...170. [18] T. Curtius, Ber. Dtsch. Chem. Ges. 1890, 23, 3023. [19] A. V. Pankratov , N. I. Savenkova, Russ. J. Inorg. Chem. 1968, 13, 1345. [20] K. O...Christe, R. D. Wilson, W. W. Wilson, R. Bau, S. Sukumar, D. A. Dixon, J. Am. Chem. Soc. 1991 , 113, 3795. [21] K. O. Christe, D. A. Dixon, D. McLemore, W

Research and Development of Methods for Estimating Physicochemical Properties of Organic Compounds of Environmental Concern. Part 2.

DTIC Science & Technology

1981-06-01

they be used outside the temperature range of 10 to 40°C. See J. Gmehling et al., Ind. Eng. Chem. Process Des. Dev., 21:118 (1982) for new set of para ...Mumford, S.A. and J.W.C. Phillips, "The Evaluation and Interpretation of Para - chors," J. Chem. Soc., 1929, 2112-33. 20. Ogata, Y. and M. Tsuchida...naphthylamnines 1.03 a. For mixed systems, Kr for the OH group takes precedence. Thus, KF for P- aminophenol is 1.15. Source: Fishtine [4]. (4) Assume A&b

SO2 Emissions and Lifetimes: Estimates from Inverse Modeling Using In Situ and Global, Space-Based (SCIAMACHY and OMI) Observations

NASA Technical Reports Server (NTRS)

Lee, Chulkyu; Martin Randall V.; vanDonkelaar, Aaron; Lee, Hanlim; Dickerson, RUssell R.; Hains, Jennifer C.; Krotkov, Nickolay; Richter, Andreas; Vinnikov, Konstantine; Schwab, James J.

2011-01-01

Top-down constraints on global sulfur dioxide (SO2) emissions are inferred through inverse modeling using SO2 column observations from two satellite instruments (SCIAMACHY and OMI). We first evaluated the S02 column observations with surface SO2 measurements by applying local scaling factors from a global chemical transport model (GEOS-Chem) to SO2 columns retrieved from the satellite instruments. The resulting annual mean surface SO2 mixing ratios for 2006 exhibit a significant spatial correlation (r=0.86, slope=0.91 for SCIAMACHY and r=0.80, slope = 0.79 for OMI) with coincident in situ measurements from monitoring networks throughout the United States and Canada. We evaluate the GEOS-Chem simulation of the SO2 lifetime with that inferred from in situ measurements to verity the applicability of GEOS-Chem for inversion of SO2 columns to emissions. The seasonal mean SO2 lifetime calculated with the GEOS-Chem model over the eastern United States is 13 h in summer and 48 h in winter, compared to lifetimes inferred from in situ measurements of 19 +/- 7 h in summer and 58 +/- 20 h in winter. We apply SO2 columns from SCIAMACHY and OMI to derive a top-down anthropogenic SO2 emission inventory over land by using the local GEOS-Chem relationship between SO2 columns and emissions. There is little seasonal variation in the top-down emissions (<15%) over most major industrial regions providing some confidence in the method. Our global estimate for annual land surface anthropogenic SO2 emissions (52.4 Tg S/yr from SCIAMACHY and 49.9 Tg S / yr from OMI) closely agrees with the bottom-up emissions (54.6 Tg S/yr) in the GEOS-Chem model and exhibits consistency in global distributions with the bottom-up emissions (r = 0.78 for SCIAMACHY, and r = 0.77 for OMI). However, there are significant regional differences.

Chemistry Comes Alive! Vol. 3: Abstract of Special Issue 23 on CD-ROM

NASA Astrophysics Data System (ADS)

Jacobsen, Jerrold J.; Moore, John W.

1999-09-01

Literature Cited

1. Jacobsen, J. J.; Moore, J. W. Chemistry Comes Alive! Vol. 1 [CD-ROM]; J. Chem. Educ. Software 1998, SP 18.

2. Jacobsen, J. J.; Moore, J. W. Chemistry Comes Alive! Vol. 2 [CD-ROM]; J. Chem. Educ. Software 1998, SP 21.

3. Moore, J. W.; Jacobsen, J. J.; Hunsberger, L. R.; Gammon, S. D.; Jetzer, K. H.; Zimmerman, J. ChemDemos Videodisc; J. Chem. Educ. Software 1994, SP 8.

4. Moore, J. W.; Jacobsen, J. J.; Jetzer, K. H.; Gilbert, G.; Mattes, F.; Phillips, D.; Lisensky, G.; Zweerink, G. ChemDemos II; J. Chem. Educ. Software 1996, SP 14.

5. Jacobsen, J. J.; Jetzer, K. H.; Patani, N.; Zimmerman, J. Titration Techniques Videodisc; J. Chem. Educ. Software 1995, SP9.

PubChemSR: A search and retrieval tool for PubChem

PubMed Central

Hur, Junguk; Wild, David J

2008-01-01

Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

A Java API for working with PubChem datasets.

PubMed

Southern, Mark R; Griffin, Patrick R

2011-03-01

PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose-response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. http://code.google.com/p/pubchemdb.

Consequences of ChemR23 Heteromerization with the Chemokine Receptors CXCR4 and CCR7

PubMed Central

de Poorter, Cédric; Baertsoen, Kevin; Lannoy, Vincent; Parmentier, Marc; Springael, Jean-Yves

2013-01-01

Recent studies have shown that heteromerization of the chemokine receptors CCR2, CCR5 and CXCR4 is associated to negative binding cooperativity. In the present study, we build on these previous results, and investigate the consequences of chemokine receptor heteromerization with ChemR23, the receptor of chemerin, a leukocyte chemoattractant protein structurally unrelated to chemokines. We show, using BRET and HTRF assays, that ChemR23 forms homomers, and provide data suggesting that ChemR23 also forms heteromers with the chemokine receptors CCR7 and CXCR4. As previously described for other chemokine receptor heteromers, negative binding cooperativity was detected between ChemR23 and chemokine receptors, i.e. the ligands of one receptor competed for the binding of a specific tracer of the other. We also showed, using mouse bone marrow-derived dendritic cells prepared from wild-type and ChemR23 knockout mice, that ChemR23-specific ligands cross-inhibited CXCL12 binding on CXCR4 in a ChemR23-dependent manner, supporting the relevance of the ChemR23/CXCR4 interaction in native leukocytes. Finally, and in contrast to the situation encountered for other previously characterized CXCR4 heteromers, we showed that the CXCR4-specific antagonist AMD3100 did not cross-inhibit chemerin binding in cells co-expressing ChemR23 and CXCR4, demonstrating that cross-regulation by AMD3100 depends on the nature of receptor partners with which CXCR4 is co-expressed. PMID:23469143

Consequences of ChemR23 heteromerization with the chemokine receptors CXCR4 and CCR7.

PubMed

de Poorter, Cédric; Baertsoen, Kevin; Lannoy, Vincent; Parmentier, Marc; Springael, Jean-Yves

2013-01-01

Recent studies have shown that heteromerization of the chemokine receptors CCR2, CCR5 and CXCR4 is associated to negative binding cooperativity. In the present study, we build on these previous results, and investigate the consequences of chemokine receptor heteromerization with ChemR23, the receptor of chemerin, a leukocyte chemoattractant protein structurally unrelated to chemokines. We show, using BRET and HTRF assays, that ChemR23 forms homomers, and provide data suggesting that ChemR23 also forms heteromers with the chemokine receptors CCR7 and CXCR4. As previously described for other chemokine receptor heteromers, negative binding cooperativity was detected between ChemR23 and chemokine receptors, i.e. the ligands of one receptor competed for the binding of a specific tracer of the other. We also showed, using mouse bone marrow-derived dendritic cells prepared from wild-type and ChemR23 knockout mice, that ChemR23-specific ligands cross-inhibited CXCL12 binding on CXCR4 in a ChemR23-dependent manner, supporting the relevance of the ChemR23/CXCR4 interaction in native leukocytes. Finally, and in contrast to the situation encountered for other previously characterized CXCR4 heteromers, we showed that the CXCR4-specific antagonist AMD3100 did not cross-inhibit chemerin binding in cells co-expressing ChemR23 and CXCR4, demonstrating that cross-regulation by AMD3100 depends on the nature of receptor partners with which CXCR4 is co-expressed.

Engaging Organic Chemistry Students Using ChemDraw for iPad

ERIC Educational Resources Information Center

Morsch, Layne A.; Lewis, Michael

2015-01-01

Drawing structures, mechanisms, and syntheses is a vital part of success in organic chemistry courses. ChemDraw for iPad has been used to increase classroom experiences in the preparation of high quality chemical drawings. The embedded Flick-to-Share allows for simple, real-time exchange of ChemDraw documents. ChemDraw for iPad also allows…

Heats of Vaporization of Room Temperature Ionic Liquids by Tunable Vacuum Ultraviolet Photoionization

DTIC Science & Technology

2009-12-07

18) Emel’yanenko, V. N.; Verevkin, S. P.; Heintz, A.; Corfield, J.-A.; deyko, A.; Lovelock , K. R. J.; Licence, P.; Jones, R. G. J. Phys. Chem. B 2008...112, 11734. (19) Armstrong, J. P.; Hurst, C.; Jones, R. G.; Licence, P.; Lovelock , K. R. J.; Satterly, C. J.; Villar-Garcia, I. J. Phys. Chem. Chem...Phys. 2007, 9, 982. (20) Lovelock , K. R. J.; Deyko, A.; Corfield, J.-A.; Gooden, P. N.; Licence, P.; Jones, R. G. ChemPhysChem 2009, 10, 337. (21

PubChem applications in drug discovery: a bibliometric analysis

PubMed Central

Cheng, Tiejun; Pan, Yongmei; Hao, Ming; Wang, Yanli; Bryant, Stephen H.

2014-01-01

A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services has been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound–target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing. PMID:25168772

The PubChem chemical structure sketcher

PubMed Central

2009-01-01

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

Bridging single and multireference coupled cluster theories with universal state selective formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran-Nair, Kiran; Kowalski, Karol

2013-05-28

The universal state selective (USS) multireference approach is used to construct new energy functionals which offers a unique possibility of bridging single and multireference coupled cluster theories (SR/MRCC). These functionals, which can be used to develop iterative and non-iterative approaches, utilize a special form of the trial wavefunctions, which assure additive separability (or size-consistency) of the USS energies in the non-interacting subsystem limit. When the USS formalism is combined with approximate SRCC theories, the resulting formalism can be viewed as a size-consistent version of the method of moments of coupled cluster equations (MMCC) employing a MRCC trial wavefunction. Special casesmore » of the USS formulations, which utilize single reference state specific CC (V.V. Ivanov, D.I. Lyakh, L. Adamowicz, Phys. Chem. Chem. Phys. 11, 2355 (2009)) and tailored CC (T. Kinoshita, O. Hino, R.J. Bartlett, J. Chem. Phys. 123, 074106 (2005)) expansions are also discussed.« less

A noniterative asymmetric triple excitation correction for the density-fitted coupled-cluster singles and doubles method: Preliminary applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozkaya, Uğur, E-mail: ugrbzky@gmail.com

2016-04-14

An efficient implementation of the asymmetric triples correction for the coupled-cluster singles and doubles [ΛCCSD(T)] method [S. A. Kucharski and R. J. Bartlett, J. Chem. Phys. 108, 5243 (1998); T. D. Crawford and J. F. Stanton, Int. J. Quantum Chem. 70, 601 (1998)] with the density-fitting [DF-ΛCCSD(T)] approach is presented. The computational time for the DF-ΛCCSD(T) method is compared with that of ΛCCSD(T). Our results demonstrate that the DF-ΛCCSD(T) method provide substantially lower computational costs than ΛCCSD(T). Further application results show that the ΛCCSD(T) and DF-ΛCCSD(T) methods are very beneficial for the study of single bond breaking problems as wellmore » as noncovalent interactions and transition states. We conclude that ΛCCSD(T) and DF-ΛCCSD(T) are very promising for the study of challenging chemical systems, where the coupled-cluster singles and doubles with perturbative triples method fails.« less

A Java API for working with PubChem datasets

PubMed Central

Southern, Mark R.; Griffin, Patrick R.

2011-01-01

Summary: PubChem is a public repository of chemical structures and associated biological activities. The PubChem BioAssay database contains assay descriptions, conditions and readouts and biological screening results that have been submitted by the biomedical research community. The PubChem web site and Power User Gateway (PUG) web service allow users to interact with the data and raw files are available via FTP. These resources are helpful to many but there can also be great benefit by using a software API to manipulate the data. Here, we describe a Java API with entity objects mapped to the PubChem Schema and with wrapper functions for calling the NCBI eUtilities and PubChem PUG web services. PubChem BioAssays and associated chemical compounds can then be queried and manipulated in a local relational database. Features include chemical structure searching and generation and display of curve fits from stored dose–response experiments, something that is not yet available within PubChem itself. The aim is to provide researchers with a fast, consistent, queryable local resource from which to manipulate PubChem BioAssays in a database agnostic manner. It is not intended as an end user tool but to provide a platform for further automation and tools development. Availability: http://code.google.com/p/pubchemdb Contact: southern@scripps.edu PMID:21216779

Preface to Special Issue of ChemSusChem on Perovskite Optoelectronics.

PubMed

Bolink, Henk J; Mhaisalkar, Subodh G

2017-10-09

This Editorial introduces one of two companion Special Issues on "Halide Perovskites for Optoelectronics Applications" in ChemSusChem and Energy Technology following the ICMAT 2017 Conference in Singapore. More information on the other Special Issue can be found in the Editorial published in Energy Technology. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Demilitarization Assembled Chemical Weapons Alternatives (Chem Demil-ACWA)

DTIC Science & Technology

2015-12-01

Weapons Alternatives (Chem Demil-ACWA) is performing a portion of the chemical warfare materiel elimination mission. In 1996, Congress and the...Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-243 Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil-ACWA) As...Date Assigned: December 19, 2010 Program Information Program Name Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil

75 FR 51440 - Solid Urea from the Russian Federation: Final Results of Antidumping Duty Administrative Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-20

... produced and exported by MCC EuroChem (EuroChem). The period of review (POR) is July 1, 2008, through June... for EuroChem. Therefore, the final results are different from the preliminary results. The final weighted-average dumping margin for EuroChem is listed below in the section entitled ``Final Results of the...

Chemerin serum levels in girls with anorexia nervosa.

PubMed

Oświecimska, Joanna M; Ziora, Katarzyna T; Suwała, Andrzej; Swietochowska, Elzbieta; Gorczyca, Piotr; Ziora-Jakutowicz, Karolina; Machura, Edyta; Szczepańska, Maria; Ostrowska, Zofia; Ziora, Dariusz; Szalecki, Mieczysław; Stojewska, Małgorzata; Matusik, Paweł; Małecka-Tendera, Ewa

2014-01-01

The regulatory function of chemerin (CHEM) in the process of adipogenesis and the metabolism of adipocytes has been confirmed. Data from several studies have shown higher serum CHEM in obesity. To date, there are no available studies on serum CHEM concentrations in patients with anorexia nervosa (AN), which is recognized as a good biological model of the chronic atrophy of adipose tissue and energy metabolism disorders in humans. The aim of the study was to assess serum CHEM concentrations in girls with AN in comparison to healthy and obese subjects and determine its relationship with body mass, BMI and insulin. CHEM serum concentrations were evaluated using commercially available ELISA kit in 65 Polish girls with restrictive AN, in 39 healthy controls (H) and 64 girls with simple obesity (OB). The mean serum CHEM concentration in the AN group was significantly lower than in the H and OB groups. After adjusting for BMI, CHEM concentrations in the AN group were significantly lower than in the H group, but statistically higher than in the OB group. Significant correlations between serum CHEM and body mass (r=0.77), BMI (r=0.82), Cole index (r=0.81) and serum insulin (r=0.78) were observed.

Electronic Structure of Ethynyl Substituted Cyclobutadienes

NASA Astrophysics Data System (ADS)

Emmert, Frank Lee Emmert, III; Thompson, Stephanie J.; Slipchenko, Lyudmila V.

2011-06-01

We investigated the effects of ethynyl substitution on the electronic structure of cyclobutadiene. These species are involved in Bergman Cyclization reactionsand are possible intermediates in the formation of fullerenes and graphite sheets. Prediction of the electronic energy of cyclobutadiene is challenging for single-reference ab initio methods such as HF, MP2 or DFT because of Jahn-Teller distortions and the diradical character of the singlet state. We determined the vertical and adiabatic singlet-triplet energy splittings, the natural charges and spin densities in substituted cyclobutadienes, using the equations of motion spin flip coupled cluster with single and double excitations (EOM-SF-CCSD) method that accurately describes diradical states. The adiabatic singlet-triplet gaps decrease upon substituent addition, but the singlet state is always lower in energy. However, we found that the results are affected by spin-contamination of the reference state and deteriorate when an unrestricted HF reference is employed. O. L. Chapman, C. L. McIntosh, J. Pacansky, "Cyclobutadiene" J. Am. Chem. Soc. 1973, 95, (2), 614-617. N. S. Goroff, "Mechanism of Fullerene Formation." Acc. Chem. Res. 1996, 29, (2), 77-83. L.V. Slipchenko and A.I. Krylov, "Singlet-triplet gaps in diradicals by the Spin-Flip approach: A benchmark study", J. Chem. Phys. 2002, 117, 4694-4708.

radEq Add-On Module for CFD Solver Loci-CHEM

NASA Technical Reports Server (NTRS)

McCloud, Peter

2013-01-01

Loci-CHEM to be applied to flow velocities where surface radiation due to heating from compression and friction becomes significant. The module adds a radiation equilibrium boundary condition to the computational fluid dynamics (CFD) code to produce accurate results. The module expanded the upper limit for accurate CFD solutions of Loci-CHEM from Mach 4 to Mach 10 based on Space Shuttle Orbiter Re-Entry trajectories. Loci-CHEM already has a very promising architecture and performance, but absence of radiation equilibrium boundary condition limited the application of Loci-CHEM to below Mach 4. The immediate advantage of the add-on module is that it allows Loci-CHEM to work with supersonic flows up to Mach 10. This transformed Loci-CHEM from a rocket engine- heritage CFD code with general subsonic and low-supersonic applications, to an aeroheating code with hypersonic applications. The follow-on advantage of the module is that it is a building block for additional add-on modules that will solve for the heating generated at Mach numbers higher than 10.

A Novel Method to Estimate Surface NO_{2} Concentrations from the Space-borne Ozone Monitoring Instrument

NASA Astrophysics Data System (ADS)

Li, Yanshun; Zhang, Qiang; Geng, Guannan; Zheng, Yixuan; Guo, Jianping

2017-04-01

Atmospheric NO2near the surface has notable health effects and is precursor of tropospheric ozone. In this work, we propose a novel method to estimate daily surface NO2 concentrations from the Ozone Monitoring Instrument (OMI) with improved accuracy. Two chemical transport models GEOS-Chem and WRF/CMAQ are used to simulate converting factors between OMI column densities and surface concentrations. GEOS-Chem is found to better capture the distribution of converting factors, while CMAQ has advantage in simulating the magnitude. We combine the two models to calculate optimal values of converting factors and further constrain them by using colocated boundary layer heights (BLH) derived from fine-resolution sounding observations made at OMI overpass time. Calculated converting factors over Chinese Mainland vary by more than three orders of magnitude (10-18 ˜10-15 μgṡcm-1ṡmolecule-1), indicating complexity of NO2 vertical structure over large spatial extent. We generate a map of surface NO2 mass concentrations during June 2013 from OMI retrievals at 0.1˚ ×0.1˚ grids. Estimated concentrations from our novel method show reasonable spatial agreement with in situ chemiluminescent measurements (R = 0.70, Slope = 0.58, N = 353), which significantly outperform estimations using only GEOS-Chem (R = 0.60, Slope = 0.20, N = 353) or WRF/CMAQ (R = 0.19, Slope = 0.52, N = 353) to simulate the converting factor. Preliminary results show that the novel method developed in this study could improve capability of satellite sensors to quantify surface NO2 pollution.

Charactering biomass burning aerosol in the Weather Research and Forecasting model with Chemistry (WRF-Chem), with evaluation against SAMBBA flight data.

NASA Astrophysics Data System (ADS)

Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W.; Freitas, S. R.; Longo, K.; Coe, H.; McFiggans, G.

2014-12-01

The burning of forests in the Amazonia region is a globally significant source of carbonaceous aerosol, containing both absorbing and scattering components. Biomass burning aerosol (BBA) are efficient CCN, modifying cloud properties and influencing atmospheric circulation and precipitation tendencies. The impacts of BBA are highly dependent on their size distribution and composition. Studies in this region can therefore benefit greatly from the use of state-of-the-art sectional aerosol representations. A bottom-up fire emissions inventory, 3BEM, has been developed by Longo et al.1. It uses satellite products to identify fire locations, applying the emissions factors of Andrei and Merlot3 to generate daily emission maps. Flaming emissions are very buoyant, and a method for injecting emissions at altitude is needed to accurately describe the vertical profile of BBA. A parameterisation has been developed to simulate this sub-grid process4, and previously implemented in WRF-Chem using a modal aerosol scheme5. For this work we have modified the WRF-Chem model to simulate 3BEM emissions using the MOSAIC sectional aerosol scheme6. This modified version of WRF-Chem v3.4.1 has been run for September 2012 over South America (25km grid-spacing). We will present model results evaluating the modelled aerosol vertical distribution, size distribution, composition and optical properties against measurements taken by the FAAM BAe-146 research aircraft during the SAMBBA field campaign. The plume-rise parameterisation was found to inject flaming emissions too high over most fires, resulting in high modelled aerosol loadings at high altitude. We probed the behaviour of the parameterisation by developing a new SAMBBA-tuned 3BEM emissions scenario, which uses more realistic estimates of fire size. Results from high-resolution (5 and 1km) nested simulations will also be presented, in order to evaluate the impacts of explicit aerosol-cloud interactions in non-parameterised clouds. 1. K. Longo et al., 2010, Atmos. Chem. Phys., 10, 5785-5795. 2. M. O. Andreae and P. Merlot, 2001, Global Biogeochem. Cy., 15(4), 955-966. 3. S. Freitas et al., 2007, Atmos. Chem. Phys., 7, 3385-3398. 4. G. Grell et al., 2011, Atmos. Chem. Phys., 11, 5289-5303. 5. R. Zavari et al., 2008, J. Geophys. Res., 113, D132024.

Spectroscopic accuracy directly from quantum chemistry: application to ground and excited states of beryllium dimer.

PubMed

Sharma, Sandeep; Yanai, Takeshi; Booth, George H; Umrigar, C J; Chan, Garnet Kin-Lic

2014-03-14

We combine explicit correlation via the canonical transcorrelation approach with the density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods to compute a near-exact beryllium dimer curve, without the use of composite methods. In particular, our direct density matrix renormalization group calculations produce a well-depth of D(e) = 931.2 cm(-1) which agrees very well with recent experimentally derived estimates D(e) = 929.7±2 cm(-1) [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D(e) = 934.6 cm(-1) [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D(e) = 938±15 cm(-1) [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D(e) = 935.1±10 cm(-1) [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)]. Our results suggest possible inaccuracies in the functional form of the potential used at shorter bond lengths to fit the experimental data [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)]. With the density matrix renormalization group we also compute near-exact vertical excitation energies at the equilibrium geometry. These provide non-trivial benchmarks for quantum chemical methods for excited states, and illustrate the surprisingly large error that remains for 1 ¹Σ(g)⁻ state with approximate multi-reference configuration interaction and equation-of-motion coupled cluster methods. Overall, we demonstrate that explicitly correlated density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods allow us to fully converge to the basis set and correlation limit of the non-relativistic Schrödinger equation in small molecules.

A rare case of haboob in Tehran: Observational and numerical study

NASA Astrophysics Data System (ADS)

Karami, S.; Ranjbar, A.; Mohebalhojeh, A. R.; Moradi, M.

2017-03-01

A great dust storm occurred in Tehran on 2 June 2014 and caused severe damage to properties and involved loss of human life. From the visual evidence available, it can be regarded as a case of haboob. As a lower latitude phenomenon, its occurrence in Tehran was unprecedented in the last 50 years. This paper aims to present a detailed analysis of the weather conditions, the pathways by which dust particles were ingested by the haboob, as well as the impact of the urban boundary layer on the intensity and propagation of the dust storm. Using numerical simulation carried out by the WRF-Chem model and various observational techniques, the coupling of a low-level small-scale deformation field with a lower-tropospheric cold pool produced by precipitating mid-tropospheric clouds is identified as the main process involved in shaping this rare dust storm.

Application of Symmetry-Broken H2-H2 Potential Energy Surface to Low Energy o-/p-H2+HD Collisions of Astrophysical Interest

NASA Astrophysics Data System (ADS)

Sultanov, R. A.; Guster, D.; Adhukari, S. K.

2011-05-01

A possibility of correct description of non-symmetrical HD+H2 collision at low temperatures (T≤300 K) is considered by applying symmetrical H2-H2 potential energy surface (PES) [Diep, P. & Johnson, K. 2000, J. Chem. Phys. 113, 3480 (DJ PES)]. With the use of a special mathematical transformation technique, which was applied to this surface, and a quantum dynamical method we obtained a quite satisfactory agreement with previous results when another H2-H2 PES was used [Boothroyd, A.I. et al. 2002, J. Chem. Phys. 116, 666 (BMKP PES)].

Halogenation effects on electron collisions with CF3Cl, CF2Cl2, and CFCl3

NASA Astrophysics Data System (ADS)

Freitas, T. C.; Lopes, A. R.; Azeredo, A. D.; Bettega, M. H. F.

2016-04-01

We report differential and integral elastic cross sections for low-energy electron collisions with CF3Cl, CF2Cl2, and CFCl3 molecules for energies ranging from 0.1 eV to 30 eV. The calculations were performed using the Schwinger multichannel method with pseudopotentials in the static-exchange and static-exchange plus polarization approximations. The influence of the permanent electric dipole moment on the cross sections was included using the Born closure scheme. A very good agreement between our calculations and the experimental results of Jones [J. Chem. Phys. 84, 813 (1986)], Mann and Linder [J. Phys. B 25, 1621 (1992); 25, 1633 (1992)] and Hoshino et al. [J. Chem. Phys. 138, 214305 (2013)] was found. We also compare our results with the calculations of Beyer et al. [Chem. Phys. 255, 1 (2000)] using the R-matrix method, where we find good agreement with respect to the location of the resonances, and with the calculations of Hoshino et al. using the independent atom method with screening corrected additivity rule, where we find qualitative agreement at energies above 20 eV. Additional electronic structure calculations were carried out in order to help in the interpretation of the scattering results. The stabilization the lowest σ∗ resonance due to the exchange of fluorine by chlorine atoms (halogenation effect) follows a simple linear relation with the energy of the lowest unoccupied molecular orbitals and can be considered as a signature of the halogenation effect.

Orbital-Optimized MP3 and MP2.5 with Density-Fitting and Cholesky Decomposition Approximations.

PubMed

Bozkaya, Uğur

2016-03-08

Efficient implementations of the orbital-optimized MP3 and MP2.5 methods with the density-fitting (DF-OMP3 and DF-OMP2.5) and Cholesky decomposition (CD-OMP3 and CD-OMP2.5) approaches are presented. The DF/CD-OMP3 and DF/CD-OMP2.5 methods are applied to a set of alkanes to compare the computational cost with the conventional orbital-optimized MP3 (OMP3) [Bozkaya J. Chem. Phys. 2011, 135, 224103] and the orbital-optimized MP2.5 (OMP2.5) [Bozkaya and Sherrill J. Chem. Phys. 2014, 141, 204105]. Our results demonstrate that the DF-OMP3 and DF-OMP2.5 methods provide considerably lower computational costs than OMP3 and OMP2.5. Further application results show that the orbital-optimized methods are very helpful for the study of open-shell noncovalent interactions, aromatic bond dissociation energies, and hydrogen transfer reactions. We conclude that the DF-OMP3 and DF-OMP2.5 methods are very promising for molecular systems with challenging electronic structures.

Decadal evaluation of regional climate, air quality, and their interactions using WRF/Chem Version 3.6.1

NASA Astrophysics Data System (ADS)

Yahya, K.; Wang, K.; Campbell, P.; Glotfelty, T.; He, J.; Zhang, Y.

2015-08-01

The Weather Research and Forecasting model with Chemistry (WRF/Chem) v3.6.1 with the Carbon Bond 2005 (CB05) gas-phase mechanism is evaluated for its first decadal application during 2001-2010 using the Representative Concentration Pathway (RCP 8.5) emissions to assess its capability and appropriateness for long-term climatological simulations. The initial and boundary conditions are downscaled from the modified Community Earth System Model/Community Atmosphere Model (CESM/CAM5) v1.2.2. The meteorological initial and boundary conditions are bias-corrected using the National Center for Environmental Protection's Final (FNL) Operational Global Analysis data. Climatological evaluations are carried out for meteorological, chemical, and aerosol-cloud-radiation variables against data from surface networks and satellite retrievals. The model performs very well for the 2 m temperature (T2) for the 10 year period with only a small cold bias of -0.3 °C. Biases in other meteorological variables including relative humidity at 2 m, wind speed at 10 m, and precipitation tend to be site- and season-specific; however, with the exception of T2, consistent annual biases exist for most of the years from 2001 to 2010. Ozone mixing ratios are slightly overpredicted at both urban and rural locations but underpredicted at rural locations. PM2.5 concentrations are slightly overpredicted at rural sites, but slightly underpredicted at urban/suburban sites. In general, the model performs relatively well for chemical and meteorological variables, and not as well for aerosol-cloud-radiation variables. Cloud-aerosol variables including aerosol optical depth, cloud water path, cloud optical thickness, and cloud droplet number concentration are generally underpredicted on average across the continental US. Overpredictions of several cloud variables over eastern US result in underpredictions of radiation variables and overpredictions of shortwave and longwave cloud forcing which are important climate variables. While the current performance is deemed to be acceptable, improvements to the bias-correction method for CESM downscaling and the model parameterizations of cloud dynamics and thermodynamics, as well as aerosol-cloud interactions can potentially improve model performance for long-term climate simulations.

Unsteady Heat Transfer Behavior of Reinforced Concrete Wall of Cold Storage

NASA Astrophysics Data System (ADS)

Nomura, Tomohiro; Murakami, Yuji; Uchikawa, Motoyuki

The authors had already clarified that the heat transfer behaviors between internal and external insulated reinforced concrete wall of cold storage are different each others when inside and outside temperature of wall is flactuating. From that conclusion, we must consider the application method of wall insulation of cold storages in actual design. The theme of the paper is to get the analyzing method and unsteady heat transfer characteristics of concrete walls of cold storage during daily variation of outside temperature of walls, and to give the basis for efficient design and cost optimization of insulate wall of cold storage. The difference of unsteady heat transfer characteristics between internal and external insulate wall, when outside temperature of the wall follewed daily varation, was clarified in experiment and in situ measurement of practical cold storage. The analyzing method with two dimentional unsteady FEM was introduced. Using this method, it is possible to obtain the time variation of heat flux, which is important basic factor for practical design of cold storage, through the wall.

Top-down estimate of dust emissions through integration of MODIS and MISR aerosol retrievals with the GEOS-Chem adjoint model

NASA Astrophysics Data System (ADS)

Wang, Jun; Xu, Xiaoguang; Henze, Daven K.; Zeng, Jing; Ji, Qiang; Tsay, Si-Chee; Huang, Jianping

2012-04-01

Predicting the influences of dust on atmospheric composition, climate, and human health requires accurate knowledge of dust emissions, but large uncertainties persist in quantifying mineral sources. This study presents a new method for combined use of satellite-measured radiances and inverse modeling to spatially constrain the amount and location of dust emissions. The technique is illustrated with a case study in May 2008; the dust emissions in Taklimakan and Gobi deserts are spatially optimized using the GEOS-Chem chemical transport model and its adjoint constrained by aerosol optical depth (AOD) that are derived over the downwind dark-surface region in China from MODIS (Moderate Resolution Imaging Spectroradiometer) reflectance with the aerosol single scattering properties consistent with GEOS-chem. The adjoint inverse modeling yields an overall 51% decrease in prior dust emissions estimated by GEOS-Chem over the Taklimakan-Gobi area, with more significant reductions south of the Gobi Desert. The model simulation with optimized dust emissions shows much better agreement with independent observations from MISR (Multi-angle Imaging SpectroRadiometer) AOD and MODIS Deep Blue AOD over the dust source region and surface PM10 concentrations. The technique of this study can be applied to global multi-sensor remote sensing data for constraining dust emissions at various temporal and spatial scales, and hence improving the quantification of dust effects on climate, air quality, and human health.

PubChem BioAssay: 2017 update

PubMed Central

Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

2017-01-01

PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

Exploiting PubChem for Virtual Screening

PubMed Central

Xie, Xiang-Qun

2011-01-01

Importance of the field PubChem is a public molecular information repository, a scientific showcase of the NIH Roadmap Initiative. The PubChem database holds over 27 million records of unique chemical structures of compounds (CID) derived from nearly 70 million substance depositions (SID), and contains more than 449,000 bioassay records with over thousands of in vitro biochemical and cell-based screening bioassays established, with targeting more than 7000 proteins and genes linking to over 1.8 million of substances. Areas covered in this review This review builds on recent PubChem-related computational chemistry research reported by other authors while providing readers with an overview of the PubChem database, focusing on its increasing role in cheminformatics, virtual screening and toxicity prediction modeling. What the reader will gain These publicly available datasets in PubChem provide great opportunities for scientists to perform cheminformatics and virtual screening research for computer-aided drug design. However, the high volume and complexity of the datasets, in particular the bioassay-associated false positives/negatives and highly imbalanced datasets in PubChem, also creates major challenges. Several approaches regarding the modeling of PubChem datasets and development of virtual screening models for bioactivity and toxicity predictions are also reviewed. Take home message Novel data-mining cheminformatics tools and virtual screening algorithms are being developed and used to retrieve, annotate and analyze the large-scale and highly complex PubChem biological screening data for drug design. PMID:21691435

77 FR 2669 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-19

... methods and would inspect additional areas, and corrective actions if necessary. This proposed AD would... and 11.45, by any of the following methods: Federal eRulemaking Portal: Go to http://www.regulations...-mill cracking in the shear wrinkle areas Inspecting for vertical chem-mill cracking at specified...

Understanding Protein-Protein Interactions: Essential Players in (Patho)physiology (Part 1).

PubMed

Wilson, Andrew J; Gunning, Patrick T

2016-04-15

This is the first of a two-part Editorial by the Guest Editors of the ChemBioChem and ChemMedChem joint Special Issue on Protein-Protein Interactions. Part 2 can be accessed via http://dx.doi.org/10.1002/cmdc.201600158; the complete issue can be viewed here: bit.ly/cbcVIppi. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

LANL Researcher Roger Wiens Discusses ChemCam

ScienceCinema

Wiens, Roger

2018-01-16

Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Red Planet on August 5, 2012.

Understanding High Wintertime Ozone Events over an Oil and Natural Gas Production Region from Air Quality Model Perspective

NASA Astrophysics Data System (ADS)

Ahmadov, R.; McKeen, S. A.; Trainer, M.; Banta, R. M.; Brown, S. S.; Edwards, P. M.; Frost, G. J.; Gilman, J.; Helmig, D.; Johnson, B.; Karion, A.; Koss, A.; Lerner, B. M.; Oltmans, S. J.; Roberts, J. M.; Schnell, R. C.; Veres, P. R.; Warneke, C.; Williams, E. J.; Wild, R. J.; Yuan, B.; Zamora, R. J.; Petron, G.; De Gouw, J. A.; Peischl, J.

2014-12-01

The huge increase in production of oil and natural gas has been associated with high wintertime ozone events over some parts of the western US. The Uinta Basin, UT, where oil and natural gas production is abundant experienced high ozone concentrations in winters of recent years, when cold stagnant weather conditions were prevalent. It has been very challenging for conventional air quality models to accurately simulate such wintertime ozone pollution cases. Here, a regional air quality model study was successfully conducted for the Uinta Basin by using the WRF-Chem model. For this purpose a new emission dataset for the region's oil/gas sector was built based on atmospheric in-situ measurements made during 2012 and 2013 field campaigns in the Uinta Basin. The WRF-Chem model demonstrates that the major factors driving high ozone in the Uinta Basin in winter are shallow boundary layers with light winds, high emissions of volatile organic compounds (VOC) compared to nitrogen oxides emissions from the oil and natural gas industry, enhancement of photolysis rates and reduction of O3 dry deposition due to snow cover. We present multiple sensitivity simulations to quantify the contribution of various factors driving high ozone over the Uinta Basin. The emission perturbation simulations show that the photochemical conditions in the Basin during winter of 2013 were VOC sensitive, which suggests that targeting VOC emissions would be most beneficial for regulatory purposes. Shortcomings of the emissions within the most recent US EPA (NEI-2011, version 1) inventory are also discussed.

Checking out ChemCam View

NASA Image and Video Library

2012-08-17

This mosaic shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover, as seen by the ChemCam remote micro-imager. The 10 images incorporated in this mosaic were taken on Aug. 15.

Chem-Braze Abradable Seal Attachment to Aircraft Gas Turbine Compressor Components.

DTIC Science & Technology

1982-01-01

seals to compressor blade tip-shrouds using the im- proved Chem-Braze system compared to attachment with gold-nickel braze. The Chem-Braze system has been...used successfully to bond abradable seals to titanium ’ cobalt, nickel and iron base alloys; however, attempts to use Chem-Braze to bond seals to...attaching FELTMETALO seals to steel, titanium , and nickel-based alloys, and ICB bonding procedures were investigated for attaching seals to selected

Synthesis and Characterization of Silyldichloramines, Their Reactions with F- Ions, Stability of N2CI2 and NCI2(-), and Formation of NCI3 (Postprint)

DTIC Science & Technology

2007-01-01

S. Can. J. Chem. 1987, 65, 88. (23) Werner, H. J.; Knowles, P. J.; Amos, R. D.; Bernhardsson, A.; Berning, A.; Celani, P.; Cooper, D. L.; Deegan , M. J...Phys. Chem. 1988, 92, 3033. (25) Knowles, P. J.; Hampel, C.; Werner, H. J. J. Chem. Phys. 1994, 99, 5219. (26) Deegan , M. J. O.; Knowles, P. J. Chem

Searching Online Chemical Data Repositories via the ChemAgora Portal.

PubMed

Zanzi, Antonella; Wittwehr, Clemens

2017-12-26

ChemAgora, a web application designed and developed in the context of the "Data Infrastructure for Chemical Safety Assessment" (diXa) project, provides search capabilities to chemical data from resources available online, enabling users to cross-reference their search results with both regulatory chemical information and public chemical databases. ChemAgora, through an on-the-fly search, informs whether a chemical is known or not in each of the external data sources and provides clikable links leading to the third-party web site pages containing the information. The original purpose of the ChemAgora application was to correlate studies stored in the diXa data warehouse with available chemical data. Since the end of the diXa project, ChemAgora has evolved into an independent portal, currently accessible directly through the ChemAgora home page, with improved search capabilities of online data sources.

Overview Of 100 Sols Of Chemcam Operations At Gale Crater

NASA Astrophysics Data System (ADS)

Maurice, Sylvestre; Wiens, Roger; MSL Science Team

2013-04-01

The Curiosity rover carries the ChemCam instrument suite, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument that can analyze the chemical composition of geological samples at distances up to 7 meters from the rover, and a high resolution camera for context imaging (RMI). In the first 100 sols after landing, ChemCam performed 343 single point measurements on approximately 50 different rocks or soil areas, for over 12,000 laser shots. Each time at least two RMI images are acquired before and after the laser shots to visualize the area of investigation and the geological context. LIBS lines are identified using primarily a martian dedicated database; to date, ChemCam has detected unambiguously major elements (Si, Al, Fe, Mg, Ca, Na, K, O), minor/trace elements of interest (Li, Cr, Mn, Rb, Sr, Ba, Ti, S, C, H). These observations allow a qualitative/quantitative assessment of the presence of dust (first few shots), the sample surface composition and chemical heterogeneity with depth. Several techniques have been developed to analyze ChemCam's data: (1) Univariate analysis refers to peak height studies of well-chosen LIBS lines and a training dataset to build calibration curves. Peak ratios K/Si, Na/Si, Al/Si, Fe+Mg/Si, or Mg/Mg+Fe have been calculated from the onboard calibration targets. The technique also applies to minor and trace elements which yield low intensity emission lines, such as Lin, Rb, H, C. (2) Multivariate methods give better results in terms of elemental composition, since they examine simultaneously and statistically several peaks of the same elements. A Partial Least Squares (PLS) regression algorithm is used for rapid major-element abundance determination. (3) Composition trends, clusters and end-members can also be identified using component analysis methods. Independent Component Analysis (ICA) identifies components that are directly related to Chemical elements: Al, Ca, Fe, H, K, Mg, Na, O, Si, Ti, but also mixture like a "soil" component. On top of this classification, clustering methods such as k-means and hierarchical clustering allow the differentiation and filation of different geochemical populations encountered so far at Mars. The ChemCam instruments are performing very well. The 100-sol dataset is rich of thousands of spectra and hundreds of images. We will present a status of the data set acquired during that period, a review of the analysis techniques and an introduction to the results which have been obtained so far.

Comparison of wildfire smoke estimation methods and associations with cardiopulmonary-related hospital admissions

PubMed Central

Gan, Ryan W.; Ford, Bonne; Lassman, William; Pfister, Gabriele; Vaidyanathan, Ambarish; Fischer, Emily; Volckens, John; Pierce, Jeffrey R.; Magzamen, Sheryl

2017-01-01

Climate forecasts predict an increase in frequency and intensity of wildfires. Associations between health outcomes and population exposure to smoke from Washington 2012 wildfires were compared using surface monitors, chemical-weather models, and a novel method blending three exposure information sources. The association between smoke particulate matter ≤2.5 μm in diameter (PM2.5) and cardiopulmonary hospital admissions occurring in Washington from 1 July to 31 October 2012 was evaluated using a time-stratified case-crossover design. Hospital admissions aggregated by ZIP code were linked with population-weighted daily average concentrations of smoke PM2.5 estimated using three distinct methods: a simulation with the Weather Research and Forecasting with Chemistry (WRF-Chem) model, a kriged interpolation of PM2.5 measurements from surface monitors, and a geographically weighted ridge regression (GWR) that blended inputs from WRF-Chem, satellite observations of aerosol optical depth, and kriged PM2.5. A 10 μg/m3 increase in GWR smoke PM2.5 was associated with an 8% increased risk in asthma-related hospital admissions (odds ratio (OR): 1.076, 95% confidence interval (CI): 1.019–1.136); other smoke estimation methods yielded similar results. However, point estimates for chronic obstructive pulmonary disease (COPD) differed by smoke PM2.5 exposure method: a 10 μg/m3 increase using GWR was significantly associated with increased risk of COPD (OR: 1.084, 95%CI: 1.026–1.145) and not significant using WRF-Chem (OR: 0.986, 95%CI: 0.931–1.045). The magnitude (OR) and uncertainty (95%CI) of associations between smoke PM2.5 and hospital admissions were dependent on estimation method used and outcome evaluated. Choice of smoke exposure estimation method used can impact the overall conclusion of the study. PMID:28868515

Exploring Natural Products from the Biodiversity of Pakistan for Computational Drug Discovery Studies: Collection, Optimization, Design and Development of A Chemical Database (ChemDP).

PubMed

Mirza, Shaher Bano; Bokhari, Habib; Fatmi, Muhammad Qaiser

2015-01-01

Pakistan possesses a rich and vast source of natural products (NPs). Some of these secondary metabolites have been identified as potent therapeutic agents. However, the medicinal usage of most of these compounds has not yet been fully explored. The discoveries for new scaffolds of NPs as inhibitors of certain enzymes or receptors using advanced computational drug discovery approaches are also limited due to the unavailability of accurate 3D structures of NPs. An organized database incorporating all relevant information, therefore, can facilitate to explore the medicinal importance of the metabolites from Pakistani Biodiversity. The Chemical Database of Pakistan (ChemDP; release 01) is a fully-referenced, evolving, web-based, virtual database which has been designed and developed to introduce natural products (NPs) and their derivatives from the biodiversity of Pakistan to Global scientific communities. The prime aim is to provide quality structures of compounds with relevant information for computer-aided drug discovery studies. For this purpose, over 1000 NPs have been identified from more than 400 published articles, for which 2D and 3D molecular structures have been generated with a special focus on their stereochemistry, where applicable. The PM7 semiempirical quantum chemistry method has been used to energy optimize the 3D structure of NPs. The 2D and 3D structures can be downloaded as .sdf, .mol, .sybyl, .mol2, and .pdb files - readable formats by many chemoinformatics/bioinformatics software packages. Each entry in ChemDP contains over 100 data fields representing various molecular, biological, physico-chemical and pharmacological properties, which have been properly documented in the database for end users. These pieces of information have been either manually extracted from the literatures or computationally calculated using various computational tools. Cross referencing to a major data repository i.e. ChemSpider has been made available for overlapping compounds. An android application of ChemDP is available at its website. The ChemDP is freely accessible at www.chemdp.com.

Development of the EarthChem Geochronology and Thermochronology database: Collaboration of the EarthChem and EARTHTIME efforts

NASA Astrophysics Data System (ADS)

Walker, J. D.; Ash, J. M.; Bowring, J.; Bowring, S. A.; Deino, A. L.; Kislitsyn, R.; Koppers, A. A.

2009-12-01

One of the most onerous tasks in rigorous development of data reporting and databases for geochronological and thermochronological studies is to fully capture all of the metadata needed to completely document both the analytical work as well as the interpretation effort. This information is available in the data reduction programs used by researchers, but has proven difficult to harvest into either publications or databases. For this reason, the EarthChem and EARTHTIME efforts are collaborating to foster the next generation of data management and discovery for age information by integrating data reporting with data reduction. EarthChem is a community-driven effort to facilitate the discovery, access, and preservation of geochemical data of all types and to support research and enable new and better science. EARTHTIME is also a community-initiated project whose aim is to foster the next generation of high-precision geochronology and thermochoronology. In addition, collaboration with the CRONUS effort for cosmogenic radionuclides is in progress. EarthChem workers have met with groups working on the Ar-Ar, U-Pb, and (U-Th)/He systems to establish data reporting requirements as well as XML schemas to be used for transferring data from reduction programs to database. At present, we have prototype systems working for the U-Pb_Redux, ArArCalc, MassSpec, and Helios programs. In each program, the user can select to upload data and metadata to the GEOCHRON system hosted at EarthChem. There are two additional requirements for upload. The first is having a unique identifier (IGSN) obtained either manually or via web services contained within the reduction program from the SESAR system. The second is that the user selects whether the sample is to be available for discovery (public) or remain hidden (private). Search for data at the GEOCHRON portal can be done using age, method, mineral, or location parameters. Data can be downloaded in the full XML format for ingestion back into the reduction program or as abbreviated tables.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

PubMed Central

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-01-01

Objective To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. Conclusions The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil. PMID:25182282

Adiabatic Variational Theory for Cold Atom-Molecule Collisions: Application to a Metastable Helium Atom Colliding with ortho- and para-Hydrogen Molecules.

PubMed

Pawlak, Mariusz; Shagam, Yuval; Klein, Ayelet; Narevicius, Edvardas; Moiseyev, Nimrod

2017-03-16

We recently developed an adiabatic theory for cold molecular collision experiments. In our previous application of this theory ( Pawlak, M.; et al. J. Chem. Phys. 2015 , 143 , 074114 ), we assumed that during the experiment the collision of an atom with a diatom takes place when the diatom is in the ground rotational state and is located in a plane. In this paper, we present how the variational approach of the adiabatic theory for low-temperature collision experiments can be used for the study a 5D collision between the atom and the diatomic molecule with no limitations on its rotational quantum states and no plane restrictions. Moreover, we show here the dramatic differences in the measured reaction rates of He(2 3 S 1 ) + ortho/para-H 2 → He(1s 2 ) + ortho/para-H 2 + + e - resulting from the anisotropic long-range interactions in the reaction. In collisions of metastable helium with molecular hydrogen in the ground rotational state, the isotropic potential term dominates the dynamics. When the collision is with molecular hydrogen in the first excited rotational state, the nonisotropic interactions play an important role in the dynamics. The agreement of our results with the latest experimental findings ( Klein , A. ; et al. Nat. Phys. 2017 , 13 , 35 - 38 ) is very good.

LANL Researcher Roger Wiens Discusses ChemCam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiens, Roger

2012-02-15

Discussion of the ChemCam instrument on the Curiosity Rover that occurred during the NASA press conference prior to launch of the Mars Science Laboratory. The ChemCam instrument was developed by Los Alamos National Laboratory and the French Space Institute. Los Alamos National Laboratory researcher Roger Wiens discusses the instrument on this video. ChemCam uses a laser to "zap" features of the Martian landscape and then uses a spectrometer to gather information about the composition of the sample. ChemCam will help the Curiosity Rover determine whether Mars is or was habitable. The Rover is expected to touch down on the Redmore » Planet on August 5, 2012.« less

Handheld Chem/Biosensor Using Extreme Conformational Changes in Designed Binding Proteins to Enhance Surface Plasmon Resonance (SPR)

DTIC Science & Technology

2016-04-01

AFCEC-CX-TY-TR-2016-0007 HANDHELD CHEM/ BIOSENSOR USING EXTREME CONFORMATIONAL CHANGES IN DESIGNED BINDING PROTEINS TO ENHANCE SURFACE PLASMON...Include area code) 03/24/2016 Abstract 08/14/2015--03/31/2016 Handheld chem/ biosensor using extreme conformational changes in designed binding...Baltimore, Maryland on 17-21 April 2016. We propose the development of a highly sensitive handheld chem/ biosensor device using a novel class of engineered

Molecular and functional roles of 6C CC chemokine 19 in defense system of striped murrel Channa striatus.

PubMed

Arockiaraj, Jesu; Bhatt, Prasanth; Harikrishnan, Ramasamy; Arasu, Mariadhas Valan; Al-Dhabi, Naif Abdullah

2015-08-01

In this study, we have reported the molecular information of chemokine-19 (Chem19) from striped murrel Channa striatus (Cs). CsCC-Chem19 cDNA sequence was 555 base pair (bp) in length which is 68bp 5' untranslated region (UTR), 339bp translated region and 149bp 3' UTR. The translated region is encoded for a polypeptide of 112 amino acids. CsCC-Chem19 peptide contains a signal sequence between 1 and 26 and an interleukin (IL) 8 like domain between 24 and 89. The multiple sequence alignment showed a 'DCCL' motif, an indispensable motif present in all CC chemokines which was conserved throughout the evolution. Phylogenetic tree showed that CsCC-Chem19 formed a cluster with chemokine 19 from fishes. Secondary structure of CsCC-Chem19 revealed that the peptide contains maximum amount of coils (61.6%) compared to α-helices (25.9%%) and β-sheet (12.5%). Further, 3D analysis indicated that the cysteine residues at 33, 34, 59 and 75 making the disulfide bridges as 33 = 59 and 34 = 75. Significantly (P < 0.05) highest CsCC-Chem19 mRNA expression was observed in blood and it was up-regulated upon fungus and bacterial infection. Utilizing the coding region of CsCC-Chem19, recombinant CsCC-Chem19 protein was produced. The recombinant CsCC-Chem19 protein induced the cellular proliferation and respiratory burst activity of C. striatus peripheral blood leukocytes (PBL) in a concentration dependent manner. Moreover, the chemotactic activity showed that the recombinant CsCC-Chem19 significantly (P < 0.05) enhanced the movement of PBL of C. striatus. Conclusively, CsCC-Chem19 is a 6C CC chemokine having an ability to perform both inflammatory and homeostatic functions. However, further research is necessary to understand the potential of 6C CC chemokine 19 of C. striatus, particularly their regulatory ability on different cellular components in the defense system. Copyright © 2015 Elsevier Ltd. All rights reserved.

Studies on the mechanism of action of 6-mercaptopurine. Interaction with copper and xanthine oxidase.

PubMed

Kela, U; Vijayvargiya, R

1981-03-01

Interaction between 6-mercaptopurine, Cu2+ and the enzyme xanthine oxidase (EC 1.2.3.2.) was examined. Whereas Cu2+ was found to inhibit the enzyme, 6-mercaptopurine could protect as well as reverse the enzyme inhibition produced by the metal ion. The formation of a complex between 6-mercaptopurine and Cu2+ seems to be responsible for the observed effect. Job's [(1928) Ann. Chem. 9, 113] method has shown the composition of the complex to be 1:1. The apparent stability constant (log K value), as determined by Subhrama Rao & Raghav Rao's [(1955) J. Sci. Chem. Ind. Res. 143, 278], method is found to be 6.74. It is suggested that the formation of a stable complex between 6-mercaptopurine molecules and Cu2+ may be an additional mechanism of action of 6-mercaptopurine, particularly with reference to its anti-inflammatory properties.

Wavepacket propagation using time-sliced semiclassical initial value methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, Brett B.; Reimers, Jeffrey R.; School of Chemistry, University of Sydney, Sydney NSW 2006

2004-12-22

A new semiclassical initial value representation (SC-IVR) propagator and a SC-IVR propagator originally introduced by Kay [J. Chem. Phys. 100, 4432 (1994)], are investigated for use in the split-operator method for solving the time-dependent Schroedinger equation. It is shown that the SC-IVR propagators can be derived from a procedure involving modified Filinov filtering of the Van Vleck expression for the semiclassical propagator. The two SC-IVR propagators have been selected for investigation because they avoid the need to perform a coherent state basis set expansion that is necessary in other time-slicing propagation schemes. An efficient scheme for solving the propagators ismore » introduced and can be considered to be a semiclassical form of the effective propagators of Makri [Chem. Phys. Lett. 159, 489 (1989)]. Results from applications to a one-dimensional, two-dimensional, and three-dimensional Hamiltonian for a double-well potential are presented.« less

Studies on the mechanism of action of 6-mercaptopurine. Interaction with copper and xanthine oxidase.

PubMed Central

Kela, U; Vijayvargiya, R

1981-01-01

Interaction between 6-mercaptopurine, Cu2+ and the enzyme xanthine oxidase (EC 1.2.3.2.) was examined. Whereas Cu2+ was found to inhibit the enzyme, 6-mercaptopurine could protect as well as reverse the enzyme inhibition produced by the metal ion. The formation of a complex between 6-mercaptopurine and Cu2+ seems to be responsible for the observed effect. Job's [(1928) Ann. Chem. 9, 113] method has shown the composition of the complex to be 1:1. The apparent stability constant (log K value), as determined by Subhrama Rao & Raghav Rao's [(1955) J. Sci. Chem. Ind. Res. 143, 278], method is found to be 6.74. It is suggested that the formation of a stable complex between 6-mercaptopurine molecules and Cu2+ may be an additional mechanism of action of 6-mercaptopurine, particularly with reference to its anti-inflammatory properties. PMID:6895465

A Comparison of Two Methods of Teaching Molecular Architecture to High School Chemistry Students.

ERIC Educational Resources Information Center

Halsted, Douglas Alan

This investigation explored the question of how high school chemistry students best learn three-dimensional molecular, ionic, and metallic structures in CHEM Study (Freeman, 1963). The experimenter compared the achievement, attitude, and instructional preferences of 110 randomly selected students taught by two different methods: (1) student…

A Comparison of Multivariate and Pre-Processing Methods for Quantitative Laser-Induced Breakdown Spectroscopy of Geologic Samples

NASA Technical Reports Server (NTRS)

Anderson, R. B.; Morris, R. V.; Clegg, S. M.; Bell, J. F., III; Humphries, S. D.; Wiens, R. C.

2011-01-01

The ChemCam instrument selected for the Curiosity rover is capable of remote laser-induced breakdown spectroscopy (LIBS).[1] We used a remote LIBS instrument similar to ChemCam to analyze 197 geologic slab samples and 32 pressed-powder geostandards. The slab samples are well-characterized and have been used to validate the calibration of previous instruments on Mars missions, including CRISM [2], OMEGA [3], the MER Pancam [4], Mini-TES [5], and Moessbauer [6] instruments and the Phoenix SSI [7]. The resulting dataset was used to compare multivariate methods for quantitative LIBS and to determine the effect of grain size on calculations. Three multivariate methods - partial least squares (PLS), multilayer perceptron artificial neural networks (MLP ANNs) and cascade correlation (CC) ANNs - were used to generate models and extract the quantitative composition of unknown samples. PLS can be used to predict one element (PLS1) or multiple elements (PLS2) at a time, as can the neural network methods. Although MLP and CC ANNs were successful in some cases, PLS generally produced the most accurate and precise results.

Quantitative determination of 5-hydroxy-N-methylpyrrolidone in urine for biological monitoring of N-methylpyrrolidone exposure.

PubMed

Ligocka, D; Lison, D; Haufroid, V

2002-10-05

The aim of this work was to validate a sensitive method for quantitative analysis of 5-hydroxy-N-methylpyrrolidone (5-HNMP) in urine. This compound has been recommended as a marker for biological monitoring of N-methylpyrrolidone (NMP) exposure. Different solvents and alternative methods of extraction including liquid-liquid extraction (LLE) on Chem Elut and solid-phase extraction (SPE) on Oasis HLB columns were tested. The most efficient extraction of 5-HNMP in urine was LLE with Chem Elut columns and dichloromethane as a solvent (consistently 22% of recovery). The urinary extracts were derivatized by bis(trimethylsilyl)trifluoroacetamide and analysed by gas chromatography-mass spectrometry (GC-MS) with tetradeutered 5-HNMP as an internal standard. The detection limit of this method is 0.017 mg/l urine with an intraassay precision of 1.6-2.6%. The proposed method of extraction is simple and reproducible. Four different m/z signal ratios of TMS-5-HNMP and tetralabelled TMS-5-HNMP have been validated and could be indifferently used in case of unexpected impurities from urine matrix. Copyright 2002 Elsevier Science B.V.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method.

PubMed

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-02-01

To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Umino, Satoru; Takahashi, Hideaki, E-mail: hideaki@m.tohoku.ac.jp; Morita, Akihiro

In a recent work, we developed a method [H. Takahashi et al., J. Chem. Phys. 143, 084104 (2015)] referred to as exchange-core function (ECF) approach, to compute exchange repulsion E{sub ex} between solute and solvent in the framework of the quantum mechanical (QM)/molecular mechanical (MM) method. The ECF, represented with a Slater function, plays an essential role in determining E{sub ex} on the basis of the overlap model. In the work of Takahashi et al. [J. Chem. Phys. 143, 084104 (2015)], it was demonstrated that our approach is successful in computing the hydrogen bond energies of minimal QM/MM systems includingmore » a cationic QM solute. We provide in this paper the extension of the ECF approach to the free energy calculation in condensed phase QM/MM systems by combining the ECF and the QM/MM-ER approach [H. Takahashi et al., J. Chem. Phys. 121, 3989 (2004)]. By virtue of the theory of solutions in energy representation, the free energy contribution δμ{sub ex} from the exchange repulsion was naturally formulated. We found that the ECF approach in combination with QM/MM-ER gives a substantial improvement on the calculation of the hydration free energy of a hydronium ion. This can be attributed to the fact that the ECF reasonably realizes the contraction of the electron density of the cation due to the deficit of an electron.« less

Solubility Prediction of Active Pharmaceutical Compounds with the UNIFAC Model

NASA Astrophysics Data System (ADS)

Nouar, Abderrahim; Benmessaoud, Ibtissem; Koutchoukali, Ouahiba; Koutchoukali, Mohamed Salah

2016-03-01

The crystallization from solution of an active pharmaceutical ingredient requires the knowledge of the solubility in the entire temperature range investigated during the process. However, during the development of a new active ingredient, these data are missing. Its experimental determination is possible, but tedious. UNIFAC Group contribution method Fredenslund et al. (Vapor-liquid equilibria using UNIFAC: a group contribution method, 1977; AIChE J 21:1086, 1975) can be used to predict this physical property. Several modifications on this model have been proposed since its development in 1977, modified UNIFAC of Dortmund Weidlich et al. (Ind Eng Chem Res 26:1372, 1987), Gmehling et al. (Ind Eng Chem Res 32:178, 1993), Pharma-modified UNIFAC Diedrichs et al. (Evaluation und Erweiterung thermodynamischer Modelle zur Vorhersage von Wirkstofflöslichkeiten, PhD Thesis, 2010), KT-UNIFAC Kang et al. (Ind Eng Chem Res 41:3260, 2002), ldots In this study, we used UNIFAC model by considering the linear temperature dependence of interaction parameters as in Pharma-modified UNIFAC and structural groups as defined by KT-UNIFAC first-order model. More than 100 binary datasets were involved in the estimation of interaction parameters. These new parameters were then used to calculate activity coefficient and solubility of some molecules in various solvents at different temperatures. The model gives better results than those from the original UNIFAC and shows good agreement between the experimental solubility and the calculated one.

NARSTO EPA SS NEW YORK AIR CHEM PM MET DATA

Atmospheric Science Data Center

2018-04-09

NARSTO EPA SS NEW YORK AIR CHEM PM MET DATA Project Title:  NARSTO ... Nitrogen Oxides Ozone Surface Winds Air Temperature Humidity Solar Irradiance Particulate Matter ... Data Guide Documents:  New York Air Chem Guide CPM Summary Report  (PDF) Nitrate ...

Hazardous Waste Cleanup: Cycle Chem Incorporated in Elizabeth, New Jersey

EPA Pesticide Factsheets

Cycle Chem is located at 217 South First Street in Elizabeth, New Jersey. Cycle Chem recovers spent solvents and treats both hazardous and non-hazardous wastes in containers and tanks. The site comprises two acres in an industrial area, surrounded by

Development of a Grid-Independent Geos-Chem Chemical Transport Model (v9-02) as an Atmospheric Chemistry Module for Earth System Models

NASA Technical Reports Server (NTRS)

Long, M. S.; Yantosca, R.; Nielsen, J. E; Keller, C. A.; Da Silva, A.; Sulprizio, M. P.; Pawson, S.; Jacob, D. J.

2015-01-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, T.; Rabitz, H.

1996-02-01

A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less

Halogenation effects on electron collisions with CF{sub 3}Cl, CF{sub 2}Cl{sub 2}, and CFCl{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freitas, T. C., E-mail: tcf03@fisica.ufpr.br; Lopes, A. R.; Bettega, M. H. F.

2016-04-28

We report differential and integral elastic cross sections for low-energy electron collisions with CF{sub 3}Cl, CF{sub 2}Cl{sub 2}, and CFCl{sub 3} molecules for energies ranging from 0.1 eV to 30 eV. The calculations were performed using the Schwinger multichannel method with pseudopotentials in the static-exchange and static-exchange plus polarization approximations. The influence of the permanent electric dipole moment on the cross sections was included using the Born closure scheme. A very good agreement between our calculations and the experimental results of Jones [J. Chem. Phys. 84, 813 (1986)], Mann and Linder [J. Phys. B 25, 1621 (1992); 25, 1633 (1992)]more » and Hoshino et al. [J. Chem. Phys. 138, 214305 (2013)] was found. We also compare our results with the calculations of Beyer et al. [Chem. Phys. 255, 1 (2000)] using the R-matrix method, where we find good agreement with respect to the location of the resonances, and with the calculations of Hoshino et al. using the independent atom method with screening corrected additivity rule, where we find qualitative agreement at energies above 20 eV. Additional electronic structure calculations were carried out in order to help in the interpretation of the scattering results. The stabilization the lowest σ{sup ∗} resonance due to the exchange of fluorine by chlorine atoms (halogenation effect) follows a simple linear relation with the energy of the lowest unoccupied molecular orbitals and can be considered as a signature of the halogenation effect.« less

Accurate treatment of total photoabsorption cross sections by an ab initio time-dependent method

NASA Astrophysics Data System (ADS)

Daud, Mohammad Noh

2014-09-01

A detailed discussion of parallel and perpendicular transitions required for the photoabsorption of a molecule is presented within a time-dependent view. Total photoabsorption cross sections for the first two ultraviolet absorption bands of the N2O molecule corresponding to transitions from the X1 A' state to the 21 A' and 11 A'' states are calculated to test the reliability of the method. By fully considering the property of the electric field polarization vector of the incident light, the method treats the coupling of angular momentum and the parity differently for two kinds of transitions depending on the direction of the vector whether it is: (a) situated parallel in a molecular plane for an electronic transition between states with the same symmetry; (b) situated perpendicular to a molecular plane for an electronic transition between states with different symmetry. Through this, for those transitions, we are able to offer an insightful picture of the dynamics involved and to characterize some new aspects in the photoabsorption process of N2O. Our calculations predicted that the parallel transition to the 21 A' state is the major dissociation pathway which is in qualitative agreement with the experimental observations. Most importantly, a significant improvement in the absolute value of the total cross section over previous theoretical results [R. Schinke, J. Chem. Phys. 134, 064313 (2011), M.N. Daud, G.G. Balint-Kurti, A. Brown, J. Chem. Phys. 122, 054305 (2005), S. Nanbu, M.S. Johnson, J. Phys. Chem. A 108, 8905 (2004)] was obtained.

Mars Rock Rocknest 3 Imaged by Curiosity ChemCam

NASA Image and Video Library

2012-11-26

This view of a rock called Rocknest 3 combines two images taken by the Chemistry and Camera ChemCam instrument on the NASA Mars rover Curiosity and indicates five spots where ChemCam had hit the rock with laser pulses to check its composition.

Elucidating the Complex Lineshapes Resulting from the Highly Sensitive, Ion Selective, Technique Nice-Ohvms

NASA Astrophysics Data System (ADS)

Hodges, James N.; Siller, Brian; McCall, Benjamin J.

2015-06-01

The technique Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy, or NICE-OHVMS, has been used to great effect to precisely and accurately measure a variety of molecular ion transitions from species such as H_3^+, CH_5^+, HeH^+, and HCO^+, achieving MHz or in some cases sub-MHz uncertainty. It is a powerful technique, but a complete theoretical understanding of the complex NICE-OHVMS lineshape is needed to fully unlock its potential. NICE-OHVMS is the direct result of the combination of the highly sensitive spectroscopic technique Noise Immune Cavity Enhanced Optical Heterodyne Molecular Spectroscopy(NICE-OHMS) with Velocity Modulation Spectroscopy(VMS), applying the most sensitive optical detection method with ion species selectivity. The theoretical underpinnings of NICE-OHMS lineshapes are well established, as are those of VMS. This presentation is the logical extension of those two preceding bodies of work. Simulations of NICE-OHVMS lineshapes under a variety of conditions and fits of experimental data to the model are presented. The significance and accuracy of the various inferred parameters, along with the prospect of using them to extract additional information from observed transitions, are discussed. J.~N. Hodges, et al. J. Chem. Phys. (2013), 139, 164201. A.~J. Perry, et al. J. Chem. Phys. (2014), 141, 101101. K.~N. Crabtree, et al. Chem. Phys. Lett. (2012), 551, 1-6. F.~M. Schmidt, et al. J. Opt. Soc. Amer. A (2008), 24, 1392--1405. J.~W. Farley, J. Chem. Phys. (1991), 95, 5590--5602.

Tropospheric ozone using an emission tagging technique in the CAM-Chem and WRF-Chem models

NASA Astrophysics Data System (ADS)

Lupascu, A.; Coates, J.; Zhu, S.; Butler, T. M.

2017-12-01

Tropospheric ozone is a short-lived climate forcing pollutant. High concentration of ozone can affect human health (cardiorespiratory and increased mortality due to long-term exposure), and also it damages crops. Attributing ozone concentrations to the contributions from different sources would indicate the effects of locally emitted or transported precursors on ozone levels in specific regions. This information could be used as an important component of the design of emissions reduction strategies by indicating which emission sources could be targeted for effective reductions, thus reducing the burden of ozone pollution. Using a "tagging" approach within the CAM-Chem (global) and WRF-Chem (regional) models, we can quantify the contribution of individual emission of NOx and VOC precursors on air quality. Hence, when precursor emissions of NOx are tagged, we have seen that the largest contributors on ozone levels are the anthropogenic sources, while in the case of precursor emissions of VOCs, the biogenic sources and methane account for more than 50% of ozone levels. Further, we have extended the NOx tagging method in order to investigate continental source region contributions to concentrations of ozone over various receptor regions over the globe, with a zoom over Europe. In general, summertime maximum ozone in most receptor regions is largely attributable to local emissions of anthropogenic NOx and biogenic VOC. During the rest of the year, especially during springtime, ozone in most receptor regions shows stronger influences from anthropogenic emissions of NOx and VOC in remote source regions.

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Development and Performance of the Modularized, High-performance Computing and Hybrid-architecture Capable GEOS-Chem Chemical Transport Model

NASA Astrophysics Data System (ADS)

Long, M. S.; Yantosca, R.; Nielsen, J.; Linford, J. C.; Keller, C. A.; Payer Sulprizio, M.; Jacob, D. J.

2014-12-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been reengineered to serve as a platform for a range of computational atmospheric chemistry science foci and applications. Development included modularization for coupling to general circulation and Earth system models (ESMs) and the adoption of co-processor capable atmospheric chemistry solvers. This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of GEOS-Chem scientific code to permit seamless transition from the GEOS-Chem stand-alone serial CTM to deployment as a coupled ESM module. In this manner, the continual stream of updates contributed by the CTM user community is automatically available for broader applications, which remain state-of-science and directly referenceable to the latest version of the standard GEOS-Chem CTM. These developments are now available as part of the standard version of the GEOS-Chem CTM. The system has been implemented as an atmospheric chemistry module within the NASA GEOS-5 ESM. The coupled GEOS-5/GEOS-Chem system was tested for weak and strong scalability and performance with a tropospheric oxidant-aerosol simulation. Results confirm that the GEOS-Chem chemical operator scales efficiently for any number of processes. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemical operator means that the relative cost goes down with increasing number of processes, making fine-scale resolution simulations possible.

Analysis of cold worked holes for structural life extension

NASA Technical Reports Server (NTRS)

Wieland, David H.; Cutshall, Jon T.; Burnside, O. Hal; Cardinal, Joseph W.

1994-01-01

Cold working holes for improved fatigue life of fastener holes are widely used on aircraft. This paper presents methods used by the authors to determine the percent of cold working to be applied and to analyze fatigue crack growth of cold worked fastener holes. An elastic, perfectly-plastic analysis of a thick-walled tube is used to determine the stress field during the cold working process and the residual stress field after the process is completed. The results of the elastic/plastic analysis are used to determine the amount of cold working to apply to a hole. The residual stress field is then used to perform damage tolerance analysis of a crack growing out of a cold worked fastener hole. This analysis method is easily implemented in existing crack growth computer codes so that the cold worked holes can be used to extend the structural life of aircraft. Analytical results are compared to test data where appropriate.

Direct Methanol Fuel Cell Battery Replacement Program

DTIC Science & Technology

2011-04-11

Matthey PtRu in operating direct methanol fuel cells” Phys. Chem. Chem. Phys., 10, 6430-6437 (2008) 2. Harry Rivera, Jamie S. Lawton , David E. Budil and...Phys. Chem. B, 112, (29) 8542-8548 (2008) 3. Jamie S. Lawton , Eugene S. Smotkin and David E. Budil, “ESR Investigation of Microviscosity, Microscopic

Synergy of SAM and ChemCam instruments (Curiosity Rover) to Search for Organic Matter at Mars

NASA Astrophysics Data System (ADS)

Dequaire, T.; Coll, P.; Szopa, C.; Maurice, S.; Mangold, N.

2014-07-01

This work proposes to determine ChemCam capabilities to detect organic molecules in the martian rocks, by coupling LIBS and passive spectroscopy using the ChemCam testbed (IRAP) in order to select at best the samples analyzed by the SAM instrument.

Pulsed Photolytic Density Scaling Experiment for BiF

DTIC Science & Technology

1989-05-01

on Lasers 86, ed. W. B. Lacina, Soc. for Opt. and Quantum Electronics, STS Press. 281 (1987). 9a. R. F. Heidner, H . Helvajian , J. S. Holloway, and J. B...Koffend, J. Chem. Phys. 84, 2137 (1986). 9b. H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. (in press). 10. J. B. Koffend and R. F...C. E. Gardner, and R. F. Heidner, J. Chem. Phys. 83, 2904 (1985). 13. R. F. Heidner, H . Helvajian , and J. B. Koffend, J. Chem. Phys. 87, 520 (1987

Reactive Removal of BiF Ground State

DTIC Science & Technology

1990-09-28

1978). 3. W E. Jones and T D. McLean, J. Mol. Spectrosc. 90, 481 (1981). 4. R. E Heidner, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem...Phys. 84, 2137 (1986). 5. C. R. Jones and H . P. Broida, J. Chem. Phys. 60, 4369 (1974). 6. H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem...Phys. Rev. A6, 631 (1972). 27. H . Hotop and W C. Lineberger, J. Phys. Chem. Ref. Data 4, 539 (1985). 28. J.M. Herbelin, Conf. Proc., Intl. Gonf. on

Photoelectronic Properties of Ternary Niobium Oxides.

DTIC Science & Technology

1980-09-01

K . /Dwi ght ,. 1 d N0,OO0l4-77-C-0387 B . PERFORMING ORGAbi)ATi0N NAME AND ADZRESS 10. PROGRAM ELEMENT. PROIECT. TASK00 Po soArn odAREA a WORK UNIT...Kershaw, R.; Dwight, K .; Wold, A. J. Solid State Chem., 1979, 27, 307. 6. Salmon, 0. N.*J. Phys. Chem., 1961, 65, 550. 7. Koenitzer, J.; Khazai, B ...Ann. Rev. Phys. Chem., 197F, 29, 189. 10. Hormadaly, J.; Subbarao , S. N.; Kershaw, R.; Dwight, K .; Wold, A. J. Solid State Chem., to be published. 1.1

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

Fabricating cooled electronic system with liquid-cooled cold plate and thermal spreader

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Methods are provided for facilitating cooling of an electronic component. The method includes providing a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to bemore » cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Fabricating cooled electronic system with liquid-cooled cold plate and thermal spreader

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Methods are provided for facilitating cooling of an electronic component. The methods include providing a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to bemore » cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Mw Spectroscopy Coupled with Ultrafast UV Laser Vaporization: {RIBOSE} Found in the Gas Phase

NASA Astrophysics Data System (ADS)

Cocinero, Emilio J.; Ecija, Patricia; Basterretxea, Francisco J.; Fernandez, Jose A.; Castano, Fernando; Lesarri, Alberto; Grabow, Jens-Uwe

2012-06-01

Sugars are aldoses or ketoses with multiple hydroxy groups which have been elusive to spectroscopic studies. Here we report a rotational study of the aldopentose ribose. According to any standard textbook aldopentoses can exhibit either linear forms, cyclic five-membered (furanose) structures or six-membered (pyranose) rings, occurring either as α- or β- anomers depending on the orientation of the hydroxy group at C-1 (anomeric carbon). β-Furanose is predominant in ribonucleosides, RNA, ATP and other biochemically relevant derivatives, but is β-furanose the native form also of free ribose? Recent condensed-phase X-ray and older NMR studies delivered conflicting results. In order to solve this question we conducted a microwave study on D-ribose that, owing to ultrafast UV laser vaporization, has become the first C-5 sugar observed with rotational resolution. The spectrum revealed six conformations of free ribose, preferentially adopting β-pyranose chairs as well as higher-energy α-pyranose forms. The method also allowed for unambiguous distinction between different orientations of the hydroxy groups, which stabilize the structures by cooperative hydrogen-bond networks. No evidence was observed of the α-/β-furanoses or linear forms found in the biochemical derivatives. i) D. Šišak, L. B. McCusker, G. Zandomeneghi, B. H. Meier, D. Bläser, R. Boese, W. B. Schweizer, R. Gylmour and J. D. Dunitz Angew. Chem. Int. Ed. 49, 4503, 2010. ii) W. Saenger Angew. Chem. Int. Ed. 49, 6487, 2010. i) M. Rudrum, and D. F. Shaw, J. Chem. Soc. 52, 1965. ii) R. U. Lemieux and J. D. Stevens Can. J. Chem. 44, 249, 1966. iii) E. Breitmaier and U. Hollstein Org. Magn. Reson. 8, 573, 1976. E. J. Cocinero, A. Lesarri, P. Écija, F. J. Basterretxea, J. U. Grabow, J. A. Fernández and F. Castaño Angew. Chem. Int. Ed. in press: DOI: 10.1002/anie.201107973, 2012.

Fixed node diffusion Monte Carlo using a genetic algorithm: a study of the CO-(4)He(N) complex, N = 1…10.

PubMed

Ramilowski, Jordan A; Farrelly, David

2012-06-14

The diffusion Monte Carlo (DMC) method is a widely used algorithm for computing both ground and excited states of many-particle systems; for states without nodes the algorithm is numerically exact. In the presence of nodes approximations must be introduced, for example, the fixed-node approximation. Recently we have developed a genetic algorithm (GA) based approach which allows the computation of nodal surfaces on-the-fly [Ramilowski and Farrelly, Phys. Chem. Chem. Phys., 2010, 12, 12450]. Here GA-DMC is applied to the computation of rovibrational states of CO-(4)He(N) complexes with N≤ 10. These complexes have been the subject of recent high resolution microwave and millimeter-wave studies which traced the onset of microscopic superfluidity in a doped (4)He droplet, one atom at a time, up to N = 10 [Surin et al., Phys. Rev. Lett., 2008, 101, 233401; Raston et al., Phys. Chem. Chem. Phys., 2010, 12, 8260]. The frequencies of the a-type (microwave) series, which correlate with end-over-end rotation in the CO-(4)He dimer, decrease from N = 1 to 3 and then smoothly increase. This signifies the transition from a molecular complex to a quantum solvated system. The frequencies of the b-type (millimeter-wave) series, which evolves from free rotation of the rigid CO molecule, initially increase from N = 0 to N∼ 6 before starting to decrease with increasing N. An interesting feature of the b-type series, originally observed in the high resolution infra-red (IR) experiments of Tang and McKellar [J. Chem. Phys., 2003, 119, 754] is that, for N = 7, two lines are observed. The GA-DMC algorithm is found to be in good agreement with experimental results and possibly detects the small (∼0.7 cm(-1)) splitting in the b-series line at N = 7. Advantages and disadvantages of GA-DMC are discussed.

Rovibrational Quantum Dynamics of the Methane-Water Dimer

NASA Astrophysics Data System (ADS)

Sarka, János; Császár, Attila; Mátyus, Edit

2017-06-01

The challenging quantum dynamical description of the CH_4.H_2O complex has been solved variationally to provide theoretical explanation and assignment to the high-resolution spectroscopic measurements of the methane-water dimer carried out some twenty years ago. The computational results are in excellent agreement with the reported experimental transitions and the experimentally observed reversed rovibrational sequences, i.e., formally negative rotational excitation energies, are also obtained in the computations. In order to better understand the origin of these peculiar features in the energy-level spectrum, we studied all four possible combinations of the light and heavy isotopologues of methane and water and analyzed their rovibrational states using two limiting model systems: the rigidly rotating (RR) molecule and the coupled rotor (CR) system corresponding to the coupling of the two rotating monomers. All rovibrational quantum dynamical computations^{a,c} were carried out with rigid monomers and J = 0,1,2 total angular momentum quantum numbers using the fourth-age quantum chemical code GENIUSH and two different methane-water potential energy surfaces (PES). The numerical and formal analysis of the wave functions give insight into a fascinating complex world worth for further theoretical and experimental inquiries. J. Sarka, A. G. Császár, S. C. Althorpe, D. J. Wales and E. Mátyus, Phys. Chem. Chem. Phys. 18, 22816 (2016). L. Dore, R. C. Cohen, C. A. Schmuttenmaer, K. L. Busarow, M. J. Elrod, J. G. Loeser and R. J. Saykally, J. Chem. Phys. 100, 863 (1994). J. Sarka, A. G. Császár and E. Mátyus, Phys. Chem. Chem. Phys. accepted for publication (2017).} E. Mátyus, G. Czakó and A. G. Császár, J. Chem. Phys. 130, 134112 (2009). C. Fábri, E. Mátyus and A. G. Császár, J. Chem. Phys. 134, 074105 (2011). O. Akin-Ojo and K. Szalewicz, J. Chem. Phys. 123, 134311 (2005). C. Qu, R. Conte, P. L. Houston and J. M. Bowman, Phys. Chem. Chem. Phys. 17, 8172 (2015).

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Pyle, B. H.; Lisle, J. T.; Broadaway, S. C.

1999-01-01

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Infrared Spectroscopy of 1-CHOLOROMETHYLALLYL and 1-METHYLALLYL Radicals Produced in a Solid Para-Hydrogen Matrix.

NASA Astrophysics Data System (ADS)

Bahou, Mohammed; Wu, Jen-Yu; Tanaka, Keiichi; Lee, Yuan-Pern

2012-06-01

The reaction of chlorine atoms with trans-1,3-butadiene in solid para-hydrogen (p-H_2) matrix has been studied using Fourier transform infrared spectroscopy. When a mixture of Cl_2, trans-1,3-butadiene and p-H_2 was deposited onto a cold target at 3 K and irradiated by UV light at 365 nm, new intense lines at 809.0, 962.1, 1240.6 cm-1 and several weaker ones appeared. The carrier of this spectrum was assigned to the 1-chloromethylallyl radical, - (CH_2CHCH)CH_2Cl, based on the anharmonic vibrational frequencies calculated with the DFT method, indicating that the addition of the Cl atom to trans-1,3-butadiene occurs primarily at the terminal carbon atom. This is in sharp contrast to the reaction of chlorine atoms with propene in a solid p-H_2 matrix in which the addition of Cl to the central carbon atom to produce selectively the 2-chloropropyl is favored due to the steric effects. The energy diagram calculated with B3PW91 method supports this selective reaction process because 1) the channel from trans-1,3-butadiene to 1-chloro-methylallyl is almost barrierless (0.4 kcal/mol), and 2) isomereization from 1-chloromethylally to the 2-chloro-3-buten-1-yl radical, CH_2CHCHClCH_2 - by migration of Cl atom from the terminal to the central C atom, hardly occur in the p-H_2 matrix because of the isomerization barrier height (18.8 kcal/mol). We also observed a second set of lines with intense ones at 781.6, 957.93, 1433.6 cm-1 and several weaker ones when the UV-irradiated Cl_2/trans-1,3-butadiene/p-H_2 matrix was further irradiated with infrared light from a globar source. These lines are assigned to the 1-methylallyl radical, - (CH_2CHCH)CH_3, produced from reaction of 1,3-butadiene with an H atom that was produced from the reaction of Cl atoms with IR-irradiated p-H_2, Cl + H_2^* → H + HCl. The energy diagram calculated at the G3//B3LYP level similarly supports the reaction process to form selectively 1-methylallyl in the p-H_2 matrix. J. C. Amicangelo and Y. P. Lee, J. Phys. Chem. Lett. 1, 1956 (2010). J. L. Millerngelo, J. Phys. Chem. A 108, 2268 (2004).

78 FR 25369 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-01

... at chem-mill areas on the crown skin panels. This AD requires repetitive inspections for cracking of the fuselage skin at certain locations at chem-mill areas, and repair if necessary. We are issuing this AD to detect and correct fatigue cracking of the skin panel at the specified chem-mill step...

77 FR 57536 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-18

... chem-mill areas on the crown skin panels. This proposed AD would require repetitive inspections for cracking of the fuselage skin at certain locations at chem-mill areas, and repair if necessary. We are proposing this AD to detect and correct fatigue cracking of the skin panel at the specified chem-mill step...

77 FR 48423 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-14

... Company Model 737-500 series airplanes. This AD was prompted by reports of chem-mill step cracking on the aft lower lobe fuselage skins. This AD requires inspections of the fuselage skin at the chem- mill... 22686). That NPRM proposed to require inspections of the fuselage skin at the chem-mill steps, and...

Engineering Analysis in the Chem-E-Car Competition

ERIC Educational Resources Information Center

Lewis, Randy S.; Moshfeghian, Aliakbar; Madihally, Sundararajan V.

2006-01-01

The AIChE Chem-E-Car competition provides students an opportunity to demonstrate their design and teamwork skills. Engineering analysis is not required at the national competition and is often not applied. This work describes an engineering analysis of a Chem-E-Car to predict the distance traveled by the car. Engineering analysis is advantageous…

77 FR 47427 - Accreditation and Approval of Chem Gas International LLC, as a Commercial Gauger and Laboratory

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-08

... Chem Gas International LLC, as a Commercial Gauger and Laboratory AGENCY: U.S. Customs and Border Protection, Department of Homeland Security. ACTION: Notice of accreditation and approval of Chem Gas... Gas International LLC, as commercial gauger and laboratory became effective on October 19, 2011. The...

Chemerin15 inhibits neutrophil-mediated vascular inflammation and myocardial ischemia-reperfusion injury through ChemR23

PubMed Central

Cash, Jenna L; Bena, Stefania; Headland, Sarah E; McArthur, Simon; Brancaleone, Vincenzo; Perretti, Mauro

2013-01-01

Neutrophil activation and adhesion must be tightly controlled to prevent complications associated with excessive inflammatory responses. The role of the anti-inflammatory peptide chemerin15 (C15) and the receptor ChemR23 in neutrophil physiology is unknown. Here, we report that ChemR23 is expressed in neutrophil granules and rapidly upregulated upon neutrophil activation. C15 inhibits integrin activation and clustering, reducing neutrophil adhesion and chemotaxis in vitro. In the inflamed microvasculature, C15 rapidly modulates neutrophil physiology inducing adherent cell detachment from the inflamed endothelium, while reducing neutrophil recruitment and heart damage in a murine myocardial infarction model. These effects are mediated through ChemR23. We identify the C15/ChemR23 pathway as a new regulator and thus therapeutic target in neutrophil-driven pathologies. PMID:23999103

Comparison of mixed layer heights from airborne high spectral resolution lidar, ground-based measurements, and the WRF-Chem model during CalNex and CARES

NASA Astrophysics Data System (ADS)

Scarino, A. J.; Obland, M. D.; Fast, J. D.; Burton, S. P.; Ferrare, R. A.; Hostetler, C. A.; Berg, L. K.; Lefer, B.; Haman, C.; Hair, J. W.; Rogers, R. R.; Butler, C.; Cook, A. L.; Harper, D. B.

2013-05-01

The California Research at the Nexus of Air Quality and Climate Change (CalNex) and Carbonaceous Aerosol and Radiative Effects Study (CARES) field campaigns during May and June 2010 provided a data set appropriate for studying characteristics of the planetary boundary layer (PBL). The NASA Langley Research Center (LaRC) airborne High Spectral Resolution Lidar (HSRL) was deployed to California onboard the NASA LaRC B-200 aircraft to aid in characterizing aerosol properties during these two field campaigns. Measurements of aerosol extinction (532 nm), backscatter (532 and 1064 nm), and depolarization (532 and 1064 nm) profiles during 31 flights, many in coordination with other research aircraft and ground sites, constitute a diverse data set for use in characterizing the spatial and temporal distribution of aerosols, as well as the depth and variability of the daytime mixed layer (ML), which is a subset within the PBL. This work illustrates the temporal and spatial variability of the ML in the vicinity of Los Angeles and Sacramento, CA. ML heights derived from HSRL measurements are compared to PBL heights derived from radiosonde profiles, ML heights measured from ceilometers, and simulated PBL heights from the Weather Research and Forecasting Chemistry (WRF-Chem) community model. Comparisons between the HSRL ML heights and the radiosonde profiles in Sacramento result in a correlation coefficient value (R) of 0.93 (root-mean-square (RMS) difference of 157 m and bias difference (HSRL - radiosonde) of 57 m). HSRL ML heights compare well with those from the ceilometer in the LA Basin with an R of 0.89 (RMS difference of 108 m and bias difference (HSRL - Ceilometer) of -9.7 m) for distances of up to 30 km between the B-200 flight track and the ceilometer site. Simulated PBL heights from WRF-Chem were compared with those obtained from all flights for each campaign, producing an R of 0.58 (RMS difference of 604 m and a bias difference (WRF-Chem - HSRL) of -157 m) for CalNex and 0.59 (RMS difference of 689 m and a bias difference (WRF-Chem - HSRL) of 220 m) for CARES. Aerosol backscatter simulations are also available from WRF-Chem and are compared to those from HSRL to examine differences among the methods used to derive ML heights.

Soot and SO2 contribution to the supersites in the MILAGRO campaign from elevated flares in the Tula Refinery

NASA Astrophysics Data System (ADS)

Almanza, V. H.; Molina, L. T.; Sosa, G.

2012-11-01

This work presents a simulation of the plume trajectory emitted by flaring activities of the Miguel Hidalgo Refinery in Mexico. The flame of a representative sour gas flare is modeled with a CFD combustion code in order to estimate emission rates of combustion by-products of interest for air quality: acetylene, ethylene, nitrogen oxides, carbon monoxide, soot and sulfur dioxide. The emission rates of NO2 and SO2 were compared with measurements obtained at Tula as part of MILAGRO field campaign. The rates of soot, VOCs and CO emissions were compared with estimates obtained by Instituto Mexicano del Petróleo (IMP). The emission rates of these species were further included in WRF-Chem model to simulate the chemical transport of the plume from 22 to 27 March of 2006. The model presents reliable performance of the resolved meteorology, with respect to the Mean Absolute Error (MAE), Root Mean Square Error (RMSE), mean bias (BIAS), vector RMSE and Index of Agreement (IOA). WRF-Chem outputs of SO2 and soot were compared with surface measurements obtained at the three supersites of MILAGRO campaign. The results suggest a contribution of Tula flaring activities to the total SO2 levels of 18% to 27% at the urban supersite (T0), and of 10% to 18% at the suburban supersite (T1). For soot, the model predicts low contribution at the three supersites, with less than 0.1% at three supersites. According to the model, the greatest contribution of both pollutants to the three supersites occurred on 23 March, which coincides with the third cold surge event reported during the campaign.

A Mechanistic Study of the Influence of Proton Transfer Processes on the Behavior of Thiol/Disulfide Redox Couples

DTIC Science & Technology

1998-06-29

acidic than its cation radical, McMT4*. Bordwell et al.20 have discussed the relative acidities of thiols (pKnA)and their cation radicals (PKHA+-), and...15) Bordwell , F. G. Ace. Chem. Res. 1988, 21, 456. 16) Parker, V. D.; Tilset, M. J. Am. Chem. Soc. 1988,110, 1649. 17) Bordwell , F. G.; Bausch, M. J...J. Am. Chem. Soc. 1986,108, 2473. 18) Bordwell , F. G.; Cheng, J.-P. J. Am. Chem. Soc. 1989,111, 1792. 19) Parker, V. D.; Handoo, K. L.; Roness, F

Photoelectron Spectroscopy of CdSe Nanocrystals in the Gas Phase: A Direct Measure of the Evanescent Electron Wave Function of Quantum Dots

DTIC Science & Technology

2013-01-01

11) Kim, S.; Fisher, B.; Eisler , H.-J.; Bawendi, M. J. Am. Chem. Soc. 2003, 125, 11466−11467. (12) Dabbousi, B. O.; Mikulec, F. V; Heine, J. R...Chem. 1982, 2291−2293. (34) Spanhel, L.; Haase, M.; Weller, H.; Henglein, A. J. Am. Chem. Soc. 1987 , 5649−5655. (35) Spanhel, L.; Weller, H...Henglein, A. J. Am. Chem. Soc. 1987 , 6632−6635. (36) Berglund, C. N.; Spicer, W. E. Phys. Rev. 1964, 136, 1030−1044. (37) Liu, P.; Ziemann, P. J.; Kittelson

Comparing the Predictive Capabilities of Level Three EVM Cost Data with Level Five EVM Cost Data

DTIC Science & Technology

2014-03-27

Management (EVM) Data Manual , 2008). Performance Assessments and Root Cause Analysis (PARCA) directly oversees EVM- CR. A contractor must submit seven...Massive Ordance Penetrator (F33657-99-D-0028) 126 66 17 9 7 Chem Demil - CMA (DAAA09-97-C-0025) 2494 1520 63 19 9 Chem Demil - CMA (DACA87-89-C-0076) 441...Engagement Capability N00024-05-C-5100 1 50 Army Chem Demil - CMA DACA87-89-C-0076 0 1 Army Chem Demil - CMA DAAA09-97-C-0025 1 2 Navy DDG 1000 - ZUMWALT

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

DOE PAGES

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar; ...

2015-06-30

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Kyle K.G.; Poulsen, Jens Aage; Nyman, Gunnar

Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3) and (T = 23.0 K, n = 24.61 nm -3), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this showsmore » that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se; Nyman, Gunnar, E-mail: nyman@chem.gu.se

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCWmore » provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.« less

Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Nyman, Gunnar; Cunsolo, Alessandro; Rossky, Peter J

2015-06-28

We apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. This shows that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.

Development of a Standardized Approach for Assessing Potential Risks to Amphibians Exposed to Sediment and Hydric Soils

DTIC Science & Technology

2004-05-01

following digestion using method 3005A. Copper concentrations were verified using atomic absorption spectroscopy/graphite furnace. Each chamber...1995. Ammonia Variation in Sediments: Spatial, Temporal and Method -Related Effects. Environ. Toxicol. Chem. 14:1499-1506. Savage, W.K., F.W...Regulator Approved Methods and Protocols for Conducting Marine and Terrestrial Risk Assessments 1.III.01.k - Improved Field Analytical Sensors

Adaptive Quantum Control of Charge Motion in Semiconductor Heterostructures

NASA Astrophysics Data System (ADS)

Reitze, David

1998-05-01

Quantum control of electronic wavepacket motion and interactions using ultrafast lasers has moved from the conceptual stage to reality, in large part driven by advances in quantum control theory (R. J. Gordon and S. A. Rice, Ann. Rev. Phys. Chem. (1997), in press.) (M. Shapiro and P. Brumer, J. Chem. Soc. Faraday Trans. V93, 1263 (1997).) (D. Neuhauser and H. Rabitz, Acc. Chem. Res. V26, 496 (1993).) and experimental pulse shaping methods (A. M. Weiner, D. E. Leaird, G. P. Wiederrecht, and K. A. Nelson, Science V247, 412 (1990).) (A. Efimov, C. Schaffer, and D. H. Reitze, J. Opt. Soc. Am VB12, 1968 (1995).). Here, we apply these methods to controlling charge motion in semiconductor heterostructures. Control of coherent charge dynamics in heterostructures enjoys an advantage in that spatial potential profiles can be adjusted almost arbitrarily. Thus, control of charge motion can be exerted by tailoring both the temporal and spatial interactions of the charges with the controlling optical and static fields. In this talk, we demonstrate an experimental feedback loop which adaptively shapes fs pulses in a quantum contol pump-probe experiment, apply it to the control of coherent wavepacket motion in DC-biased asymmetric double quantum well(ADQW) structures, and compare to theoretical predictions of quantum control in ADQWs (N. M. Beach, D. H. Reitze, and J. L. Krause, submitted to Opt. Exp.) (J. L. Krause, D. H. Reitze, G. D. Sanders, A. Kuznetsov, and C. J. Stanton, to appear in Phys. Rev. B).

The Cl + O3 reaction: a detailed QCT simulation of molecular beam experiments.

PubMed

Menéndez, M; Castillo, J F; Martínez-Haya, B; Aoiz, F J

2015-10-14

We have studied in detail the dynamics of the Cl + O3 reaction in the 1-56 kcal mol(-1) collision energy range using quasi-classical trajectory (QCT) calculations on a recent potential energy surface (PES) [J. F. Castillo et al., Phys. Chem. Chem. Phys., 2011, 13, 8537]. The main goal of this work has been to assess the accuracy of the PES and the reliability of the QCT method by comparison with the existing crossed molecular beam results [J. Zhang and Y. T. Lee J. Phys. Chem. A, 1997, 101, 6485]. For this purpose, we have developed a methodology that allows us to determine the experimental observables in crossed molecular beam experiments (integral and differential cross sections, recoil velocity distributions, scattering angle-recoil velocity polar maps, etc.) as continuous functions of the collision energy. Using these distributions, raw experimental data in the laboratory frame (angular distributions and time-of-flight spectra) have been simulated from first principles with the sole information on the instrumental parameters and taking into account the energy spread. A general good agreement with the experimental data has been found, thereby demonstrating the adequacy of the QCT method and the quality of the PES to describe the dynamics of this reaction at the level of resolution of the existing crossed beam experiments. Some features which are apparent in the differential cross sections have also been analysed in terms of the dynamics of the reaction and its evolution with the collision energy.

Application of Coamplification at Lower Denaturation Temperature-PCR Sequencing for Early Detection of Antiviral Drug Resistance Mutations of Hepatitis B Virus

PubMed Central

Wong, Danny Ka-Ho; Tsoi, Ottilia; Huang, Fung-Yu; Seto, Wai-Kay; Fung, James; Lai, Ching-Lung

2014-01-01

Nucleoside/nucleotide analogue for the treatment of chronic hepatitis B virus (HBV) infection is hampered by the emergence of drug resistance mutations. Conventional PCR sequencing cannot detect minor variants of <20%. We developed a modified co-amplification at lower denaturation temperature-PCR (COLD-PCR) method for the detection of HBV minority drug resistance mutations. The critical denaturation temperature for COLD-PCR was determined to be 78°C. Sensitivity of COLD-PCR sequencing was determined using serially diluted plasmids containing mixed proportions of HBV reverse transcriptase (rt) wild-type and mutant sequences. Conventional PCR sequencing detected mutations only if they existed in ≥25%, whereas COLD-PCR sequencing detected mutations when they existed in 5 to 10% of the viral population. The performance of COLD-PCR was compared to conventional PCR sequencing and a line probe assay (LiPA) using 215 samples obtained from 136 lamivudine- or telbivudine-treated patients with virological breakthrough. Among these 215 samples, drug resistance mutations were detected in 155 (72%), 148 (69%), and 113 samples (53%) by LiPA, COLD-PCR, and conventional PCR sequencing, respectively. Nineteen (9%) samples had mutations detectable by COLD-PCR but not LiPA, while 26 (12%) samples had mutations detectable by LiPA but not COLD-PCR, indicating both methods were comparable (P = 0.371). COLD-PCR was more sensitive than conventional PCR sequencing. Thirty-five (16%) samples had mutations detectable by COLD-PCR but not conventional PCR sequencing, while none had mutations detected by conventional PCR sequencing but not COLD-PCR (P < 0.0001). COLD-PCR sequencing is a simple method which is comparable to LiPA and superior to conventional PCR sequencing in detecting minor lamivudine/telbivudine resistance mutations. PMID:24951803

Investigating fire emissions and smoke transport during the Summer of 2013 using an operational smoke modeling system and chemical transport model

NASA Astrophysics Data System (ADS)

ONeill, S. M.; Chung, S. H.; Wiedinmyer, C.; Larkin, N. K.; Martinez, M. E.; Solomon, R. C.; Rorig, M.

2014-12-01

Emissions from fires in the Western US are substantial and can impact air quality and regional climate. Many methods exist that estimate the particulate and gaseous emissions from fires, including those run operationally for use with chemical forecast models. The US Forest Service Smartfire2/BlueSky modeling framework uses satellite data and reported information about fire perimeters to estimate emissions of pollutants to the atmosphere. The emission estimates are used as inputs to dispersion models, such as HYSPLIT, and chemical transport models, such as CMAQ and WRF-Chem, to assess the chemical and physical impacts of fires on the atmosphere. Here we investigate the use of Smartfire2/BlueSky and WRF-Chem to simulate emissions from the 2013 fire summer fire season, with special focus on the Rim Fire in northern California. The 2013 Rim Fire ignited on August 17 and eventually burned more than 250,000 total acres before being contained on October 24. Large smoke plumes and pyro-convection events were observed. In this study, the Smartfire2/BlueSky operational emission estimates are compared to other estimation methods, such as the Fire INventory from NCAR (FINN) and other global databases to quantify variations in emission estimation methods for this wildfire event. The impact of the emissions on downwind chemical composition is investigated with the coupled meteorology-chemistry WRF-Chem model. The inclusion of aerosol-cloud and aerosol-radiation interactions in the model framework enables the evaluation of the downwind impacts of the fire plume. The emissions and modeled chemistry can also be evaluated with data collected from the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) aircraft field campaign, which intersected the fire plume.

ConfChem Conference on Flipped Classroom: Spring 2014 ConfChem Virtual Poster Session

ERIC Educational Resources Information Center

Belford, Robert E.; Stoltzfus, Matthew; Houseknecht, Justin B.

2015-01-01

This communication describes the virtual poster session of the Flipped Classroom online ConfChem conference that was hosted by the ACS CHED Committee on Computers in Chemical Education (CCCE) from May 9 to June 12, 2014. During the conference's online discussions, it became evident that multiple participants who were not presenting papers had been…

ScrubChem: Cleaning of PubChem Bioassay Data to Create Diverse and Massive Bioactivity Datasets for Use in Modeling Applications (SOT)

EPA Science Inventory

The PubChem Bioassay database is a non-curated public repository with bioactivity data from 64 sources, including: ChEMBL, BindingDb, DrugBank, Tox21, NIH Molecular Libraries Screening Program, and various academic, government, and industrial contributors. However, this data is d...

Supramolecular Polymers with Orthogonal Functionality

DTIC Science & Technology

2014-12-11

Weder, C. J. Am. Chem. Soc. 2014, 136, 10493−10498. (17) Burnworth, M.; Tang , L.; Kumpfer, J. R.; Duncan, A. J.; Beyer, F. L.; Fiore, G. L.; Rowan, S. J...J. Am. Chem. Soc. 2005, 127, 2913−2921. (29) Holyer, R. H.; Hubbard, C. D.; Kettle, S. F. A.; Wilkins , R. G. Inorg. Chem. 1966, 5, 622−625. (30

pH and temperature dual-sensitive liposome gel based on novel cleavable mPEG-Hz-CHEMS polymeric vaginal delivery system

PubMed Central

Chen, Daquan; Sun, Kaoxiang; Mu, Hongjie; Tang, Mingtan; Liang, Rongcai; Wang, Aiping; Zhou, Shasha; Sun, Haijun; Zhao, Feng; Yao, Jianwen; Liu, Wanhui

2012-01-01

Background In this study, a pH and temperature dual-sensitive liposome gel based on a novel cleavable hydrazone-based pH-sensitive methoxy polyethylene glycol 2000-hydrazone-cholesteryl hemisuccinate (mPEG-Hz-CHEMS) polymer was used for vaginal administration. Methods The pH-sensitive, cleavable mPEG-Hz-CHEMS was designed as a modified pH-sensitive liposome that would selectively degrade under locally acidic vaginal conditions. The novel pH-sensitive liposome was engineered to form a thermogel at body temperature and to degrade in an acidic environment. Results A dual-sensitive liposome gel with a high encapsulation efficiency of arctigenin was formed and improved the solubility of arctigenin characterized by Fourier transform infrared spectroscopy and differential scanning calorimetry. The dual-sensitive liposome gel with a sol-gel transition at body temperature was degraded in a pH-dependent manner, and was stable for a long period of time at neutral and basic pH, but cleavable under acidic conditions (pH 5.0). Arctigenin encapsulated in a dual-sensitive liposome gel was more stable and less toxic than arctigenin loaded into pH-sensitive liposomes. In vitro drug release results indicated that dual-sensitive liposome gels showed constant release of arctigenin over 3 days, but showed sustained release of arctigenin in buffers at pH 7.4 and pH 9.0. Conclusion This research has shed some light on a pH and temperature dual-sensitive liposome gel using a cleavable mPEG-Hz-CHEMS polymer for vaginal delivery. PMID:22679372

ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds

PubMed Central

Naveja, J. Jesús; Medina-Franco, José L.

2017-01-01

We present a novel approach called ChemMaps for visualizing chemical space based on the similarity matrix of compound datasets generated with molecular fingerprints’ similarity. The method uses a ‘satellites’ approach, where satellites are, in principle, molecules whose similarity to the rest of the molecules in the database provides sufficient information for generating a visualization of the chemical space. Such an approach could help make chemical space visualizations more efficient. We hereby describe a proof-of-principle application of the method to various databases that have different diversity measures. Unsurprisingly, we found the method works better with databases that have low 2D diversity. 3D diversity played a secondary role, although it seems to be more relevant as 2D diversity increases. For less diverse datasets, taking as few as 25% satellites seems to be sufficient for a fair depiction of the chemical space. We propose to iteratively increase the satellites number by a factor of 5% relative to the whole database, and stop when the new and the prior chemical space correlate highly. This Research Note represents a first exploratory step, prior to the full application of this method for several datasets. PMID:28794856

ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds.

PubMed

Naveja, J Jesús; Medina-Franco, José L

2017-01-01

We present a novel approach called ChemMaps for visualizing chemical space based on the similarity matrix of compound datasets generated with molecular fingerprints' similarity. The method uses a 'satellites' approach, where satellites are, in principle, molecules whose similarity to the rest of the molecules in the database provides sufficient information for generating a visualization of the chemical space. Such an approach could help make chemical space visualizations more efficient. We hereby describe a proof-of-principle application of the method to various databases that have different diversity measures. Unsurprisingly, we found the method works better with databases that have low 2D diversity. 3D diversity played a secondary role, although it seems to be more relevant as 2D diversity increases. For less diverse datasets, taking as few as 25% satellites seems to be sufficient for a fair depiction of the chemical space. We propose to iteratively increase the satellites number by a factor of 5% relative to the whole database, and stop when the new and the prior chemical space correlate highly. This Research Note represents a first exploratory step, prior to the full application of this method for several datasets.

Cold Plasma Welding System for Surgical Skin Closure: In Vivo Porcine Feasibility Assessment.

PubMed

Harats, Moti; Lam, Amnon; Maller, Michael; Kornhaber, Rachel; Haik, Josef

2016-09-29

Cold plasma skin welding is a novel technology that bonds skin edges through soldering without the use of synthetic materials or conventional wound approximation methods such as sutures, staples, or skin adhesives. The cold plasma welding system uses a biological solder applied to the edges of a skin incision, followed by the application of cold plasma energy. The objectives of this study were to assess the feasibility of a cold plasma welding system in approximating and fixating skin incisions compared with conventional methods and to evaluate and define optimal plasma welding parameters and histopathological tissue response in a porcine model. The cold plasma welding system (BioWeld1 System, IonMed Ltd, Yokneam, Israel) was used on porcine skin incisions using variable energy parameters. Wound healing was compared macroscopically and histologically to incisions approximated with sutures. When compared to sutured skin closure, cold plasma welding in specific system parameters demonstrated comparable and favorable wound healing results histopathologically as well as macroscopically. No evidence of epidermal damage, thermal or otherwise, was encountered in the specified parameters. Notably, bleeding, infection, and wound dehiscence were not detected at incision sites. Skin incisions welded at extreme energy parameters presented second-degree burns. Implementation of cold plasma welding has been shown to be feasible for skin closure. Initial in vivo results suggest cold plasma welding might provide equal, if not better, healing results than traditional methods of closure.

Method of manufacturing metallic products such as sheet by cold working and flash anealing

DOEpatents

Hajaligol, Mohammad R.; Sikka, Vinod K.

2001-01-01

A metallic alloy composition is manufactured into products such as press formed or stamped products or rolled products such as sheet, strip, rod, wire or band by one or more cold working steps with intermediate or final flash annealing. The method can include cold rolling an iron, nickel or titanium aluminide alloy and annealing the cold worked product in a furnace by infrared heating. The flash annealing is preferably carried out by rapidly heating the cold worked product to an elevated temperature for less than one minute. The flash annealing is effective to reduce surface hardness of the cold worked product sufficiently to allow further cold working. The product to be cold worked can be prepared by casting the alloy or by a powder metallurgical technique such as tape casting a mixture of metal powder and a binder, roll compacting a mixture of the powder and a binder or plasma spraying the powder onto a substrate. In the case of tape casting or roll compaction, the initial powder product can be heated to a temperature sufficient to remove volatile components. The method can be used to form a cold rolled sheet which is formed into an electrical resistance heating element capable of heating to 900.degree. C. in less than 1 second when a voltage up to 10 volts and up to 6 amps is passed through the heating element.

Method of manufacturing metallic products such as sheet by cold working and flash annealing

DOEpatents

Hajaligol, Mohammad R.; Sikka, Vinod K.

2000-01-01

A metallic alloy composition is manufactured into products such as press formed or stamped products or rolled products such as sheet, strip, rod, wire or band by one or more cold working steps with intermediate or final flash annealing. The method can include cold rolling an iron, nickel or titanium aluminide alloy and annealing the cold worked product in a furnace by infrared heating. The flash annealing is preferably carried out by rapidly heating the cold worked product to an elevated temperature for less than one minute. The flash annealing is effective to reduce surface hardness of the cold worked product sufficiently to allow further cold working. The product to be cold worked can be prepared by casting the alloy or by a powder metallurgical technique such as tape casting a mixture of metal powder and a binder, roll compacting a mixture of the powder and a binder or plasma spraying the powder onto a substrate. In the case of tape casting or roll compaction, the initial powder product can be heated to a temperature sufficient to remove volatile components. The method can be used to form a cold rolled sheet which is formed into an electrical resistance heating element capable of heating to 900.degree. C. in less than 1 second when a voltage up to 10 volts and up to 6 amps is passed through the heating element.

Isolation of Ion-Driven Conformations in Diphenylacetylene Molecular Switches Using Cryogenic Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Wolk, Arron B.; Garand, Etienne; Jones, Ian M.; Kamrath, Michael Z.; Hamilton, Rew; Johnson, Mark A.

2012-06-01

We report the infrared predissociation spectra of a family of ionic diphenylacetylene molecular switch complexes. The electrosprayed complexes were trapped and cooled in a cryogenic (10K) quadrupole ion trap and tagged with molecular deuterium. The infrared spectra of the vibrationally cold species reveal sharp transitions over a wide energy range (800 - 3800 cm-1), facilitating comparison to harmonic spectra. The evolution of the band pattern upon derivatization of the complexes exposes the signatures of the amide, urea, and carbonyl functionalities, enabling unambiguous identification of the non-covalent interactions that control the secondary structure of the molecule. Complexation with the tetramethylammonium cation reveals a conformation analogous to that of the neutral molecule, while halide ion attachment induces a conformational change similar to that observed earlier in solution. In several cases, both the donor and acceptor groups involved in the multidentate H-bonds are observed, providing a microscopic mechanical picture of the interactions at play. I. Jones, and A. Hamilton, Angew. Chem. Intl. Edit. 50, 4597 (2011).

A CK2 site is reversibly phosphorylated in the photosystem II subunit CP29.

PubMed

Testi, M G; Croce, R; Polverino-De Laureto, P; Bassi, R

1996-12-16

Protein phosphorylation is a major mechanism in the regulation of protein function. In chloroplast thylakoids several photosystem II subunits, including the major antenna light-harvesting complex II and several core complex components, are reversibly phosphorylated depending on the redox state of the electron carriers. A previously unknown reversible phosphorylation event has recently been described on the CP29 subunit which leads to conformational changes and protection from cold stress (Bergantino, E., Dainese, P., Cerovic, Z. Sechi, S. and Bassi, R. (1995) J. Biol Chem. 270, 8474-8481). In this study, we have identified the phosphorylation site on the N-terminal, stroma-exposed domain, showing that it is located in a sequence not homologous to the other members of the Lhc family. The phosphorylated sequence is unique in chloroplast membranes since it meets the requirements for CK2 (casein kinase II) kinases. The possibility that this phosphorylation is involved in a signal transduction pathway is discussed.

Actively controlling coolant-cooled cold plate configuration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Parida, Pritish R.

A method is provided to facilitate active control of thermal and fluid dynamic performance of a coolant-cooled cold plate. The method includes: monitoring a variable associated with at least one of the coolant-cooled cold plate or one or more electronic components being cooled by the cold plate; and dynamically varying, based on the monitored variable, a physical configuration of the cold plate. By dynamically varying the physical configuration, the thermal and fluid dynamic performance of the cold plate are adjusted to, for example, optimally cool the one or more electronic components, and at the same time, reduce cooling power consumptionmore » used in cooling the electronic component(s). The physical configuration can be adjusted by providing one or more adjustable plates within the coolant-cooled cold plate, the positioning of which may be adjusted based on the monitored variable.« less

Conformation-selective resonant photoelectron imaging from dipole-bound states of cold 3-hydroxyphenoxide

NASA Astrophysics Data System (ADS)

Zhu, Guo-Zhu; Huang, Dao-Ling; Wang, Lai-Sheng

2017-07-01

We report a photoelectron imaging and photodetachment study of cryogenically cooled 3-hydroxyphenoxide (3HOP) anions, m-HO(C6H4)O-. In a previous preliminary study, two conformations of the cold 3HOP anions with different dipole bound states were observed [D. L. Huang et al., J. Phys. Chem. Lett. 6, 2153 (2015)]. Five near-threshold vibrational resonances were revealed in the photodetachment spectrum from the dipole-bound excited states of the two conformations. Here, we report a more extensive investigation of the two conformers with observation of thirty above-threshold vibrational resonances in a wide spectral range between 18 850 and 19 920 cm-1 (˜1000 cm-1 above the detachment thresholds). By tuning the detachment laser to the vibrational resonances in the photodetachment spectrum, high-resolution conformation-selective resonant photoelectron images are obtained. Using information of the autodetachment channels and theoretical vibrational frequencies, we are able to assign the resonant peaks in the photodetachment spectrum: seventeen are assigned to vibrational levels of anti-3HOP, eight to syn-3HOP, and five to overlapping vibrational levels of both conformers. From the photodetachment spectrum and the conformation-selective resonant photoelectron spectra, we have obtained fourteen fundamental vibrational frequencies for the neutral syn- and anti-m-HO(C6H4)Oṡ radicals. The possibility to produce conformation-selected neutral beams using resonant photodetachment via dipole-bound excited states of anions is discussed.

Cold Atmospheric Plasma: methods of production and application in dentistry and oncology

PubMed Central

2013-01-01

Cold Atmospheric Plasma is an ionized gas that has recently been extensively studied by researchers as a possible therapy in dentistry and oncology. Several different gases can be used to produce Cold Atmospheric Plasma such as Helium, Argon, Nitrogen, Heliox, and air. There are many methods of production by which cold atmospheric plasma is created. Each unique method can be used in different biomedical areas. In dentistry, researchers have mostly investigated the antimicrobial effects produced by plasma as a means to remove dental biofilms and eradicate oral pathogens. It has been shown that reactive oxidative species, charged particles, and UV photons play the main role. Cold Atmospheric Plasma has also found a minor, but important role in tooth whitening and composite restoration. Furthermore, it has been demonstrated that Cold Atmospheric Plasma induces apoptosis, necrosis, cell detachment, and senescence by disrupting the S phase of cell replication in tumor cells. This unique finding opens up its potential therapy in oncology. PMID:24083477

ChemPreview: an augmented reality-based molecular interface.

PubMed

Zheng, Min; Waller, Mark P

2017-05-01

Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www.metavision.com/. ChemPreview can be used to interact with a protein in an intuitive way using natural hand gestures, thereby making it appealing to computational chemists or structural biologists. The ability to manipulate atoms in real world could eventually provide new and more efficient ways of extracting structural knowledge, or designing new molecules in silico. Copyright © 2017 Elsevier Inc. All rights reserved.

Chem Ed Compacts.

ERIC Educational Resources Information Center

Wolf, Walter A., Ed.

1978-01-01

Reported here are brief descriptions of a common grading and scaling formula for large multi-section courses, an ion exchange amino acid separation and thin layer chromatography identification experiment, a conservation of energy demonstration, a catalyst for synthesizing esters from fatty aids, and an inexpensive method for preparing platinum…

Scrubchem: Building Bioactivity Datasets from Pubchem Bioassay Data (SOT)

EPA Science Inventory

The PubChem Bioassay database is a non-curated public repository with data from 64 sources, including: ChEMBL, BindingDb, DrugBank, EPA Tox21, NIH Molecular Libraries Screening Program, and various other academic, government, and industrial contributors. Methods for extracting th...

Sources of Mercury Exposure for U.S. Seafood Consumers: Implications for Policy

EPA Science Inventory

Recent policies attempting to reduce adverse effects of methylmercury exposure from fish consumption in the U.S. have targeted reductions in anthropogenic emissions from U.S. sources. Methods: We use models that simulate global atmospheric chemistry (GEOS-Chem); the fate, transp...

DEVELOPMENT AND APPLICATION OF A NEW AIR POLLUTION MODELING SYSTEM--II. AEROSOL MODULE STRUCTURE AND DESIGN (R823186)

EPA Science Inventory

The methods used for simulating aerosol physical and chemical processes in a new air pollution modeling system are discussed and analyzed. Such processes include emissions, nucleation, coagulation, reversible chemistry, condensation, dissolution, evaporation, irreversible chem...

Semi-stochastic full configuration interaction quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Holmes, Adam; Petruzielo, Frank; Khadilkar, Mihir; Changlani, Hitesh; Nightingale, M. P.; Umrigar, C. J.

2012-02-01

In the recently proposed full configuration interaction quantum Monte Carlo (FCIQMC) [1,2], the ground state is projected out stochastically, using a population of walkers each of which represents a basis state in the Hilbert space spanned by Slater determinants. The infamous fermion sign problem manifests itself in the fact that walkers of either sign can be spawned on a given determinant. We propose an improvement on this method in the form of a hybrid stochastic/deterministic technique, which we expect will improve the efficiency of the algorithm by ameliorating the sign problem. We test the method on atoms and molecules, e.g., carbon, carbon dimer, N2 molecule, and stretched N2. [4pt] [1] Fermion Monte Carlo without fixed nodes: a Game of Life, death and annihilation in Slater Determinant space. George Booth, Alex Thom, Ali Alavi. J Chem Phys 131, 050106, (2009).[0pt] [2] Survival of the fittest: Accelerating convergence in full configuration-interaction quantum Monte Carlo. Deidre Cleland, George Booth, and Ali Alavi. J Chem Phys 132, 041103 (2010).

Chem-Braze Abradable Seal Attachment

DTIC Science & Technology

1980-05-01

bonding system for attaching sintered abradable seals such as FELTMETAL® to titanium -, steel- and nickel-base compressor blade tip-shrouds has been... blade tip-shrouds was developed. The improved Chem-Braze system incorporates glycerin as an inhibitor to prevent premature evaporation which prolongs...compressor blade tip-shrouds using the improved Chem-Braze system compared to attachment with gold-nickel braze. p. p. FORM . . yn

76 FR 35405 - Solid Urea From the Russian Federation: Preliminary Results of Antidumping Duty Administrative...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-17

... Federation (Russia). The review covers one producer/ exporter of the subject merchandise, MCC EuroChem (Euro... duty order on solid urea from Russia with respect to EuroChem on July 28, 2010. On August 31, 2010, in... To determine whether EuroChem's sales of solid urea from Russia were made in the United States at...

Outreach within the Bristol ChemLabS CETL (Centre for Excellence in Teaching and Learning)

ERIC Educational Resources Information Center

Shallcross, Dudley E.; Harrison, Tim G.; Obey, Tim M.; Croker, Steve J.; Norman, Nick C.

2013-01-01

This paper presents an overview of the Bristol ChemLabS project. In particular, it describes the development and impacts of the outreach project within Bristol ChemLabS, the UK's Centre for Excellence in Teaching and Learning (CETL) in practical chemistry, and its continuation beyond the funded project. The major elements of working with both…

ConfChem Conference on Select 2016 BCCE Presentations: Radical Awakenings--A New Teaching Paradigm Using Social Media

ERIC Educational Resources Information Center

Sorensen-Unruh, Clarissa

2017-01-01

This Communication summarizes one of the invited papers to the Select 2016 BCCE Presentations ACS CHED Committee on Computers in Chemical Education online ConfChem held from October 30 to November 22, 2016. The ConfChem paper (included within Supporting Information) focuses on the results of one instructor's incorporation of social media into her…

ChemOkey: A Game to Reinforce Nomenclature

ERIC Educational Resources Information Center

Kavak, Nusret

2012-01-01

Learning the symbolic language of chemistry is a difficult task that can be frustrating for students. This article introduces a game, ChemOkey, that can help students learn the names and symbols of common ions and their compounds in a fun environment. ChemOkey, a game similar to Rummikub, is played with a set of 106 plastic or wooden tiles. The…

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Long-range transport of Asian pollution to the northeast Pacific: Seasonal variations and transport pathways of carbon monoxide

NASA Astrophysics Data System (ADS)

Liang, Qing; Jaeglé, Lyatt; Jaffe, Daniel A.; Weiss-Penzias, Peter; Heckman, Anna; Snow, Julie A.

2004-12-01

Continuous CO measurements were obtained at Cheeka Peak Observatory (CPO, 48.3°N, 124.6°W, 480 m), a coastal site in Washington state, between 9 March 2001 and 31 May 2002. We analyze these observations as well as CO observations at ground sites throughout the North Pacific using the GEOS-CHEM global tropospheric chemistry model to examine the seasonal variations of Asian long-range transport. The model reproduces the observed CO levels, their seasonal cycle and day-to-day variability, with a 5-20 ppbv negative bias in winter/spring and 5-10 ppbv positive bias during summer. Asian influence on CO levels in the North Pacific troposphere maximizes during spring and minimizes during summer, ranging from 91 ppbv (44% of total CO) to 52 ppbv (39%) along the Asian Pacific Rim and from 44 ppbv (30%) to 24 ppbv (23%) at CPO. Maximum export of Asian pollution to the western Pacific occurs at 20°-50°N during spring throughout the tropospheric column, shifting to 30°-60°N during summer, mostly in the upper troposphere. The model captures five particularly strong transpacific transport events reaching CPO (four in spring, one in winter) resulting in 20-40 ppbv increases in observed CO levels. Episodic long-range transport of pollutants from Asia to the NE Pacific occurs throughout the year every 10, 15, and 30 days in the upper, middle, and lower troposphere, respectively. Lifting ahead of cold fronts followed by transport in midlatitude westerlies accounts for 78% of long-range transport events reaching the NE Pacific middle and upper troposphere. During summer, convective injection into the upper troposphere competes with frontal mechanisms in this export. Most events reaching the NE Pacific lower troposphere below 2 km altitude result from boundary layer outflow behind cold fronts (for spring) or ahead of cold fronts (for other seasons) followed by low-level transpacific transport.

Dynamic Kerr effect in a strong uniform AC electric field for interacting polar and polarizable molecules in the mean field approximation

NASA Astrophysics Data System (ADS)

Deshmukh, Snehal D.; Déjardin, Pierre-Michel; Kalmykov, Yuri P.

2017-09-01

Analytical formulas for the electric birefringence response of interacting polar and anisotropically polarizable molecules due to a uniform alternating electric field are derived using Berne's forced rotational diffusion model [B. J. Berne, J. Chem. Phys. 62, 1154 (1975)] in the nonlinear version described by Warchol and Vaughan [J. Chem. Phys. 71, 502 (1979)]. It is found for noninteracting molecules that the signal consists of a frequency-dependent DC component superimposed on an oscillatory part with a frequency twice that of the AC driving field. However, unlike noninteracting molecules, the AC part strongly deviates from its dilute counterpart. This suggests a possible way of motivating new experimental studies of intermolecular interactions involving electro-optical methods and complementary nonlinear dielectric relaxation experiments.

Comment on 'The diatomic dication CuZn{sup 2+} in the gas phase' [J. Chem. Phys. 135, 034306 (2011)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fiser, Jiri; Diez, Reinaldo Pis; Franzreb, Klaus

2013-02-21

In this Comment, the density functional theory (DFT) calculations carried out by Diez et al. [J. Chem. Phys. 135, 034306 (2011)] are revised within the framework of the coupled-cluster single double triple method. These more sophisticated calculations allow us to show that the {sup 2}{Sigma}{sup +} electronic ground state of CuZn{sup 2+}, characterized as the metastable ground state by DFT calculations, is a repulsive state instead. The {sup 2}{Delta} and {sup 2}{Pi} metastable states of CuZn{sup 2+}, on the other hand, should be responsible for the formation mechanism of the dication through the near-resonant electron transfer CuZn{sup +}+ Ar{sup +}{yields}more » CuZn{sup 2+}+ Ar reaction.« less

Transition-density-fragment interaction combined with transfer integral approach for excitation-energy transfer via charge-transfer states

NASA Astrophysics Data System (ADS)

Fujimoto, Kazuhiro J.

2012-07-01

A transition-density-fragment interaction (TDFI) combined with a transfer integral (TI) method is proposed. The TDFI method was previously developed for describing electronic Coulomb interaction, which was applied to excitation-energy transfer (EET) [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)] and exciton-coupled circular dichroism spectra [K. J. Fujimoto, J. Chem. Phys. 133, 124101 (2010)]. In the present study, the TDFI method is extended to the exchange interaction, and hence it is combined with the TI method for applying to the EET via charge-transfer (CT) states. In this scheme, the overlap correction is also taken into account. To check the TDFI-TI accuracy, several test calculations are performed to an ethylene dimer. As a result, the TDFI-TI method gives a much improved description of the electronic coupling, compared with the previous TDFI method. Based on the successful description of the electronic coupling, the decomposition analysis is also performed with the TDFI-TI method. The present analysis clearly shows a large contribution from the Coulomb interaction in most of the cases, and a significant influence of the CT states at the small separation. In addition, the exchange interaction is found to be small in this system. The present approach is useful for analyzing and understanding the mechanism of EET.

Determination of iodide with 1,3-dibromo-5,5-dimethylhydantoin (DBH) in comparison with the ICl-method. Analytical methods of pharmacopeias with DBH in respect to environmental and economical concern. Part 3.

PubMed

Hilp, M; Senjuk, S

2001-06-01

USP 1995 (The United States Pharmacopeia, 23rd Edit., (1995), potassium iodide p. 1265, sodium iodide p. 1424), PH. EUR. 1997 (European Pharmacopoeia, third ed., Council of Europe, Strasbourg, (1997), potassium iodide p. 1367, sodium iodide p. 1493) and JAP 1996 (The Japanes Pharmacopoeia, 13th ed. (1996), potassium iodide p. 578, sodium iodide p. 630) determine iodide with the ICl-method (J. Am. Chem. Soc. 25 (1903) 756-761; Z. Anorg. Chem. 36 (1903) 76-83; Fresenius Z. Anal. Chem. 106 (1936) 12-23; Arzneibuch-Kommentar, Wissenschaftliche Erläuterungen zum Europäischen Arzneibuch, Wissenschaftliche Verlagsgesellschaft mbH, Stuttgart, Govi-Verlag - Pharmazeutischer Verlag GmbH, Eschborn, 12th suppl. (1999), K10 p. 2), using chloroform, which is toxic and hazardous to environment. Without the application of chlorinated hydrocarbons USP 2000 (The United State Pharmacopeia, 24th ed. (2000), potassium iodide p. 1368, sodium iodide p. 1535) and Brit 1999 (British Pharmacopoeia London, (1999), Appendix VIII C, p. A162) titrate iodide with the redox indicator amaranth. A titration with potentiometric indication giving two end-points at the step of I(2) and [ICl(2)](-) is described. Due to the high concentration of hydrochloric acid required for the ICl-method, the determination with DBH (1,3-dibromo-5,5-dimethylhydantoin; 1,3-dibromo-5,5-dimethyl-2,4-imidazolidinedione) can be recommended and is performed easily. Similarly, the iodide content of gallamine triethiodide may be analyzed with DBH by application of a visual two-phase titration in water and ethyl acetate or with potentiometric indication in a mixture of 2-propanol and water. During the removal of the excess of DBH 4-bromo-triethylgallamine (2,2',2"-[1-bromo-benzene-2,3,4-triyltris(oxy)]N,N,N-triethylethanium) is formed.

Development of Ultrafast Indirect Flash Heating Methods for RDX

DTIC Science & Technology

2014-02-01

8 1 1. Introduction The mission of the Multiscale Response of Energetic Materials program is to establish...vinyl nitrate ) Films. J. Phys. Chem. A 2004, 108 (43), 9342–9347. 11 12. Gottfried, J. L.; de Lucia, F. C., Jr.; Piraino, S. M. Ultrafast Laser

A Field-Portable, Fiber-Optic Based Near-Infrared Spectrometer and its Applications to Fuels Analysis

DTIC Science & Technology

1991-05-28

R.E., Anal. Chem., 1991, 63, 114. 14. Ozubko, R.S., Clungston, D.M., Furimsky , E., Anal. Chem., 1981, 53, 183. 15. Hayes, P.C., Jr., Anderson, S.D...Adv. Study Inst. Sec. A, 1983, 46, 471. Ozubko, R.S., Clunqston, D.M., Furimsky , E., Anal. Chem., 1981, 53, 183. PC-MATLAB for 80386-based MS-DOS

Emission, transport, and radiative effects of mineral dust from the Taklimakan and Gobi deserts: comparison of measurements and model results

NASA Astrophysics Data System (ADS)

Chen, Siyu; Huang, Jianping; Kang, Litai; Wang, Hao; Ma, Xiaojun; He, Yongli; Yuan, Tiangang; Yang, Ben; Huang, Zhongwei; Zhang, Guolong

2017-02-01

The Weather Research and Forecasting Model with chemistry (WRF-Chem model) was used to investigate a typical dust storm event that occurred from 18 to 23 March 2010 and swept across almost all of China, Japan, and Korea. The spatial and temporal variations in dust aerosols and the meteorological conditions over East Asia were well reproduced by the WRF-Chem model. The simulation results were used to further investigate the details of processes related to dust emission, long-range transport, and radiative effects of dust aerosols over the Taklimakan Desert (TD) and Gobi Desert (GD). The results indicated that weather conditions, topography, and surface types in dust source regions may influence dust emission, uplift height, and transport at the regional scale. The GD was located in the warm zone in advance of the cold front in this case. Rapidly warming surface temperatures and cold air advection at high levels caused strong instability in the atmosphere, which strengthened the downward momentum transported from the middle and low troposphere and caused strong surface winds. Moreover, the GD is located in a relatively flat, high-altitude region influenced by the confluence of the northern and southern westerly jets. Therefore, the GD dust particles were easily lofted to 4 km and were the primary contributor to the dust concentration over East Asia. In the dust budget analysis, the dust emission flux over the TD was 27.2 ± 4.1 µg m-2 s-1, which was similar to that over the GD (29 ± 3.6 µg m-2 s-1). However, the transport contribution of the TD dust (up to 0.8 ton d-1) to the dust sink was much smaller than that of the GD dust (up to 3.7 ton d-1) because of the complex terrain and the prevailing wind in the TD. Notably, a small amount of the TD dust (PM2.5 dust concentration of approximately 8.7 µg m-3) was lofted to above 5 km and transported over greater distances under the influence of the westerly jets. Moreover, the direct radiative forcing induced by dust was estimated to be -3 and -7 W m-2 at the top of the atmosphere, -8 and -10 W m-2 at the surface, and +5 and +3 W m-2 in the atmosphere over the TD and GD, respectively. This study provides confidence for further understanding the climate effects of the GD dust.

Artichoke (Cynara cardunculus L. var. scolymus) waste as a natural source of carbonyl trapping and antiglycative agents.

PubMed

Maietta, Mariarosa; Colombo, Raffaella; Lavecchia, Roberto; Sorrenti, Milena; Zuorro, Antonio; Papetti, Adele

2017-10-01

The role of polyphenolic compounds extractable from artichoke solid wastes in the formation of advanced glycation end products (AGEs) was studied. Outer bracts and stems were extracted using different water-ethanol mixtures and HPLC-DAD analyses indicated aqueous and hydro-alcoholic 20:80 stem extracts as the richest in polyphenols. The samples were characterized in their phenolic composition (using mass spectrometry) and antioxidant capacity. Antiglycative capacity was evaluated by in vitro BSA-sugars (glucose, fructose, and ribose) and BSA-methylglyoxal (MGO) tests, formation of Amadori products assay, direct glyoxal (GO) and MGO trapping capacity. Results indicated both extracts as effective inhibitors of fructosamine formation and antiglycative agents. In particular, aqueous extract showed the best activity in the systems containing glucose and fructose, differently from ethanolic extract, that was demonstrated able to better inhibit AGEs formation when ribose or MGO act as precursors. Ethanolic extract was also shown to be able to trap MGO and GO, with efficiency increasing after 24hours of incubation time. These activities are partially correlated with the antioxidant effect of the extract, as demonstrated by the scavenger capacity against ABTS cation and DPPH stable radicals; this relationship is evident when the model system, containing protein incubated with ribose or MGO, is considered. The different activities of the tested extracts could probably be ascribed to the different composition in chlorogenic acids (CQAs), being aqueous extract richer in 1-CQA, 3-CQA, and 1,3-di-CQA, and ethanolic extract in 5-CQA, caffeic acid, 1,5-di-CQA. These findings support further investigations to study the stability of the different CQAs in simil-physiological conditions and the feasibility of artichoke waste as antiglycative agents in food or pharmacological preparations. 5-caffeoylquinic acid (PubChem CID 5280633); 3-caffeoylquinic acid (PubChem CID 1794427); 1-caffeoylquinic acid (PubChem CID 10155076); 1,3-di-caffeoylquinic acid (PubChem CID 24720973); 1,5 - di-caffeoylquinic acid (PubChem CID 122685); caffeic acid (PubChem CID 689043); apigenin-7-glucuronide (PubChem CID 5319484); methylglyoxal PubChem CID (880); aminoguanidine hydrochloride (PubChem CID 2734687). Copyright © 2017 Elsevier Ltd. All rights reserved.

The Another Assimilation System for WRF-Chem (AAS4WRF): a new mass-conserving emissions pre-processor for WRF-Chem regional modelling

NASA Astrophysics Data System (ADS)

Vara Vela, A. L.; Muñoz, A.; Lomas, A., Sr.; González, C. M.; Calderon, M. G.; Andrade, M. D. F.

2017-12-01

The Weather Research and Forecasting with Chemistry (WRF-Chem) community model have been widely used for the study of pollutants transport, formation of secondary pollutants, as well as for the assessment of air quality policies implementation. A key factor to improve the WRF-Chem air quality simulations over urban areas is the representation of anthropogenic emission sources. There are several tools that are available to assist users in creating their own emissions based on global emissions information (e.g. anthro_emiss, prep_chem_src); however, there is no single tool that will construct local emissions input datasets for any particular domain at this time. Because the official emissions pre-processor (emiss_v03) is designed to work with domains located over North America, this work presents the Another Assimilation System for WRF-Chem (AAS4WRF), a ncl based mass-conserving emissions pre-processor designed to create WRF-Chem ready emissions files from local inventories on a lat/lon projection. AAS4WRF is appropriate to scale emission rates from both surface and elevated sources, providing the users an alternative way to assimilate their emissions to WRF-Chem. Since it was successfully tested for the first time for the city of Lima, Peru in 2014 (managed by SENAMHI, the National Weather Service of the country), several studies on air quality modelling have applied this utility to convert their emissions to those required for WRF-Chem. Two case studies performed in the metropolitan areas of Sao Paulo and Manizales in Brazil and Colombia, respectively, are here presented in order to analyse the influence of using local or global emission inventories in the representation of regulated air pollutants such as O3 and PM2.5. Although AAS4WRF works with local emissions information at the moment, further work is being conducted to make it compatible with global/regional emissions data file format. The tool is freely available upon request to the corresponding author.

Prospective randomized comparison of cold snare polypectomy and conventional polypectomy for small colorectal polyps.

PubMed

Ichise, Yasuyuki; Horiuchi, Akira; Nakayama, Yoshiko; Tanaka, Naoki

2011-01-01

The ideal method to remove small colorectal polyps is unknown. We compared removal by colon snare transection without electrocautery (cold snare polypectomy) with conventional electrocautery snare polypectomy (hot polypectomy) in terms of procedure duration, difficulty in retrieving polyps, bleeding, and post-polypectomy symptoms. Patients with colorectal polyps up to 8 mm in diameter were randomized to polypectomy by cold snare technique (cold group) or conventional polypectomy (conventional group). The principal outcome measures were abdominal symptoms within 2 weeks after polypectomy. Secondary outcome measures were the rates of retrieval of colorectal polyps and bleeding. Eighty patients were randomized: cold group, n = 40 (101 polyps) and conventional group, n = 40 (104 polyps). The patients' demographic characteristics and the number and size of polyps removed were similar between the two techniques. Procedure time was significantly shorter with cold polypectomy vs. conventional polypectomy (18 vs. 25 min, p < 0.0001). Complete polyp retrieval rates were identical [96% (97/101) vs. 96% (100/104)]. No bleeding requiring hemostasis occurred in either group. Abdominal symptoms shortly after polypectomy were more common with conventional polypectomy (i.e. 20%; 8/40) than with cold polypectomy (i.e. 2.5%; 1/40; p = 0.029). Cold polypectomy was superior to conventional polypectomy in terms of procedure time and post-polypectomy abdominal symptoms. The two methods were otherwise essentially identical in terms of bleeding risk and complete polyp retrieval. Cold polypectomy is therefore the preferred method for removal of small colorectal polyps. Copyright © 2011 S. Karger AG, Basel.

Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2)

DOE PAGES

Tilmes, S.; Lamarque, J. -F.; Emmons, L. K.; ...

2015-01-01

The Community Atmosphere Model (CAM), version 5, is now coupled to extensive tropospheric and stratospheric chemistry, called CAM5-chem, and is available in addition to CAM4-chem in the Community Earth System Model (CESM) version 1.2. The main focus of this paper is to compare the performance of configurations with internally derived "free running" (FR) meteorology and "specified dynamics" (SD) against observations from surface, aircraft, and satellite, as well as understand the origin of the identified differences. We focus on the representation of aerosols and chemistry. All model configurations reproduce tropospheric ozone for most regions based on in situ and satellite observations.more » However, shortcomings exist in the representation of ozone precursors and aerosols. Tropospheric ozone in all model configurations agrees for the most part with ozonesondes and satellite observations in the tropics and the Northern Hemisphere within the variability of the observations. Southern hemispheric tropospheric ozone is consistently underestimated by up to 25%. Differences in convection and stratosphere to troposphere exchange processes are mostly responsible for differences in ozone in the different model configurations. Carbon monoxide (CO) and other volatile organic compounds are largely underestimated in Northern Hemisphere mid-latitudes based on satellite and aircraft observations. Nitrogen oxides (NO x) are biased low in the free tropical troposphere, whereas peroxyacetyl nitrate (PAN) is overestimated in particular in high northern latitudes. The present-day methane lifetime estimates are compared among the different model configurations. These range between 7.8 years in the SD configuration of CAM5-chem and 8.8 years in the FR configuration of CAM4-chem and are therefore underestimated compared to observational estimations. We find that differences in tropospheric aerosol surface area between CAM4 and CAM5 play an important role in controlling the burden of the tropical tropospheric hydroxyl radical (OH), which causes differences in tropical methane lifetime of about half a year between CAM4-chem and CAM5-chem. In addition, different distributions of NO x from lightning explain about half of the difference between SD and FR model versions in both CAM4-chem and CAM5-chem. Remaining differences in the tropical OH burden are due to enhanced tropical ozone burden in SD configurations compared to the FR versions, which are not only caused by differences in chemical production or loss but also by transport and mixing. For future studies, we recommend the use of CAM5-chem configurations, due to improved aerosol description and inclusion of aerosol–cloud interactions. However, smaller tropospheric surface area density in the current version of CAM5-chem compared to CAM4-chem results in larger oxidizing capacity in the troposphere and therefore a shorter methane lifetime.« less

Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tilmes, S.; Lamarque, J. -F.; Emmons, L. K.

The Community Atmosphere Model (CAM), version 5, is now coupled to extensive tropospheric and stratospheric chemistry, called CAM5-chem, and is available in addition to CAM4-chem in the Community Earth System Model (CESM) version 1.2. The main focus of this paper is to compare the performance of configurations with internally derived "free running" (FR) meteorology and "specified dynamics" (SD) against observations from surface, aircraft, and satellite, as well as understand the origin of the identified differences. We focus on the representation of aerosols and chemistry. All model configurations reproduce tropospheric ozone for most regions based on in situ and satellite observations.more » However, shortcomings exist in the representation of ozone precursors and aerosols. Tropospheric ozone in all model configurations agrees for the most part with ozonesondes and satellite observations in the tropics and the Northern Hemisphere within the variability of the observations. Southern hemispheric tropospheric ozone is consistently underestimated by up to 25%. Differences in convection and stratosphere to troposphere exchange processes are mostly responsible for differences in ozone in the different model configurations. Carbon monoxide (CO) and other volatile organic compounds are largely underestimated in Northern Hemisphere mid-latitudes based on satellite and aircraft observations. Nitrogen oxides (NO x) are biased low in the free tropical troposphere, whereas peroxyacetyl nitrate (PAN) is overestimated in particular in high northern latitudes. The present-day methane lifetime estimates are compared among the different model configurations. These range between 7.8 years in the SD configuration of CAM5-chem and 8.8 years in the FR configuration of CAM4-chem and are therefore underestimated compared to observational estimations. We find that differences in tropospheric aerosol surface area between CAM4 and CAM5 play an important role in controlling the burden of the tropical tropospheric hydroxyl radical (OH), which causes differences in tropical methane lifetime of about half a year between CAM4-chem and CAM5-chem. In addition, different distributions of NO x from lightning explain about half of the difference between SD and FR model versions in both CAM4-chem and CAM5-chem. Remaining differences in the tropical OH burden are due to enhanced tropical ozone burden in SD configurations compared to the FR versions, which are not only caused by differences in chemical production or loss but also by transport and mixing. For future studies, we recommend the use of CAM5-chem configurations, due to improved aerosol description and inclusion of aerosol–cloud interactions. However, smaller tropospheric surface area density in the current version of CAM5-chem compared to CAM4-chem results in larger oxidizing capacity in the troposphere and therefore a shorter methane lifetime.« less

AEGIS Automated Targeting for the MSL ChemCam Instrument

NASA Astrophysics Data System (ADS)

Estlin, T.; Anderson, R. C.; Blaney, D. L.; Bornstein, B.; Burl, M. C.; Castano, R.; Gaines, D.; Judd, M.; Thompson, D. R.; Wiens, R. C.

2013-12-01

The Autonomous Exploration for Gathering Increased Science (AEGIS) system enables automated science data collection by a planetary rover. AEGIS has been in use on the Mars Exploration Rover (MER) mission Opportunity rover since 2010 to provide onboard targeting of the MER Panoramic Camera based on scientist-specified objectives. AEGIS is now being applied for use with the Mars Science Laboratory (MSL) mission ChemCam spectrometer. ChemCam uses a Laser Induced Breakdown Spectrometer (LIBS) to analyze the elemental composition of rocks and soil from up to seven meters away. ChemCam's tightly-focused laser beam (350-550 um) enables targeting of very fine-scale terrain features. AEGIS is being applied in two ways to help ChemCam collect valuable science data. The first application is to enable automated targeting of ChemCam during or after or in the middle of long drives. The majority of ChemCam measurements are collected by allowing the science team to select specific targets in rover images. However this requires the rover to stay in the same area while images are downlinked, analyzed for targets, and new commands uplinked. The only data that can be acquired without this communication cycle is via blind targeting, where measurements are often of soil patches vs. instead of more valuable targets such as rocks with specific properties. AEGIS is being applied to automatically analyze images onboard and select targets for ChemCam analysis. This approach allows the rover to autonomously select and sequence targeted measurements in an opportunistic fashion at different points along the rover's drive path. Rock targets can be prioritized for measurement based on various geologically relevant features, including size, shape and albedo. A second application is to enable intelligent pointing refinement of ChemCam when acquiring data of small targets, such as veins or concretions that are only a few millimeters wide. Due to backlash and other pointing challenges, it can often require several downlink cycles for LIBS measurements to be acquired on small targets. Often targets must first be imaged using the high resolution ChemCam Remote Micro Imager (RMI) and then ground analysis performed to enable a fine-tuned pointing correction on the next commanding cycle. AEGIS is being applied to analyze RMI images onboard and automatically determine the pointing refinement necessary to acquire LIBS data on small targets. This significantly decreases the amount of time and resources required to acquire ChemCam data on such targets. Work is currently in progress to adapt AEGIS algorithm for these applications and integrate the system with MSL flight software. Once integration and testing is complete, AEGIS will be uploaded to the spacecraft for operational use.

The Effect of Time, Roasting Temperature, and Grind Size on Caffeine and Chlorogenic Acid Concentrations in Cold Brew Coffee.

PubMed

Fuller, Megan; Rao, Niny Z

2017-12-21

The extraction kinetics and equilibrium concentrations of caffeine and 3-chlorogenic acid (3-CGA) in cold brew coffee were investigated by brewing four coffee samples (dark roast/medium grind, dark roast/coarse grind, medium roast/medium grind, medium roast/coarse grind) using cold and hot methods. 3-CGA and caffeine were found at higher concentrations in cold brew coffee made with medium roast coffees, rather than dark roast. The grind size did not impact 3-CGA and caffeine concentrations of cold brew samples significantly, indicating that the rate determining step in extraction for these compounds did not depend on surface area. Caffeine concentrations in cold brew coarse grind samples were substantially higher than their hot brew counterparts. 3-CGA concentrations and pH were comparable between cold and hot brews. This work suggests that the difference in acidity of cold brew coffee is likely not due to 3-CGA or caffeine concentrations considering that most acids in coffee are highly soluble and extract quickly. It was determined that caffeine and 3-CGA concentrations reached equilibrium according to first order kinetics between 6 and 7 hours in all cold brew samples instead of 10 to 24 hours outlined in typical cold brew methods.

ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

NASA Technical Reports Server (NTRS)

Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

2005-01-01

ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. [1]. Here we present the science objectives for the ChemCam instrument package.

ChemTS: an efficient python library for de novo molecular generation.

PubMed

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

ChemTS: an efficient python library for de novo molecular generation

NASA Astrophysics Data System (ADS)

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-12-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

ChemCam Science Objectives for the Mars Science Laboratory (MSL) Rover

NASA Technical Reports Server (NTRS)

Wiens, R.; Maurice, S.; Bridges, N.; Clark, B.; Cremers, D.; Herkenhoff, K.; Kirkland, L.; Mangold, N.; Manhes, G.; Mauchien, P.

2005-01-01

ChemCam consists of two remote sensing instruments. One, a Laser-Induced Breakdown Spectroscopy (LIBS) instrument provides rapid elemental composition data on rocks and soils within 13 m of the rover. By using laser pulses, it can remove dust or profile through weathering layers remotely. The other instrument, the Remote Micro-Imager (RMI), provides the highest resolution images between 2 m and infinity. At approximately 80 Rad field of view, its resolution exceeds that of MER Pancam by at least a factor of four. The ChemCam instruments are described in a companion paper by Maurice et al. Here we present the science objectives for the ChemCam instrument package.

Full-dimensional global potential energy surfaces describing abstraction and exchange for the H + H{sub 2}S reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Dandan; Li, Jun, E-mail: jli15@cqu.edu.edu

2016-07-07

For the H + H{sub 2}S system, ∼34 000 data points are sampled over a large configuration space including both abstraction and exchange channels, and calculated at the level of explicitly correlated unrestricted coupled cluster method with singles, doubles, and perturbative triples excitations with the augmented correlation-consistent polarized triple zeta basis set (UCCSD(T)-F12a/aug-cc-pVTZ). The data set was fit using the newly proposed permutation invariant polynomial-neural network (PIP-NN) method with three different vectors as the input: two redundant sets of PIPs, one with the maximum order four (PES-I) and one with the maximum order three (PES-II), and nine non-redundant PIPs (PES-III). Allmore » these PESs show small fitting errors and essentially the same performance in representing the title system. Various kinetics and dynamical properties are calculated using the tunneling corrected transition state theory and quasi-classical trajectory, and compared with available experimental results. At a collision energy of 10 kcal/mol, both the H{sub 2} and SH products are found to be internally cold, with ∼20% of H{sub 2} at its first vibrational excited state, while SH is essentially a spectator. The angular distributions of the products are mainly in backward with considerable contributions from sideway direction. In addition, analytical partial derivatives of any PIP-NN PES with respect to the coordinates of atoms are derived by making use of the monomial symmetrization algorithm [Z. Xie and J. M. Bowman, J. Chem. Theory Comput. 6, 26–34 (2010)]. It can not only accelerate the evaluation of the derivatives, but also improve the energy convergence significantly.« less

Syngas generation from n-butane with an integrated MEMS assembly for gas processing in micro-solid oxide fuel cell systems.

PubMed

Bieberle-Hütter, A; Santis-Alvarez, A J; Jiang, B; Heeb, P; Maeder, T; Nabavi, M; Poulikakos, D; Niedermann, P; Dommann, A; Muralt, P; Bernard, A; Gauckler, L J

2012-11-21

An integrated system of a microreformer and a carrier allowing for syngas generation from liquefied petroleum gas (LPG) for micro-SOFC application is discussed. The microreformer with an overall size of 12.7 mm × 12.7 mm × 1.9 mm is fabricated with micro-electro-mechanical system (MEMS) technologies. As a catalyst, a special foam-like material made from ceria-zirconia nanoparticles doped with rhodium is used to fill the reformer cavity of 58.5 mm(3). The microreformer is fixed onto a microfabricated structure with built-in fluidic channels and integrated heaters, the so-called functional carrier. It allows for thermal decoupling of the cold inlet gas and the hot fuel processing zone. Two methods for heating the microreformer are compared in this study: a) heating in an external furnace and b) heating with the two built-in heaters on the functional carrier. With both methods, high butane conversion rates of 74%-85% are obtained at around 550 °C. In addition, high hydrogen and carbon monoxide yields and selectivities are achieved. The results confirm those from classical lab reformers built without MEMS technology (N. Hotz et al., Chem. Eng. Sci., 2008, 63, 5193; N. Hotz et al., Appl. Catal., B, 2007, 73, 336). The material combinations and processing techniques enable syngas production with the present MEMS based microreformer with high performance for temperatures up to 700 °C. The functional carrier is the basis for a new platform, which can integrate the micro-SOFC membranes and the gas processing unit as subsystem of an entire micro-SOFC system.

Method for achieving sustained anisotropic crystal growth on the surface of a silicon melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mackintosh, Brian H.; Kellerman, Peter L.; Sun, Dawei

An apparatus for growing a crystalline sheet from a melt includes a cold block assembly. The cold block assembly may include a cold block and a shield surrounding the cold block and being at an elevated temperature with respect to that of the cold block, the shield defining an opening disposed along a surface of the cold block proximate a melt surface that defines a cold area comprising a width along a first direction of the cold block, the cold area operable to provide localized cooling of a region of the melt surface proximate the cold block. The apparatus maymore » further include a crystal puller arranged to draw a crystalline seed in a direction perpendicular to the first direction when the cold block assembly is disposed proximate the melt surface.« less

Identification and Optimization of Short Helical Peptides with Novel Reactive Functionality as Catalysts for Acyl Transfer by Reactive Tagging

DTIC Science & Technology

2014-01-21

269–278. 4 M. H. Fonseca and B. List, Curr. Opin. Chem. Biol., 2004, 8, 319–326. 5 P. Krattiger, C. McCarthy, A. Pfaltz and H. Wennemers, Angew. Chem...Benedetti, Trends Biochem. Sci., 1991, 16, 350–353. 33 C. Toniolo, A. Polese, F. Formaggio, M. Crisma and J. Kamphuis, J. Am. Chem. Soc., 1996 , 118, 2744

Effects on Student Achievement in General Chemistry following Participation in an Online Preparatory Course: ChemPrep, a Voluntary, Self-Paced, Online Introduction to Chemistry

ERIC Educational Resources Information Center

Botch, Beatrice; Day, Roberta; Vining, William; Stewart, Barbara; Rath, Kenneth; Peterfreund, Alan; Hart, David

2007-01-01

ChemPrep was developed to be a stand-alone preparatory short-course to help students succeed in general chemistry. It is Web-based and delivered using the OWL system. Students reported that the ChemPrep materials (short information pages, parameterized questions with detailed feedback, tutorials, and answers to questions through the OWL message…

Chem-2-Chem: A One-to-One Supportive Learning Environment for Chemistry

NASA Astrophysics Data System (ADS)

Báez-Galib, Rosita; Colón-Cruz, Héctor; Resto, Wilfredo; Rubin, Michael R.

2005-12-01

The Chem-2-Chem (C2C) tutoring mentoring program was developed at the University of Puerto Rico at Cayey, an undergraduate institution serving Hispanic students, to increase student retention and help students achieve successful general chemistry course outcomes. This program provides a supportive learning environment designed to address students' academic and emotional needs in a holistic way. Advanced chemistry students offered peer-led, personalized, and individualized learning experiences through tutoring and mentoring to approximately 21% of students enrolled in the general chemistry course. Final grades from official class lists of all general chemistry course sections were analyzed using Student's t -test, paired t -test, and χ 2 analysis. Results during the seven semesters studied show an increase of 29% in successful course outcomes defined as final letter grades of A, B, and C obtained by Chem-2-Chem participants. For each final grade, highly statistically significant differences between participants and nonparticipants were detected. There were also statistically significant differences between successful course outcomes obtained by participants and nonparticipants for each of the semesters studied. This research supports recent trends in chemical education to provide a social context for learning experiences. This peer-led learning strategy can serve as an effective model to achieve excellence in science courses at a wide range of educational institutions.

Chem I Supplement: Nuclear Synthesis and Identification of New Elements.

ERIC Educational Resources Information Center

Seaborg, Glenn T.

1985-01-01

As background material for a paper on the transuranium elements (SE 537 837), this article reviews: (1) several descriptive terms; (2) nuclear reactions; (3) radioactive decay modes; (4) chemical background; and (5) experimental methods used in this field of research and more broadly in nuclear chemistry. (Author/JN)

Chem I Supplement. Chemistry Related to Isolation of High-Level Nuclear Waste.

ERIC Educational Resources Information Center

Hoffman, Darleane C.; Choppin, Gregory R.

1986-01-01

Discusses some of the problems associated with the safe disposal of high-level nuclear wastes. Describes several waste disposal plans developed by various nations. Outlines the multiple-barrier concept of isolation in deep geological questions associated with the implementation of such a method. (TW)

Population Viability Analysis of the Endangered Shortnose Sturgeon

DTIC Science & Technology

2011-12-01

Processing techniques for caviar and their effects on product composition. International Review of Hydrobiology 87(5-6):645-650. Homer CCH, Yang L...Inc. 1998). We measured NO3 concentration using cadmium reduction of nitrate, followed by azo- dye colorimetry (QuickChem method 31-107-04-1-C

Python Spectral Analysis Tool (PySAT) for Preprocessing, Multivariate Analysis, and Machine Learning with Point Spectra

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Finch, N.; Clegg, S.; Graff, T.; Morris, R. V.; Laura, J.

2017-06-01

We present a Python-based library and graphical interface for the analysis of point spectra. The tool is being developed with a focus on methods used for ChemCam data, but is flexible enough to handle spectra from other instruments.

Symmetry of extremely floppy molecules: Molecular states beyond rotation-vibration separation

NASA Astrophysics Data System (ADS)

Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per

2015-10-01

Traditionally, molecules are theoretically described as near-static structures rotating in space. Vibrational motion causing small structural deformations induces a perturbative treatment of the rotation-vibration interaction, which fails in highly fluxional molecules, where all vibrational motions have amplitudes comparable in size to the linear dimensions of the molecule. An example is protonated methane (CH 5+ ) [P. Kumar and D. Marx, Phys. Chem. Chem. Phys. 8, 573 (2006); Z. Jin et al., J. Phys. Chem. A 110, 1569 (2006); and A. S. Petit et al., J. Phys. Chem. A 118, 7206 (2014)]. For these molecules, customary theory fails to simulate reliably even the low-energy spectrum [T. Oka, Science 347, 1313-1314 (2015) and O. Asvany et al., Science 347, 1346-1349 (2015)]. Within the traditional view of rotation and vibration being near-separable, rotational and vibrational wavefunctions can be symmetry classified separately in the molecular symmetry (MS) group [P. Bunker and P. Jensen, Molecular Symmetry and Spectroscopy, NRC Monograph Publishing Program (NRC Research Press, 2006)]. In this article, we discuss a fundamental group theoretical approach to the problem of determining the symmetries of molecular rotation-vibration states. We will show that all MS groups discussed so far are isomorphic to subgroups of the special orthogonal group in three dimensions SO(3). This leads to a group theoretical foundation of the technique of equivalent rotations [H. Longuet-Higgins, Mol. Phys. 6, 445 (1963)]. The group G240 (the MS group of protonated methane) represents, to the best of our knowledge, the first example of a MS group which is not isomorphic to a subgroup of SO(3) (nor of O(3) or of SU(2)). Because of this, a separate symmetry classification of vibrational and rotational wavefunctions becomes impossible in this MS group, consistent with the fact that a decoupling of vibrational and rotational motion is impossible. We discuss here the consequences of this. In conclusion, we show that the prototypical, extremely floppy molecule CH 5+ represents a new class of molecules, where customary group theoretical methods for determining selection rules and spectral assignments fail so that new methods have to be developed.

Rydberg States of Alkali Metal Atoms on Superfluid Helium Droplets - Theoretical Considerations

NASA Astrophysics Data System (ADS)

Pototschnig, Johann V.; Lackner, Florian; Hauser, Andreas W.; Ernst, Wolfgang E.

2017-06-01

The bound states of electrons on the surface of superfluid helium have been a research topic for several decades. One of the first systems treated was an electron bound to an ionized helium cluster. Here, a similar system is considered, which consists of a helium droplet with an ionized dopant inside and an orbiting electron on the outside. In our theoretical investigation we select alkali metal atoms (AK) as central ions, stimulated by recent experimental studies of Rydberg states for Na, Rb, and Cs attached to superfluid helium nanodroplets. Experimental spectra , obtained by electronic excitation and subsequent ionization, showed blueshifts for low lying electronic states and redshifts for Rydberg states. In our theoretical treatment the diatomic AK^+-He potential energy curves are first computed with ab initio methods. These potentials are then used to calculate the solvation energy of the ion in a helium droplet as a function of the number of atoms. Additional potential terms, derived from the obtained helium density distribution, are added to the undisturbed atomic pseudopotential in order to simulate a 'modified' potential felt by the outermost electron. This allows us to compute a new set of eigenstates and eigenenergies, which we compare to the experimentally observed energy shifts for highly excited alkali metal atoms on helium nanodroplets. A. Golov and S. Sekatskii, Physica B, 1994, 194, 555-556 E. Loginov, C. Callegari, F. Ancilotto, and M. Drabbels, J. Phys. Chem. A, 2011, 115, 6779-6788 F. Lackner, G. Krois, M. Koch, and W. E. Ernst, J. Phys. Chem. Lett., 2012, 3, 1404-1408 F. Lackner, G. Krois, M. Theisen, M. Koch, and W. E. Ernst, Phys. Chem. Chem. Phys., 2011, 13, 18781-18788

Photodissociation of OCS: deviations between theory and experiment, and the importance of higher order correlation effects.

PubMed

Schmidt, J A; Olsen, J M H

2014-11-14

The photodissociation of carbonyl sulfide (OCS) was investigated theoretically in a series of studies by Schmidt and co-workers. Initial studies [J. A. Schmidt, M. S. Johnson, G. C. McBane, and R. Schinke, J. Chem. Phys. 136, 131101 (2012); J. A. Schmidt, M. S. Johnson, G. C. McBane, and R. Schinke, J. Chem. Phys. 137, 054313 (2012)] found photodissociation in the first UV-band to occur mainly by excitation of the 2(1)A' (A) excited state. However, in a later study [G. C. McBane, J. A. Schmidt, M. S. Johnson, and R. Schinke, J. Chem. Phys. 138, 094314 (2013)] it was found that a significant fraction of photodissociation must occur by excitation of 1(1)A″ (B) excited state to explain the product angular distribution. The branching between excitation of the A and B excited states is determined by the magnitude of the transition dipole moment vectors in the Franck-Condon region. This study examines the sensitivity of these quantities to changes in the employed electronic structure methodology. This study benchmarks the methodology employed in previous studies against highly correlated electronic structure methods (CC3 and MRAQCC) and provide evidence in support of the picture of the OCS photodissociation process presented in [G. C. McBane, J. A. Schmidt, M. S. Johnson, and R. Schinke, J. Chem. Phys. 138, 094314 (2013)] showing that excitation of A and B electronic states both contribute significantly to the first UV absorption band of OCS. In addition, this study presents evidence in support of the assertion that the A state potential energy surface employed in previous studies underestimates the energy at highly bent geometries (γ ∼ 70°) leading to overestimated rotational energy in the product CO.

Validating the WRF-Chem model for wind energy applications using High Resolution Doppler Lidar data from a Utah 2012 field campaign

NASA Astrophysics Data System (ADS)

Mitchell, M. J.; Pichugina, Y. L.; Banta, R. M.

2015-12-01

Models are important tools for assessing potential of wind energy sites, but the accuracy of these projections has not been properly validated. In this study, High Resolution Doppler Lidar (HRDL) data obtained with high temporal and spatial resolution at heights of modern turbine rotors were compared to output from the WRF-chem model in order to help improve the performance of the model in producing accurate wind forecasts for the industry. HRDL data were collected from January 23-March 1, 2012 during the Uintah Basin Winter Ozone Study (UBWOS) field campaign. A model validation method was based on the qualitative comparison of the wind field images, time-series analysis and statistical analysis of the observed and modeled wind speed and direction, both for case studies and for the whole experiment. To compare the WRF-chem model output to the HRDL observations, the model heights and forecast times were interpolated to match the observed times and heights. Then, time-height cross-sections of the HRDL and WRF-Chem wind speed and directions were plotted to select case studies. Cross-sections of the differences between the observed and forecasted wind speed and directions were also plotted to visually analyze the model performance in different wind flow conditions. A statistical analysis includes the calculation of vertical profiles and time series of bias, correlation coefficient, root mean squared error, and coefficient of determination between two datasets. The results from this analysis reveals where and when the model typically struggles in forecasting winds at heights of modern turbine rotors so that in the future the model can be improved for the industry.

Can ferric-superoxide act as a potential oxidant in P450(cam)? QM/MM investigation of hydroxylation, epoxidation, and sulfoxidation.

PubMed

Lai, Wenzhen; Shaik, Sason

2011-04-13

In view of recent reports of high reactivity of ferric-superoxide species in heme and nonheme systems (Morokuma et al. J. Am. Chem. Soc. 2010, 132, 11993-12005; Que et al. Inorg. Chem. 2010, 49, 3618-3628; Nam et al. J. Am. Chem. Soc. 2010, 132, 5958-5959; J. Am. Chem. Soc. 2010, 132, 10668-10670), we use herein combined quantum mechanics/molecular mechanics (QM/MM) methods to explore the potential reactivity of P450(cam) ferric-superoxide toward hydroxylation, epoxidation, and sulfoxidation. The calculations demonstrate that P450 ferric-superoxide is a sluggish oxidant compared with the high-valent oxoiron porphyrin cation-radical species. As such, unlike heme enzymes with a histidine axial ligand, the P450 superoxo species does not function as an oxidant in P450(cam). The origin of this different behavior of the superoxo species of P450 vis-à-vis other heme enzymes like tryptophan 2, 3-dioxygenase (TDO) is traced to the ability of the latter superoxo species to make a stronger FeOO-X (X = H,C) bond and to stabilize the corresponding bond-activation transition states by resonance with charge-transfer configurations. By contrast, the negatively charged thiolate ligand in the P450 superoxo species minimizes the mixing of charge transfer configurations in the transition state and raises the reaction barrier. However, as we demonstrate, an external electric field oriented along the Fe-O axis with a direction pointing from Fe toward O will quench Cpd I formation by slowing the reduction of ferric-superoxide and will simultaneously lower the barriers for oxidation by the latter species, thereby enabling observation of superoxo chemistry in P450. Other options for nascent superoxo reactivity in P450 are discussed. © 2011 American Chemical Society

Pyrosequencing®-Based Identification of Low-Frequency Mutations Enriched Through Enhanced-ice-COLD-PCR.

PubMed

How-Kit, Alexandre; Tost, Jörg

2015-01-01

A number of molecular diagnostic assays have been developed in the last years for mutation detection. Although these methods have become increasingly sensitive, most of them are incompatible with a sequencing-based readout and require prior knowledge of the mutation present in the sample. Consequently, coamplification at low denaturation (COLD)-PCR-based methods have been developed and combine a high analytical sensitivity due to mutation enrichment in the sample with the identification of known or unknown mutations by downstream sequencing experiments. Among these methods, the recently developed Enhanced-ice-COLD-PCR appeared as the most powerful method as it outperformed the other COLD-PCR-based methods in terms of the mutation enrichment and due to the simplicity of the experimental setup of the assay. Indeed, E-ice-COLD-PCR is very versatile as it can be used on all types of PCR platforms and is applicable to different types of samples including fresh frozen, FFPE, and plasma samples. The technique relies on the incorporation of an LNA containing blocker probe in the PCR reaction followed by selective heteroduplex denaturation enabling amplification of the mutant allele while amplification of the wild-type allele is prevented. Combined with Pyrosequencing(®), which is a very quantitative high-resolution sequencing technology, E-ice-COLD-PCR can detect and identify mutations with a limit of detection down to 0.01 %.

ChemCam passive reflectance spectroscopy of surface materials at the Curiosity landing site, Mars

NASA Astrophysics Data System (ADS)

Johnson, Jeffrey R.; Bell, J. F.; Bender, S.; Blaney, D.; Cloutis, E.; DeFlores, L.; Ehlmann, B.; Gasnault, O.; Gondet, B.; Kinch, K.; Lemmon, M.; Le Mouélic, S.; Maurice, S.; Rice, M.; Wiens, R. C.

2015-03-01

The spectrometers on the Mars Science Laboratory (MSL) ChemCam instrument were used in passive mode to record visible/near-infrared (400-840 nm) radiance from the martian surface. Using the onboard ChemCam calibration targets' housing as a reflectance standard, we developed methods to collect, calibrate, and reduce radiance observations to relative reflectance. Such measurements accurately reproduce the known reflectance spectra of other calibration targets on the rover, and represent the highest spatial resolution (0.65 mrad) and spectral sampling (<1 nm) visible/near-infrared reflectance spectra from a landed platform on Mars. Relative reflectance spectra of surface rocks and soils match those from orbital observations and multispectral data from the MSL Mastcam camera. Preliminary analyses of the band depths, spectral slopes, and reflectance ratios of the more than 2000 spectra taken during the first year of MSL operations demonstrate at least six spectral classes of materials distinguished by variations in ferrous and ferric components. Initial comparisons of ChemCam spectra to laboratory spectra of minerals and Mars analog materials demonstrate similarities with palagonitic soils and indications of orthopyroxene in some dark rocks. Magnesium-rich "raised ridges" tend to exhibit distinct near-infrared slopes. The ferric absorption downturn typically found for martian materials at <600 nm is greatly subdued in brushed rocks and drill tailings, consistent with their more ferrous nature. Calcium-sulfate veins exhibit the highest relative reflectances observed, but are still relatively red owing to the effects of residual dust. Such dust is overall less prominent on rocks sampled within the "blast zone" immediately surrounding the landing site. These samples were likely affected by the landing thrusters, which partially removed the ubiquitous dust coatings. Increased dust coatings on the calibration targets during the first year of the mission were documented by the ChemCam passive measurements as well. Ongoing efforts to model and correct for this dust component should improve calibration of the relative reflectance spectra. This will be useful as additional measurements are acquired during the rover's future examinations of hematite-, sulfate-, and phyllosilicate-bearing materials near the base of Mt. Sharp that are spectrally active in the 400-840 nm region.

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

PubMed

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.

Rational design of protamine nanocapsules as antigen delivery carriers.

PubMed

González-Aramundiz, José Vicente; Presas, Elena; Dalmau-Mena, Inmaculada; Martínez-Pulgarín, Susana; Alonso, Covadonga; Escribano, José M; Alonso, María J; Csaba, Noemi Stefánia

2017-01-10

Current challenges in global immunization indicate the demand for new delivery strategies, which could be applied to the development of new vaccines against emerging diseases, as well as to improve safety and efficacy of currently existing vaccine formulations. Here, we report a novel antigen nanocarrier consisting of an oily core and a protamine shell, further stabilized with pegylated surfactants. These nanocarriers, named protamine nanocapsules, were rationally designed to promote the intracellular delivery of antigens to immunocompetent cells and to trigger an efficient and long-lasting immune response. Protamine nanocapsules have nanometric size, positive zeta potential and high association capacity for H1N1 influenza hemagglutinin, a protein that was used here as a model antigen. The new formulation shows an attractive stability profile both, as an aqueous suspension or a freeze-dried powder formulation. In vitro studies showed that protamine nanocapsules were efficiently internalized by macrophages without eliciting significant toxicity. In vivo studies indicate that antigen-loaded nanocapsules trigger immune responses comparable to those achieved with alum, even when using significantly lower antigen doses, thus indicating their adjuvant properties. These promising in vivo data, alongside with their versatility for the loading of different antigens and oily immunomodulators and their excellent stability profile, make these nanocapsules a promising platform for the delivery of antigens. Protamine sulphate (PubChem SID: 7849283), Sodium Cholate (PubChem CID: 23668194), Miglyol (PubChem CID: 53471835), α tocopherol (PubChem CID: 14985), Tween® 20(PubChem CID: 443314), Tween® 80(PubChem CID: 5281955), TPGS (PubChem CID: 71406). Copyright © 2016 Elsevier B.V. All rights reserved.

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR.

PubMed

Gupta, Sebanti; Tycko, Robert

2018-02-01

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15 N, 13 C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.

Possible Outcomes of Coplanar High-eccentricity Migration: Hot Jupiters, Close-in Super-Earths, and Counter-orbiting Planets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Yuxin; Masuda, Kento; Suto, Yasushi, E-mail: yuxin@utap.phys.s.u-tokyo.ac.jp

We investigate the formation of close-in planets in near-coplanar eccentric hierarchical triple systems via the secular interaction between an inner planet and an outer perturber (Coplanar High-eccentricity Migration; CHEM). We generalize the previous work on the analytical condition for successful CHEM for point masses interacting only through gravity by taking into account the finite mass effect of the inner planet. We find that efficient CHEM requires that the systems should have m {sub 1}≪m {sub 0} and m {sub 1} ≪ m {sub 2}. In addition to the gravity for point masses, we examine the importance of the short-range forces,more » and provide an analytical estimate of the migration timescale. We perform a series of numerical simulations in CHEM for systems consisting of a Sun-like central star, giant gas inner planet, and planetary outer perturber, including the short-range forces and stellar and planetary dissipative tides. We find that most of such systems end up with a tidal disruption; a small fraction of the systems produce prograde hot Jupiters (HJs), but no retrograde HJ. In addition, we extend CHEM to super-Earth mass range, and show that the formation of close-in super-Earths in prograde orbits is also possible. Finally, we carry out CHEM simulation for the observed hierarchical triple and counter-orbiting HJ systems. We find that CHEM can explain a part of the former systems, but it is generally very difficult to reproduce counter-orbiting HJ systems.« less

Treatment with sodium nitroprusside improves the endothelial function in aortic rings with endothelial dysfunction.

PubMed

Buzinari, Tereza Cristina; Oishi, Jorge Camargo; De Moraes, Thiago Francisco; Vatanabe, Izabela Pereira; Selistre-de-Araújo, Heloisa Sobreiro; Pestana, Cezar Rangel; Rodrigues, Gerson Jhonatan

2017-07-15

Verify if sodium nitroprusside (SNP) is able to improve endothelial function and if this effect is independent of nitric oxide (NO) release of the compound. Normotensive (2K) and hypertensive (2K-1C) wistar rats were used. Intact endothelium aortas were placed in a myograph and incubated with SNP: 0.1nM; 1nM or 10nM during 30min. Cumulative concentration-effect curves for acetylcholine (Ach) were realized to measure the relaxing capacity. Intracellular NO were measured (by DAF-2DA probe) in HUVEC treated with SNP 0.1nM or DETA/NO 0.1μM. The detection of intracellular superoxide radical (O 2 •- ) was obtained by using DHE probe. Treatment of 2K-1C aortic rings with SNP (0.1; 1.0 and 10nM) improved endothelium dependent relaxation induced by acetylcholine. This improvement induced by SNP was verified at the concentration of 0.1nM, which does not release NO, suggesting that this effect was not induced due to NO release by SNP compound. Besides, we show that the cell treatment with 0.1nM of SNP decreased the fluorescence intensity to DHE in cells stimulated with angiotensin II. These results indicate that SNP decreases the concentration of O 2 •- in HUVEC cells. The SNP at a concentration that does not release NO inside the cells is able to attenuate endothelial dysfunction. Acetylcholine (Ach) (PubChem CID:6060); angiotensin II human (Ang II) (PubChem CID: 16211177); diethylenetriamine/nitric oxide (DETA-NO) (PubChem CID 4518); dihydroethidium (DHE) (PubChem CID: 128682); phenylephrine (Phe) (PubChem CID: 5284443); sodium nitroprusside (SNP) (PubChem CID: 11963579); Thiazolyl Blue Tetrazolium Bromide (MTT) (PubChem CID: 64965); 4,5-diaminofluorescein diacetate (DAF-2DA); 4-hidroxy-Tempo (Tempol) (PubChem CID: 137994), were purchased from Sigma-Aldrich (St. Louis, MO, USA). Copyright © 2017 Elsevier B.V. All rights reserved.

Exploiting the spatial locality of electron correlation within the parametric two-electron reduced-density-matrix method

NASA Astrophysics Data System (ADS)

DePrince, A. Eugene; Mazziotti, David A.

2010-01-01

The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.

Genetic and epigenetic stability of cryopreserved and cold-stored hops (Humulus lupulus L.).

PubMed

Peredo, Elena L; Arroyo-García, Rosa; Reed, Barbara M; Revilla, M Angeles

2008-12-01

Conventional cold storage and cryopreservation methods for hops (Humulus lupulus L.) are available but, to our knowledge, the genetic and epigenetic stability of the recovered plants have not been tested. This study analyzed 51 accessions of hop using the molecular techniques, Random Amplified DNA Polymorphism (RAPD) and Amplified Fragment Length Polymorphism (AFLP), revealing no genetic variation among greenhouse-grown controls and cold stored or cryopreserved plants. Epigenetic stability was evaluated using Methylation Sensitive Amplified Polymorphism (MSAP). Over 36% of the loci were polymorphic when the cold and cryo-treated plants were compared to greenhouse plants. The main changes were demethylation events and they were common to the cryopreserved and cold stored plants indicating the possible effect of the in vitro establishment process, an essential step in both protocols. Protocol-specific methylation patterns were also detected indicating that both methods produced epigenetic changes in plants following cold storage and cryopreservation.

Inverse modelling of radionuclide release rates using gamma dose rate observations

NASA Astrophysics Data System (ADS)

Hamburger, Thomas; Evangeliou, Nikolaos; Stohl, Andreas; von Haustein, Christoph; Thummerer, Severin; Wallner, Christian

2015-04-01

Severe accidents in nuclear power plants such as the historical accident in Chernobyl 1986 or the more recent disaster in the Fukushima Dai-ichi nuclear power plant in 2011 have drastic impacts on the population and environment. Observations and dispersion modelling of the released radionuclides help to assess the regional impact of such nuclear accidents. Modelling the increase of regional radionuclide activity concentrations, which results from nuclear accidents, underlies a multiplicity of uncertainties. One of the most significant uncertainties is the estimation of the source term. That is, the time dependent quantification of the released spectrum of radionuclides during the course of the nuclear accident. The quantification of the source term may either remain uncertain (e.g. Chernobyl, Devell et al., 1995) or rely on estimates given by the operators of the nuclear power plant. Precise measurements are mostly missing due to practical limitations during the accident. The release rates of radionuclides at the accident site can be estimated using inverse modelling (Davoine and Bocquet, 2007). The accuracy of the method depends amongst others on the availability, reliability and the resolution in time and space of the used observations. Radionuclide activity concentrations are observed on a relatively sparse grid and the temporal resolution of available data may be low within the order of hours or a day. Gamma dose rates, on the other hand, are observed routinely on a much denser grid and higher temporal resolution and provide therefore a wider basis for inverse modelling (Saunier et al., 2013). We present a new inversion approach, which combines an atmospheric dispersion model and observations of radionuclide activity concentrations and gamma dose rates to obtain the source term of radionuclides. We use the Lagrangian particle dispersion model FLEXPART (Stohl et al., 1998; Stohl et al., 2005) to model the atmospheric transport of the released radionuclides. The inversion method uses a Bayesian formulation considering uncertainties for the a priori source term and the observations (Eckhardt et al., 2008, Stohl et al., 2012). The a priori information on the source term is a first guess. The gamma dose rate observations are used to improve the first guess and to retrieve a reliable source term. The details of this method will be presented at the conference. This work is funded by the Bundesamt für Strahlenschutz BfS, Forschungsvorhaben 3612S60026. References Davoine, X. and Bocquet, M., Atmos. Chem. Phys., 7, 1549-1564, 2007. Devell, L., et al., OCDE/GD(96)12, 1995. Eckhardt, S., et al., Atmos. Chem. Phys., 8, 3881-3897, 2008. Saunier, O., et al., Atmos. Chem. Phys., 13, 11403-11421, 2013. Stohl, A., et al., Atmos. Environ., 32, 4245-4264, 1998. Stohl, A., et al., Atmos. Chem. Phys., 5, 2461-2474, 2005. Stohl, A., et al., Atmos. Chem. Phys., 12, 2313-2343, 2012.

A statistical downscaling approach for roadside NO2 concentrations: Application to a WRF-Chem study for Berlin

NASA Astrophysics Data System (ADS)

Kuik, Friderike; Lauer, Axel; von Schneidemesser, Erika; Butler, Tim

2017-04-01

Many European cities continue to struggle with meeting the European air quality limits for NO2. In Berlin, Germany, most of the exceedances in NO2 recorded at monitoring sites near busy roads can be largely attributed to emissions from traffic. In order to assess the impact of changes in traffic emissions on air quality at policy relevant scales, we combine the regional atmosphere-chemistry transport model WRF-Chem at a resolution of 1kmx1km with a statistical downscaling approach. Here, we build on the recently published study evaluating the performance of a WRF-Chem setup in representing observed urban background NO2 concentrations from Kuik et al. (2016) and extend this setup by developing and testing an approach to statistically downscale simulated urban background NO2 concentrations to street level. The approach uses a multilinear regression model to relate roadside NO2 concentrations observed with the municipal monitoring network with observed NO2 concentrations at urban background sites and observed traffic counts. For this, the urban background NO2 concentrations are decomposed into a long term, a synoptic and a diurnal component using the Kolmogorov-Zurbenko filtering method. We estimate the coefficients of the regression model for five different roadside stations in Berlin representing different street types. In a next step we combine the coefficients with simulated urban background concentrations and observed traffic counts, in order to estimate roadside NO2 concentrations based on the results obtained with WRF-Chem at the five selected stations. In a third step, we extrapolate the NO2 concentrations to all major roads in Berlin. The latter is based on available data for Berlin of daily mean traffic counts, diurnal and weekly cycles of traffic as well as simulated urban background NO2 concentrations. We evaluate the NO2 concentrations estimated with this method at street level for Berlin with additional observational data from stationary measurements and mobile measurements conducted during a campaign in summer 2014. The results show that this approach allows us to estimate NO2 concentrations at roadside reasonably well. The approach can be applied when observations show a strong correlation between roadside NO2 concentrations and traffic emissions from a single type of road. The method, however, shows weaknesses for intersections where observed NO2 concentrations are influenced by traffic on several different roads. We then apply this downscaling approach to estimate the impact of different traffic emission scenarios both on urban background and street level NO2 concentrations. References Kuik, F., Lauer, A., Churkina, G., Denier van der Gon, H. A. C., Fenner, D., Mar, K. A., and Butler, T. M.: Air quality modelling in the Berlin-Brandenburg region using WRF-Chem v3.7.1: sensitivity to resolution of model grid and input data, Geosci. Model Dev., 9, 4339-4363, doi:10.5194/gmd-9-4339-2016, 2016.

Comparison of Mixed Layer Heights from Airborne High Spectral Resolution Lidar, Ground-based Measurements, and the WRP-Chem Model during CalNex and CARES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scarino, Amy Jo; Obland, Michael; Fast, Jerome D.

2014-06-05

The California Research at the Nexus of Air Quality and Climate Change (CalNex) and Carbonaceous Aerosol and Radiative Effects Study (CARES) field campaigns during May and June 2010 provided a data set appropriate for studying characteristics of the planetary boundary layer (PBL). The NASA Langley Research Center (LaRC) airborne High Spectral Resolution Lidar (HSRL) was deployed to California onboard the NASA LaRC B-200 aircraft to aid incharacterizing aerosol properties during these two field campaigns. Measurements of aerosol extinction (532 nm), backscatter (532 and 1064 nm), and depolarization (532 and 1064 nm) profiles during 31 flights, many in coordination with othermore » research aircraft and ground sites, constitute a diverse data set for use in characterizing the spatial and temporal distribution of aerosols, as well as the depth and variability of the daytime mixed layer (ML), which is a subset within the PBL. This work illustrates the temporal and spatial variability of the ML in the vicinity of Los Angeles and Sacramento, CA. ML heights derived from HSRL measurements are compared to PBL heights derived from radiosonde profiles, ML heights measured from ceilometers, and simulated PBL heights from the Weather Research and Forecasting Chemistry (WRF-Chem) community model. Comparisons between the HSRL ML heights and the radiosonde profiles in Sacramento result in a correlation coefficient value (R) of 0.93 (root7 mean-square (RMS) difference of 157 m and bias difference (HSRL radiosonde) of 5 m). HSRL ML heights compare well with those from the ceilometer in the LA Basin with an R of 0.89 (RMS difference of 108 m and bias difference (HSRL Ceilometer) of -9.7 m) for distances of up to 30 km between the B-200 flight track and the ceilometer site. Simulated PBL heights from WRF-Chem were compared with those obtained from all flights for each campaign, producing an R of 0.58 (RMS difference of 604 m and a bias difference (WRF-Chem HSRL) of -157 m) for CalNex and 0.59 (RMS difference of 689 m and a bias difference (WRF-Chem HSRL) of 220 m) for CARES. Aerosol backscatter simulations are also available from WRF15 Chem and are compared to those from HSRL to examine differences among the methods used to derive ML heights.« less

Impact of improved soil climatology and intialization on WRF-chem dust simulations over West Asia

NASA Astrophysics Data System (ADS)

Omid Nabavi, Seyed; Haimberger, Leopold; Samimi, Cyrus

2016-04-01

Meteorological forecast models such as WRF-chem are designed to forecast not only standard atmospheric parameters but also aerosol, particularly mineral dust concentrations. It has therefore become an important tool for the prediction of dust storms in West Asia where dust storms have the considerable impact on living conditions. However, verification of forecasts against satellite data indicates only moderate skill in prediction of such events. Earlier studies have already indicated that the erosion factor, land use classification, soil moisture, and temperature initializations play a critical role in the accuracy of WRF-chem dust simulations. In the standard setting the erosion factor and land use classification are based on topographic variations and post-processed images of the advanced very high-resolution radiometer (AVHRR) during the period April 1992-March 1993. Furthermore, WRF-chem is normally initialized by the soil moisture and temperature of Final Analysis (FNL) model on 1.0x1.0 degree grids. In this study, we have changed boundary initial conditions so that they better represent current changing environmental conditions. To do so, land use (only bare soil class) and the erosion factor were both modified using information from MODIS deep blue AOD (Aerosol Optical Depth). In this method, bare soils are where the relative frequency of dust occurrence (deep blue AOD > 0.5) is more than one-third of a given month. Subsequently, the erosion factor, limited within the bare soil class, is determined by the monthly frequency of dust occurrence ranging from 0.3 to 1. It is worth to mention, that 50 percent of calculated erosion factor is afterward assigned to sand class while silt and clay classes each gain 25 percent of it. Soil moisture and temperature from the Global Land Data Assimilation System (GLDAS) were utilized to provide these initializations in higher resolution of 0.25 degree than in the standard setting. Modified and control simulations were conducted for the summertime of 2008-2012 and verified by satellite data (MODIS deep blue AOD, TOMs Aerosol Index and MISR AOD 550nm) and two well-known modeling systems of atmospheric composition (MACC and DREAM). All comparisons show a significant improvement in WRF-chem dust simulations after implementing the modifications. In comparison to the control run, the modified run bears an average increase of spearman correlation of 17-20 percent points when it is compared with satellite data. Our runs with modified WRF-chem even outperform MACC and DREAM dust simulations for the region.

A molecular dynamics study of water nucleation using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Pérez, Alejandro; Rubio, Angel

2011-12-01

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

EPA Method 245.2: Mercury (Automated Cold Vapor Technique)

EPA Pesticide Factsheets

Method 245.2 describes procedures for preparation and analysis of drinking water samples for analysis of mercury using acid digestion and cold vapor atomic absorption. Samples are prepared using an acid digestion technique.

Time-independent quantum dynamics for diatom-surface scattering

NASA Astrophysics Data System (ADS)

Saalfrank, Peter; Miller, William H.

1993-06-01

Two time-independent quantum reactive scattering methods, namely, the S-matrix Kohn technique to compute the full S-matrix, and the absorbing boundary Green's function method to compute cumulative reaction probabilities, are applied here to the case of diatom-surface scattering. In both cases a discrete variable representation for the operators is used. We test the methods for two- and three-dimensional uncorrugated potential energy surfaces, which have been used earlier by Halstead et al. [J. Chem. Phys. 93, 2359 (1990)] and by Sheng et al. [J. Chem. Phys. 97, 684 (1992)] in studies of H2 dissociating on metal substrates with theoretical techniques different from those applied here. We find overall but not always perfect agreement with these earlier studies. Based on ab initio data and experiment, a new, six-dimensional potential energy surface for the dissociative chemisorption of H2 on Ni(100) is proposed. Two- and three-dimensional cuts through the new potential are performed to illustrate special dynamical aspects of this particular molecule-surface reaction: (i) the role of corrugation effects, (ii) the importance of the ``cartwheel'' rotation of H2, and (iii) the role of the ``helicopter'' degree of freedom for the adsorbing molecule.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

New developments on ChemCam laser transmitter and potential applications for other planetology programs

NASA Astrophysics Data System (ADS)

Faure, Benoît; Durand, Eric; Maurice, Sylvestre; Bruneau, Didier; Montmessin, Franck

2017-11-01

ChemCam is a LIBS Instrument mounted on the MSL 2011 NASA mission. The laser transmitter of this Instrument has been developed by the French society Thales Optronique (former Thales Laser) with a strong technical support from CNES. The paper will first rapidly present the performance of this laser and will then describe the postChemCam developments realized on and around this laser for new planetology programs.

Ultraviolet Photoionization Efficiency of the Vaporized Ionic Liquid 1-Butyl-3-Methylimidazolium Tricyanomethanide: Direct Detection of the Intact Ion Pair (Post Print)

DTIC Science & Technology

2012-09-21

Lovelock , K. R. J.; Satterly, C. J.; Villar-Garcia, I. J. Phys. Chem. Chem. Phys. 2007, 9, 982−990. (11) Strasser, D.; Goulay, F.; Kelkar, M. S.; Maginn, E...J.; Leone, S. R. J. Phys. Chem. A 2007, 111, 3191−3915. (12) Lovelock , K. R. J.; Deyko, A.; Corfield, J.-A.; Gooden, P. N.; Licence, P.; Jones, R. G

Studies in Aromatic and Amine Nitration.

DTIC Science & Technology

1980-05-20

of Commerce, May 1978. 4. J. Hoggett , R. Moodie, F. Penton, and K. Schofield, Nitration and Aromatic Reactivity (Cambridge University Press, 1971). 5...Moodie, K. Schofield, and G. Tobin, J. Chem. Soc., Chem. Comm., 180 (1978); (b) J. Hoggett , R. Moodie, and K. Schofield, Chem. Comm. 605 (1969). 10. (a) S...W. Benson, Thermochemical Kinetics (John Wiley and Sons, Inc., New York, 1968); (b) G. Charlot, D. Bezier, and J. Courtot, Selected Constants--Oxydo

ChemTS: an efficient python library for de novo molecular generation

PubMed Central

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Abstract Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS. PMID:29435094

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: a path for the optimization of low-energy many-body bases.

PubMed

Reboredo, Fernando A; Kim, Jeongnim

2014-02-21

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

NASA Astrophysics Data System (ADS)

Reboredo, Fernando A.; Kim, Jeongnim

2014-02-01

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.

The Transcorrelated Method Combined with the Variational Monte Carlo Calculation: Application to Atoms

NASA Astrophysics Data System (ADS)

Umezawa, Naoto; Tsuneyuki, Shinji; Ohno, Takahisa; Shiraishi, Kenji; Chikyow, Toyohiro

2005-03-01

The transcorrelated (TC) method is a useful approach to optimize the Jastrow-Slater-type many-body wave function FD. The basic idea of the TC method [1] is based on the similarity transformation of a many-body Hamiltonian H with respect to the Jastrow factor F: HTC=frac1F H F in order to incorporate the correlation effect into HTC. Both the F and D are optimized by minimizing the variance ^2=|Hrm TCD - E D |^2 d^3N x. The optimization for F is implemented by the variational Monte Carlo calculation, and D is determined by the TC self-consistent-field equation for the one-body wave functions φμ(x), which is derived from the functional derivative of ^2 with respect to φmu(x). In this talk, we will present the results given by the transcorrelated variational Monte Carlo (TC-VMC) method for the ground state [2] and the excited states of atoms [3]. [1]S. F. Boys and N. C. Handy, Proc. Roy. Soc. A, 309, 209; 310, 43; 310, 63; 311, 309 (1969). [2]N. Umezawa and S. Tsuneyuki, J. Chem. Phys. 119, 10015 (2003). [3]N. Umezawa and S. Tsuneyuki, J. Chem. Phys. 121, 7070 (2004).

Application of COLD-PCR for improved detection of KRAS mutations in clinical samples.

PubMed

Zuo, Zhuang; Chen, Su S; Chandra, Pranil K; Galbincea, John M; Soape, Matthew; Doan, Steven; Barkoh, Bedia A; Koeppen, Hartmut; Medeiros, L Jeffrey; Luthra, Rajyalakshmi

2009-08-01

KRAS mutations have been detected in approximately 30% of all human tumors, and have been shown to predict response to some targeted therapies. The most common KRAS mutation-detection strategy consists of conventional PCR and direct sequencing. This approach has a 10-20% detection sensitivity depending on whether pyrosequencing or Sanger sequencing is used. To improve detection sensitivity, we compared our conventional method with the recently described co-amplification-at-lower denaturation-temperature PCR (COLD-PCR) method, which selectively amplifies minority alleles. In COLD-PCR, the critical denaturation temperature is lowered to 80 degrees C (vs 94 degrees C in conventional PCR). The sensitivity of COLD-PCR was determined by assessing serial dilutions. Fifty clinical samples were used, including 20 fresh bone-marrow aspirate specimens and the formalin-fixed paraffin-embedded (FFPE) tissue of 30 solid tumors. Implementation of COLD-PCR was straightforward and required no additional cost for reagents or instruments. The method was specific and reproducible. COLD-PCR successfully detected mutations in all samples that were positive by conventional PCR, and enhanced the mutant-to-wild-type ratio by >4.74-fold, increasing the mutation detection sensitivity to 1.5%. The enhancement of mutation detection by COLD-PCR inversely correlated with the tumor-cell percentage in a sample. In conclusion, we validated the utility and superior sensitivity of COLD-PCR for detecting KRAS mutations in a variety of hematopoietic and solid tumors using either fresh or fixed, paraffin-embedded tissue.

Watching Conformations of Biomolecules: a Microwave Spectroscopy Approach

NASA Astrophysics Data System (ADS)

Lopez, J. C.

2011-06-01

The combination of laser ablation with Fourier transform microwave spectroscopy in supersonic jets (LA-MB-FTMW) has made possible the gas-phase study of solid biomolecules with high melting points. In the experiment, solids are efficiently vaporized by a high-energy laser pulse, supersonically expanded into a evacuated Fabry-Perot cavity and characterised by their rotational spectra. Recent improvements such as the use of picosecond pulse lasers, new ablation nozzles and the extension of the range of the spectrometers to low frequecy have notably increased the sensitivity of our experimental setup. To date different α-, β- and γ-amino acids have been studied using this technique, making possible the characterization of their preferred conformations and gaining insight in the role of intramolecular interactions. Even in conformationally challenging systems the different rotamers of such biomolecules can be identified by rotational spectroscopy as can be illustrated by the assignment of six low-energy conformers in cysteine and aspartic acid, seven in serine and threonine,^a and nine in γ-amino butyric acid (GABA). In all cases the low-energy conformers have been conclusive identified from their experimental rotational and 14N quadrupole coupling constants. The spectra of neurotransmitters and of the nucleic acid bases uracil, thymine, cytosine and guanine have also been studied and their preferred conformers or tautomeric forms determined. The complexes between amino acids and nucleic acid bases with water have also been investigated to obtain information on the possible changes induced in the conformational or tautomeric preferences by the addition of solvent molecules. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11, 617-627 (2009) and references therein M. E. Sanz, J. C. López, J. L. Alonso, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010) S. Blanco, J. C. López, S. Mata and J. L. Alonso, Angew. Chem. Int. Ed. 49, 9187 (2010) J. L. Alonso, M. E. Sanz, J. C. López, V. Cortijo, J. Am. Chem. Soc. 131, 4320 (2009) J. L. Alonso, I. Peña, J. C. López, V. Vaquero, Angew. Chem. Int. Ed. 49, 6141 (2009) J. C. López, J. L. Alonso, I. Peña, V. Vaquero, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010)

Lynn Westdal | NREL

Science.gov Websites

Process-relevant Biomass-derived Pentoses in a Biphasic Reaction System," ACS Sustainable Chem. Eng Biomass-derived Pentoses in a Biphasic Reaction System." ACS Sustainable Chem. Eng. (2017)

Methods to Estimate Acclimatization to Urban Heat Island Effects on Heat- and Cold-Related Mortality.

PubMed

Milojevic, Ai; Armstrong, Ben G; Gasparrini, Antonio; Bohnenstengel, Sylvia I; Barratt, Benjamin; Wilkinson, Paul

2016-07-01

Investigators have examined whether heat mortality risk is increased in neighborhoods subject to the urban heat island (UHI) effect but have not identified degrees of difference in susceptibility to heat and cold between cool and hot areas, which we call acclimatization to the UHI. We developed methods to examine and quantify the degree of acclimatization to heat- and cold-related mortality in relation to UHI anomalies and applied these methods to London, UK. Case-crossover analyses were undertaken on 1993-2006 mortality data from London UHI decile groups defined by anomalies from the London average of modeled air temperature at a 1-km grid resolution. We estimated how UHI anomalies modified excess mortality on cold and hot days for London overall and displaced a fixed-shape temperature-mortality function ("shifted spline" model). We also compared the observed associations with those expected under no or full acclimatization to the UHI. The relative risk of death on hot versus normal days differed very little across UHI decile groups. A 1°C UHI anomaly multiplied the risk of heat death by 1.004 (95% CI: 0.950, 1.061) (interaction rate ratio) compared with the expected value of 1.070 (1.057, 1.082) if there were no acclimatization. The corresponding UHI interaction for cold was 1.020 (0.979, 1.063) versus 1.030 (1.026, 1.034) (actual versus expected under no acclimatization, respectively). Fitted splines for heat shifted little across UHI decile groups, again suggesting acclimatization. For cold, the splines shifted somewhat in the direction of no acclimatization, but did not exclude acclimatization. We have proposed two analytical methods for estimating the degree of acclimatization to the heat- and cold-related mortality burdens associated with UHIs. The results for London suggest relatively complete acclimatization to the UHI effect on summer heat-related mortality, but less clear evidence for cold-related mortality. Milojevic A, Armstrong BG, Gasparrini A, Bohnenstengel SI, Barratt B, Wilkinson P. 2016. Methods to estimate acclimatization to urban heat island effects on heat- and cold-related mortality. Environ Health Perspect 124:1016-1022; http://dx.doi.org/10.1289/ehp.1510109.

Air Quality Modeling and Forecasting over the United States Using WRF-Chem

NASA Astrophysics Data System (ADS)

Boxe, C.; Hafsa, U.; Blue, S.; Emmanuel, S.; Griffith, E.; Moore, J.; Tam, J.; Khan, I.; Cai, Z.; Bocolod, B.; Zhao, J.; Ahsan, S.; Gurung, D.; Tang, N.; Bartholomew, J.; Rafi, R.; Caltenco, K.; Rivas, M.; Ditta, H.; Alawlaqi, H.; Rowley, N.; Khatim, F.; Ketema, N.; Strothers, J.; Diallo, I.; Owens, C.; Radosavljevic, J.; Austin, S. A.; Johnson, L. P.; Zavala-Gutierrez, R.; Breary, N.; Saint-Hilaire, D.; Skeete, D.; Stock, J.; Salako, O.

2016-12-01

WRF-Chem is the Weather Research and Forecasting (WRF) model coupled with Chemistry. The model simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. The model is used for investigation of regional-scale air quality, field program analysis, and cloud-scale interactions between clouds and chemistry. The development of WRF-Chem is a collaborative effort among the community led by NOAA/ESRL scientists. The Official WRF-Chem web page is located at the NOAA web site. Our model development is closely linked with both NOAA/ESRL and DOE/PNNL efforts. Description of PNNL WRF-Chem model development is located at the PNNL web site as well as the PNNL Aerosol Modeling Testbed. High school and undergraduate students, representative of academic institutions throughout USA's Tri-State Area (New York, New Jersey, Connecticut), set up WRF-Chem on CUNY CSI's High Performance Computing Center. Students learned the back-end coding that governs WRF-Chems structure and the front-end coding that displays visually specified weather simulations and forecasts. Students also investigated the impact, to select baseline simulations/forecasts, due to the reaction, NO2 + OH + M → HOONO + M (k = 9.2 × 10-12 cm3 molecule-1 s-1, Mollner et al. 2010). The reaction of OH and NO2 to form gaseous nitric acid (HONO2) is among the most influential and in atmospheric chemistry. Till a few years prior, its rate coefficient remained poorly determined under tropospheric conditions because of difficulties in making laboratory measurements at 760 torr. These activities fosters student coding competencies and deep insights into weather forecast and air quality.

Size- and Shape-Dependent Fluorescence Quenching of Gold Nanoparticles on Perylene Dye

DTIC Science & Technology

2013-01-01

Am. Chem. Soc. 2005 , 127 , 1216 . [10] S. Vukovic , S. Corni , B. Mennucci , J . Phys. Chem. C 2009 , 113 , 121 . procedure [ 11... J . Halas , S. Lal , W. S. Chang , S. Link , P. Nordlander , Chem. Rev. 2011 , 111 , 3913 . [3] S.-Y. Chen , J . J . Mock , R. T...Hill , A. Chilkoti , D. R. Smith , A. A. Lazarides , ACS Nano 2010 , 4 , 6535 . [4] C. J . Murphy , T. K. San , A. M. Gole , C. J

Quantum Mechanical Studies of Molecular Hyperpolarizabilities.

DTIC Science & Technology

1980-04-30

exponent , reflects the screening of an electron in a given orbital by the interior electrons in the atom or molecule. In practice, when studying...Basis sets have evolved over the years in molecular quantum mechanics until sets of orbital exponents for the different atoms composing the molecule have...and R. P. Hurst , J. Chem. Phys. 46, 2356 (1967); S. P. LickmannI and J. W. Moskowitz, J. Chem. Phys. 54, 3622 7T971). 26. T. H. Dunning, J. Chem. Phys

Studies of a Ras Antagonist in Breast Cancer

DTIC Science & Technology

2005-05-01

growth by Farensylthiosalicylic acid. J Biol Chem 1995; 270: 22268- 22270 . [19] Egozi Y, Weisz B, Gana-Weisz M, Ben-Baruch G, and Kloog Y, Growth...growth by Farensylthiosalisylic acid. J Biol Chem 270(35) (1995) 22268- 22270 . [71] Y. Egozi, B. Weisz, M. Gana-Weisz, G. Ben-Baruch, and Y. Kloog, Growth...G, Marciano D, Egozi Y, Kloog Y 1995 Selective inhibition of Ras- dependent cell growth by farnesylthiosalisylic acid. J Biol Chem 270:22263- 22270 40

Automated Discovery of New Chemical Reactions and Accurate Calculation of Their Rates

DTIC Science & Technology

2015-06-02

formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones . Phys. Chem. Chem. Phys. 2013, 15, 16841-16852. [39...dioxolan-3-ol – our second case study - we confirmed that fragmentation of the cyclic peroxide leads to two possible pairs of acid and aldehyde products...Rate Prediction via Group Additivity, Part 2: H-Abstraction from Alkenes, Alkynes, Alcohols, Aldehydes , and Acids by H Atoms. J. Phys. Chem. A 2001, 105

Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design.

PubMed

Huang, Ri-Bo; Du, Qi-Shi; Wei, Yu-Tuo; Pang, Zong-Wen; Wei, Hang; Chou, Kuo-Chen

2009-02-07

Predicting the bioactivity of peptides and proteins is an important challenge in drug development and protein engineering. In this study we introduce a novel approach, the so-called "physics and chemistry-driven artificial neural network (Phys-Chem ANN)", to deal with such a problem. Unlike the existing ANN approaches, which were designed under the inspiration of biological neural system, the Phys-Chem ANN approach is based on the physical and chemical principles, as well as the structural features of proteins. In the Phys-Chem ANN model the "hidden layers" are no longer virtual "neurons", but real structural units of proteins and peptides. It is a hybridization approach, which combines the linear free energy concept of quantitative structure-activity relationship (QSAR) with the advanced mathematical technique of ANN. The Phys-Chem ANN approach has adopted an iterative and feedback procedure, incorporating both machine-learning and artificial intelligence capabilities. In addition to making more accurate predictions for the bioactivities of proteins and peptides than is possible with the traditional QSAR approach, the Phys-Chem ANN approach can also provide more insights about the relationship between bioactivities and the structures involved than the ANN approach does. As an example of the application of the Phys-Chem ANN approach, a predictive model for the conformational stability of human lysozyme is presented.

System And Method Of Applying Energetic Ions For Sterlization

DOEpatents

Schmidt, John A.

2002-06-11

A method of sterilization of a container is provided whereby a cold plasma is caused to be disposed near a surface to be sterilized, and the cold plasma is then subjected to a pulsed voltage differential for producing energized ions in the plasma. Those energized ions then operate to achieve spore destruction on the surface to be sterilized. Further, a system for sterilization of a container which includes a conductive or non-conductive container, a cold plasma in proximity to the container, and a high voltage source for delivering a pulsed voltage differential between an electrode and the container and across the cold plasma, is provided.

The ORNL Chemical Technology Division, 1950-1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jolley, R.L.; Genung, R.K.; McNeese, L.E.

1994-10-01

This document attempts to reconstruct the role played by the Chemical Technology Division (Chem Tech) of the Oak Ridge National Laboratory (ORNL) in the atomic era since the 1940`s related to the development and production of nuclear weapons and power reactors. Chem Tech`s early contributions were landmark pioneering studies. Unknown and dimly perceived problems like chemical hazards, radioactivity, and criticality had to be dealt with. New chemical concepts and processes had to be developed to test the new theories being developed by physicists. New engineering concepts had to be developed and demonstrated in order to build facilities and equipment thatmore » had never before been attempted. Chem Tech`s role was chemical separations, especially uranium and plutonium, and nuclear fuel reprocessing. With diversification of national and ORNL missions, Chem Tech undertook R&D studies in many areas including biotechnology; clinical and environmental chemistry; nuclear reactors; safety regulations; effective and safe waste management and disposal; computer modeling and informational databases; isotope production; and environmental control. The changing mission of Chem Tech are encapsulated in the evolving activities.« less

New investigation of the ν3 C-H stretching region of 12CH4 through the analysis of high temperature infrared emission spectra

NASA Astrophysics Data System (ADS)

Amyay, Badr; Gardez, Aline; Georges, Robert; Biennier, Ludovic; Vander Auwera, Jean; Richard, Cyril; Boudon, Vincent

2018-04-01

The ν3 C-H stretching region of methane was reinvestigated in this work using high temperature (620-1715 K) emission spectra recorded in Rennes at Doppler limited resolution. This work follows our recent global analysis of the Dyad system Δn = ±1 (1000-1500 cm-1), with n being the polyad number [B. Amyay et al., J. Chem. Phys. 144, 24312 (2016)]. Thanks to the high temperature, new assignments of vibration-rotation methane line positions have been achieved successfully in the Pentad system and some associated hot bands (Δn = ±2) observed in the spectral region 2600-3300 cm-1. In particular, rotational assignments in the cold band [Pentad-ground state (GS)] and in the first related hot band (Octad-Dyad) were extended up to J = 30 and 27, respectively. In addition, 1525 new transitions belonging to the Tetradecad-Pentad hot band system were assigned for the first time, up to J = 20. The effective global model used to deal with the new assignments was developed to the 6th order for the first three polyads (Monad, Dyad, and Pentad), and to the 5th order for both the Octad and the Tetradecad. 1306 effective parameters were fitted with a dimensionless standard deviation σ = 2.64. The root mean square deviations dRMS obtained are 4.18 × 10-3 cm-1 for the Pentad-GS cold band, 2.48 × 10-3 cm-1 for the Octad-Dyad, and 1.43 × 10-3 cm-1 for the Tetradecad-Pentad hot bands.

Detecting Patterns of Changing Carbon Uptake in Alaska Using Sustained In Situ and Remote Sensing CO2 Observations

NASA Astrophysics Data System (ADS)

Parazoo, N.; Miller, C. E.; Commane, R.; Wofsy, S. C.; Koven, C.; Lawrence, D. M.; Lindaas, J.; Chang, R. Y. W.; Sweeney, C.

2015-12-01

The future trajectory of Arctic ecosystems as a carbon sink or source is of global importance due to vast quantities of carbon in permafrost soils. Over the last few years, a sustained set of airborne (NOAA-PFA, NOAA-ACG, and CARVE) and satellite (OCO-2 and GOSAT) atmospheric CO2 mole fraction measurements have provided unprecedented space and time scale sampling density across Alaska, making it possible to study the Arctic carbon cycle in more detail than ever before. Here, we use a synthesis of airborne and satellite CO2 over the 2009-2013 period with simulated concentrations from CLM4.5 and GEOS-Chem to examine the extent to which regional-scale carbon cycle changes in Alaska can be distinguished from interannual variability and long-range transport. We show that observational strategies focused on sustained profile measurements spanning continental interiors provide key insights into magnitude, duration, and variability of Summer sink activity, but that cold season sources are currently poorly resolved due to lack of sustained spatial sampling. Consequently, although future CO2 budgets dominated by enhanced cold season emission sources under climate warming and permafrost thaw scenarios are likely to produce substantial changes to near-surface CO2 gradients and seasonal cycle amplitude, they are unlikely to be detected by current observational strategies. We conclude that airborne and ground-based networks that provide more spatial coverage in year round profiles will help compensate for systematic sampling gaps in NIR passive satellite systems and provide essential constraints for Arctic carbon cycle changes.

78 FR 25372 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-01

... fuselage skin along chem-mill steps at certain crown skin and shear wrinkle areas, and repair if necessary... at certain crown skin and shear wrinkle areas, and repair if necessary. Comments We gave the public... airplanes on which STC ST00830SE is installed, a ``change in product'' alternative method of compliance...

78 FR 24338 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-25

... the fuselage skin along chem-mill steps at certain crown skin and shear wrinkle areas, and repair if... at certain crown skin and shear wrinkle areas, and repair if necessary. Comments We gave the public...'' alternative method of compliance (AMOC) approval request is not necessary to comply with the requirements of...

COMPARISON OF RAPID METHODS TO EVALUATE CHLORINE INACTIVATION OF THE BIOLOGICAL AGENT E. COLI 0157:H7

EPA Science Inventory

Rapid viability tests of the Catagory B agent Escherichia coli O157:H7 were evaluated after disinfection with chlorine. The metabolic activity dyes ChemChrome V6, a modified fluorescein diacetate (FDA) and 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) were compared to standard ...

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method.

PubMed

Zhang, Yanan; Ren, Weiqing

2014-12-28

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results are obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method

NASA Astrophysics Data System (ADS)

Zhang, Yanan; Ren, Weiqing

2014-12-01

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results are obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.

An eight-dimensional quantum dynamics study of the Cl + CH{sub 4}→ HCl + CH{sub 3} reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Na; Yang, Minghui, E-mail: yangmh@wipm.ac.cn

2015-10-07

In this work, the later-barrier reaction Cl + CH{sub 4} → HCl + CH{sub 3} is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH{sub 4} initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. Themore » good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations.« less

An Overview of Signaling Regulons During Cold Stress Tolerance in Plants

PubMed Central

Pareek, Amit; Khurana, Ashima; Sharma, Arun K.; Kumar, Rahul

2017-01-01

Plants, being sessile organisms, constantly withstand environmental fluctuations, including low-temperature, also referred as cold stress. Whereas cold poses serious challenges at both physiological and developmental levels to plants growing in tropical or sub-tropical regions, plants from temperate climatic regions can withstand chilling or freezing temperatures. Several cold inducible genes have already been isolated and used in transgenic approach to generate cold tolerant plants. The conventional breeding methods and marker assisted selection have helped in developing plant with improved cold tolerance, however, the development of freezing tolerant plants through cold acclimation remains an unaccomplished task. Therefore, it is essential to have a clear understanding of how low temperature sensing strategies and corresponding signal transduction act during cold acclimation process. Herein, we synthesize the available information on the molecular mechanisms underlying cold sensing and signaling with an aim that the summarized literature will help develop efficient strategies to obtain cold tolerant plants. PMID:29204079

Dinitrogen Difluoride Chemistry. Improved Synthesis of cis- and trans-N2F2, Synthesis and Characterization of N2F+Sn2F9 High-Level Electronic Structure Calculations of cis-N2F2, trans-N2F2, F2N=N, and N2F+, and Mechanism of the trans-cis Isomerization of N2F2 (Preprint)

DTIC Science & Technology

2010-05-01

measurements of Pankratov and Sokolov who found that within experimental error this value was close to zero.48 We note that the current calculations are...Z. Chem. Phys. Lett. 1977, 50, 418. 9. Christe, K. O.; Wilson, R. D.; Wilson, W. W.; Bau, R.; Sukumar, S.; Dixon, D. A. J. Am. Chem. Soc. 1991 , 113...Phys. Chem. Ref. Data, Mono. 9, Suppl. 1 (1998). 48. Pankratov , A. V.; Sokolov, O. M. Russ. J. Inorg. Chem. 1966, 11, 943. 49. Christe, K. O

Cold/hot pad differentiating assay of property differences of Mahuang and Maxingshigan decoctions.

PubMed

Zhao, Yanling; Jia, Lei; Wang, Jiabo; Zou, Wenjun; Yang, Hongbo; Xiao, Xiaohe

2016-07-01

Chinese medicines with different cold/hot properties have various pharmacological actions on multiple organisms. The objective of this study was to explore the cold/hot property differences of traditional Chinese medicine formulas of Mahuang and Maxingshigan decoctions. A novel cold/hot pad differentiating assay method based on the Intelligent Animal Temperature Tropism Behavior monitoring system at 20 °C (cold pad) and 30 °C (hot pad) was introduced to investigate the variability of temperature tropism among the mice treated by 0.4 mL/20 g (drug volume/body weight) of Mahuang decoction and Maxingshigan decoction, respectively. Meanwhile, the oxygen consumption and activities of adenosine triphosphatase (ATPase) were measured to explore the energy metabolism mechanism. Results showed that the differences between cold/hot properties of Mahuang decoction and Maxingshigan decoction were significant (p < 0.05). Mahuang decoction produced significant synergic effect (a combination index of 1.60), while Maxingshigan decoction expressed significant antagonistic effect (a combination index of 0.35). The changes of energy metabolism including ATPase activity and oxygen consumption might be the possible factors to result in the differences. Those influences tended to be coherent with the definition of cold/hot properties of Chinese medicines based on traditional Chinese medicinal theory. The results indicated that the method based on cold/hot pad differentiating array could objectively and quantitatively represent the cold/hot properties of different compatibilities of traditional Chinese medicines in an ethological way according to the changes of animal's temperature tropism. These findings would provide some experimental basis and data references as well as a novel evaluation method for the study of the regularity of recipe composition.

Explicit formula of finite difference method to estimate human peripheral tissue temperatures during exposure to severe cold stress.

PubMed

Khanday, M A; Hussain, Fida

2015-02-01

During cold exposure, peripheral tissues undergo vasoconstriction to minimize heat loss to preserve the maintenance of a normal core temperature. However, vasoconstricted tissues exposed to cold temperatures are susceptible to freezing and frostbite-related tissue damage. Therefore, it is imperative to establish a mathematical model for the estimation of tissue necrosis due to cold stress. To this end, an explicit formula of finite difference method has been used to obtain the solution of Pennes' bio-heat equation with appropriate boundary conditions to estimate the temperature profiles of dermal and subdermal layers when exposed to severe cold temperatures. The discrete values of nodal temperature were calculated at the interfaces of skin and subcutaneous tissues with respect to the atmospheric temperatures of 25 °C, 20 °C, 15 °C, 5 °C, -5 °C and -10 °C. The results obtained were used to identify the scenarios under which various degrees of frostbite occur on the surface of skin as well as the dermal and subdermal areas. The explicit formula of finite difference method proposed in this model provides more accurate predictions as compared to other numerical methods. This model of predicting tissue temperatures provides researchers with a more accurate prediction of peripheral tissue temperature and, hence, the susceptibility to frostbite during severe cold exposure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Part I: Reverse-docking studies of a squaramide-catalyzed conjugate addition of a diketone to a nitro-olefin Part II: The development of ChemSort: an education game for organic chemistry

NASA Astrophysics Data System (ADS)

Granger, Jenna Christine

Part 1: Reverse-docking studies of a squaramide-catalyzed conjugate addition of a diketone to a nitro-olefin. Asymmetric organocatalysis, the catalysis of asymmetric reactions by small organic molecules, is a rapidly growing field within organic synthesis. The ability to rationally design organocatalysts is therefore of increasing interest to organic chemists. Computational chemistry is quickly proving to be an extremely successful method for understanding and predicting the roles of organocatalysts, and therefore is certain to be of use in the rational design of such catalysts. A methodology for reverse-docking flexible organocatalysts to rigid transition state models of asymmetric reactions has been previously developed by the Deslongchamps group. The investigation of Rawal's squaramide-based organocatalyst for the addition of a diketone to a nitro-olefin is described, and the results of the reverse docking of Rawal's catalyst to the geometry optimized transition state models of the uncatalyzed reaction for both the R and S-product enantiomers are presented. The results of this study indicate a preference for binding of the organocatalyst to the R-enantiomer transition state model with a predicted enantiomeric excess of 99%, which is consistent with the experimental results. A plausible geometric model of the transition state for the catalyzed reaction is also presented. The success of this study demonstrates the credibility of using reverse docking methods for the rational design of asymmetric organocatalysts. Part 2: The development of ChemSort: an educational game for organic chemistry. With the advent of the millennial learner, we need to rethink traditional classroom approaches to science learning in terms of goals, approaches, and assessments. Digital simulations and games hold much promise in support of this educational shift. Although the idea of using games for education is not a new one, well-designed computer-based "serious games" are only beginning to emerge as exceptional tools for helping learners understand concepts and processes. The use of computer games for learning college-level organic chemistry is still relatively unexplored and underrepresented within the realm of "serious gaming". In this section, ideas for games as a way for teaching and learning organic chemistry will be introduced and the development process of ChemSort, a web-based Flash game for learning college-level organic chemistry topics, will be outlined. ChemSort is a path-based game, in which the player, or in this case the learner, must match the chemical structures with their appropriate functional groups. At the end of this section a 4-level useable prototype of ChemSort will be unveiled.

The Development and Study of Molecular Electronic Switches and their Field-Effect Transistor (FET) Device Properties

DTIC Science & Technology

2015-02-27

Grand Rapids, MI) meetings and conferences. References 1. L.N Lucas, J.J.D. de Jong, J.H. van Esch, R.M. Kellogg , B.L. Berringa. Eur. J. Org...R.M. Kellogg , H.L. Feringa, H.L. Eur. J. Org. Chem., 2003, 155-166. 6. B. Qin, R. Yao, X. Zhao, H. Tian. Org. Biomol. Chem., 1, 2003, 2187-2191...7. L.N. Lucas, J.H. van Euch, R.M. Kellogg , B. Feringa. Chem. Comm., 1998, 2313-2314.

Studies on Relaxation Behavior of Corona Poled Aromatic Dipolar Molecules in a Polymer Matrix

DTIC Science & Technology

1990-08-03

concentration upto 30 weight percent. Orientation As expected optically responsive molecules are randomly oriented in the polymer matrix although a small amount...INSERT Figure 4 The retention of SH intensity of the small molecule such as MNA was found to be very poor in the PMMA matrix while the larger rodlike...Polym. Prepr. Am. Chem. Soc., Div. Polym. Chem. 24(2), 309 (1983). 16.- H. Ringsdorf and H. W. Schmidt. Makromol. Chem. 185, 1327 (1984). 17. S. Musikant

History of the AFRL/USC DARPA Program on Polynitrogen Chemistry. Volume 2

DTIC Science & Technology

2004-10-01

published by Pyykkoe and Runeberg in 1991 as part of a systematic study of the isoelectronic dicyanamide series, but little emphasis was given to N5+ as...2003, 244, 93. [3] K. O. Christe, R. D. Wilson, W. W. Wilson, R. Bau, S. Sukumar, D. A. Dixon, J. Am. Chem. Soc. 1991 , 113, 1991 . [4] P...Pyykkoe, N. Runeberg, J. Mol. Struct. (Theochem.) 1991 , 234, 279. [5] R. Rawls, Chem. & Eng. News, Jan. 25 issue, 1999, pg. 7. [6] P. Zurer, Chem

Mechanism of Hydrogen Production in [Fe-Fe]-Hydrogenase: A Density Functional Theory Study (Postprint)

DTIC Science & Technology

2007-03-01

Chem. Soc. 2001, 123, 1596-1601. (8) Volbeda, A.; Fontecilla-Camps, J. C. The Active Site and Catalytic Mechanism of NiFe Hydrogenases. Dalton Trans... Properties of Diiron Complexes Related to the [2Fe]H Subcluster of Fe-Only Hydrogenases. Inorg. Chem. 2002, 41, 1421-1429. (16) Bruschi, M.; Fantucci, P...Structural, Electronic, and Reactivity Properties of Complexes Related to the [2Fe]H Subcluster. Inorg. Chem. 2003, 42, 4773-4781. (17) Bruschi, M.; Fantucci

Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

DTIC Science & Technology

2013-01-01

Narten, J. Chem. Phys., 1975, 63, 3624–3631. 10 A. Botti, F. Bruni, S. Imberti, M. A. Ricci and A. K. Soper , J. Chem. Phys., 2004, 121, 7840–7848. 11 D...10478. 48 I. Harsányi and L. Pusztai, J. Phys.: Condens. Matter, 2005, 17, S59–S65. 49 A. Botti, F. Bruni, M. A. Ricci and A. K. Soper , J. Chem. Phys

Inverse Coarse-Graining: A New Tool for Molecular Design

DTIC Science & Technology

2010-12-16

simulations. When compared with the more general multiscale coarse-graining (MS-CG) method, the EF-CG method retains the transferable part of the CG...Y.; Yan, T.; Voth, G. A., A Multiscale coarse-graining study of liquid/vacuum interface of room-temperature ionic liquids with alkyl substituents of...Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B 2008, 112, 3121-3131. 6. Liu, P

Test Operations Procedure (TOP) 1-1-003 Cold Regions Personnel Effects

DTIC Science & Technology

2008-09-15

4 3.3 Freezing Injuries : Frostnip and Frostbite...4 3.4 Non-freezing injuries ........................................................................... 5 3.5 Snow...3. Information concerning the symptoms, methods of prevention, and treatment of various types of cold injuries is also provided. 2.2 Cold Weather

Cold thermal injury from cold caps used for the prevention of chemotherapy-induced alopecia

PubMed Central

Belum, Viswanath Reddy; de Barros Silva, Giselle; Laloni, Mariana Tosello; Ciccolini, Kathryn; Sklarin, Nancy T.; Lacouture, Mario E.

2017-01-01

INTRODUCTION The use of scalp cooling for the prevention of chemotherapy-induced alopecia (CIA) is increasing. Cold caps are placed onto the hair-bearing areas of the scalp for varying time periods before, during, and after cytotoxic chemotherapy cycles. Although not yet reported, improper application procedures could result in undesirable adverse events (AEs). At present, there are no evidence-based scalp cooling protocols, and there is no regulatory oversight of their use. OBJECTIVE To report the occurrence of cold thermal injury (frostbite) on the scalp, following the use of cold caps for the prevention of CIA. MATERIALS AND METHODS We identified four patients who developed cold thermal injuries on the scalp following the application of cold caps. Medical records were analyzed to retrieve the demographic, clinical, and histologic characteristics. RESULTS The cold thermal injuries in our patients were grade 1/2 in severity and improved with topical interventions, although mild persistent alopecia ensued in 3 patients. The true incidence of such injuries in this setting however, remains unknown. CONCLUSIONS Cold thermal cold injuries are likely an infrequent and preventable AE that may result from improper device application procedures during scalp cooling. Although these untoward events are usually mild to moderate in severity, the potential occurrence of long-term sequelae (e.g. permanent alopecia, scarring) are not known. Future prospective studies are needed to further elucidate the risk and standardized delivery methods, and patient/clinical education. PMID:27146710

Chlorophyll fluorescence emission as a reporter on cold tolerance in Arabidopsis thaliana accessions

PubMed Central

Mishra, Anamika; Höermiller, Imke I; Heyer, Arnd G; Nedbal, Ladislav

2011-01-01

Non-invasive, high-throughput screening methods are valuable tools in breeding for abiotic stress tolerance in plants. Optical signals such as chlorophyll fluorescence emission can be instrumental in developing new screening techniques. In order to examine the potential of chlorophyll fluorescence to reveal plant tolerance to low temperatures, we used a collection of nine Arabidopsis thaliana accessions and compared their fluorescence features with cold tolerance quantified by the well established electrolyte leakage method on detached leaves. We found that, during progressive cooling, the minimal chlorophyll fluorescence emission rose strongly and that this rise was highly dependent on the cold tolerance of the accessions. Maximum quantum yield of PSII photochemistry and steady state fluorescence normalized to minimal fluorescence were also highly correlated to the cold tolerance measured by the electrolyte leakage method. In order to further increase the capacity of the fluorescence detection to reveal the low temperature tolerance, we applied combinatorial imaging that employs plant classification based on multiple fluorescence features. We found that this method, by including the resolving power of several fluorescence features, can be well employed to detect cold tolerance already at mild sub-zero temperatures. Therefore, there is no need to freeze the screened plants to the largely damaging temperatures of around −15°C. This, together with the method's easy applicability, represents a major advantage of the fluorescence technique over the conventional electrolyte leakage method. PMID:21427532

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries.

PubMed

do Rosário, Denes Kaic Alves; da Silva Mutz, Yhan; Peixoto, Jaqueline Moreira Curtis; Oliveira, Syllas Borburema Silva; de Carvalho, Raquel Vieira; Carneiro, Joel Camilo Souza; de São José, Jackline Freitas Brilhante; Bernardes, Patrícia Campos

2017-01-16

New sanitization methods have been evaluated to improve food safety and food quality and to replace chlorine compounds. However, these new methods can lead to physicochemical and sensory changes in fruits and vegetables. The present study evaluated the effects of acetic acid, peracetic acid, and sodium dodecylbenzenesulfonate isolated or combined with 5min of ultrasound treatment (40kHz, 500W) on strawberry quality over 9days of storage at 8°C. The strawberry natural contaminant microbiota (molds and yeasts, mesophilic aerobic and lactic acid bacteria), physicochemical quality (pH, total titratable acidity, total soluble solids, vitamin C, and color), sensory quality (triangle test) and inactivation of Salmonella enterica subsp. enterica intentionally inoculated onto strawberries were analyzed. Ultrasound increased the effect of all chemical compounds in the reduction of aerobic mesophilic, molds and yeasts. The best treatment for those groups of microorganisms was ultrasound combined with peracetic acid (US+PA) that reduced 1.8 and 2.0logcfu/g during 9days of storage. Bactericidal effect of peracetic acid was also improved by ultrasound inactivation of S. enterica, reaching a decimal reduction of 2.1logcfu/g. Moreover, synergistic effects were observed in contaminant natural microbiota inactivation for all tested compounds during storage, without any major physicochemical or sensory alteration to the strawberries. Therefore, ultrasound treatment can improve the effect of sanitizers that are substitutes of chlorine compounds without altering the quality of strawberries during storage. Acetic acid (PubChem CID: 176); Peracetic acid (PubChem CID: 6585); Sodium dodecylbenzenesulfonate (PubChem CID: 18372154). Copyright © 2016 Elsevier B.V. All rights reserved.

A novel approach to the pacemaker infection with non-thermal atmospheric pressure plasma

NASA Astrophysics Data System (ADS)

Zhang, Yuchen; Li, Yu; Li, Yinglong; Yu, Shuang; Li, Haiyan; Zhang, Jue

2017-08-01

Although the pacemaker (PM) is a key cardiac implantable electrical device for life-threatening arrhythmias treatment, the related infection is a challenge. Thus, the aim of this study is to validate cold plasma as a potential technology for the disinfection of infected pacemakers. Fifty donated PMs were cleaned and sterilized before use and then infected with Staphylococcus aureus ( S. aureus). Then, each experimental group was treated with cold plasma treatment for 1 min, 3 min, 5 min and 7 min, while the control group was immersed with sterilized water. Effectiveness of disinfection was evaluated by using CFU counting method and confocal laser scanning microscopy (CLSM). The physicochemical properties of water treated with cold plasma at different time were evaluated, including water temperature change and oxidation reduction potential (ORP). The major reactive species generated by the cold plasma equipment during cold plasma were analyzed with optical emission spectroscopy (OES). No live bacteria were detected with CFU counting method after 7 min of cold plasma treatment, which matches with the CLSM results. The ORP value of water and H2O2 concentration changed significantly after treating with cold plasma. Furthermore, reactive oxygen species (ROS) and reactive nitrogen species (RNS), especially NO, O (777 nm) and O (844 nm) were probably key inactivation agents in cold plasma treatment. These results indicate that cold plasma could be an effective technology for the disinfection of implantable devices.

Study on site selection of cold chain logistics in northwest territories

NASA Astrophysics Data System (ADS)

Liu, Yubin; Ren, Zongwei

2017-08-01

In this research, we mainly studied the Site selection problem of cold chain logistics in northwest of China. In the first place, we counted the demands of cold chain products in northwest territories, and then classified it into the Site selection problem in five provinces in northwest territories(Xinjiang, Qinghai, Gansu, Ningxia, Shanxi); Next, we used the Center of gravity Method to select initial location; Finally, we established the location of distribution by using Analytic Hierarchy Process (AHP)and fuzzy comprehensive evaluation method. Comparing with the traditional method, this method not only considered the cost of transportation and distance, but also deliberated the physical condition, social environment and economics condition which associated with Site selection problem.

Dynamic thermal-time model of cold hardiness for dormant grapevine buds

USDA-ARS?s Scientific Manuscript database

Grapevine (Vitis spp.) cold hardiness varies dynamically throughout the dormant season, primarily in response to changes in temperature. We describe development and possible uses of a discrete-dynamic model of bud cold hardiness for three Vitis genotypes. Iterative methods were used to optimize and ...

VUV Photoionisation of hydrocarbon radicals

NASA Astrophysics Data System (ADS)

Alcaraz, C.; Noller, Bastian; Hemberger, Patrick; Fischer, Ingo; Gans, Bérenger; Boyé-Peronne, Séverine; Douin, Stéphane; Gauyacq, Dolorès; Soldi-Lose, Héloïse; Garcia, Gustavo

2008-09-01

Hydrocarbon radicals CxHy are constituents of various planetary atmospheres, in particular Titan, as a result of the methane photochemistry induced by the solar radiation. They contribute to the neutral chemistry, but are also important for the ionosphere through their photoionisation leading to their cations CxHy +. These cations are also produced by ion-molecule reactions starting from the reaction of the primary ions CH4 + and CH3 + which are created in the non-dissociative and dissociative photoionisation of CH4. This work aims at caracterizing the VUV photoionisation of small hydrocarbon radicals as a function of photon energy. The objective is to provide laboratory data for modelers on the spectroscopy, the thermochemistry, and the reactivity of the radicals and their cations. The hydrocarbon radicals are much less caracterized than stable molecules since they have to be produced in situ in the laboratory experiment. We have adapted at Orsay [1-3] a pyrolysis source (Figure 1) well suited to produce cold beams of hydrocarbon radicals to our experimental setups. Available now at Orsay, we have two new sources of VUV radiation, complementary in terms of tunability and resolution, that can be used for these studies. The first one is the DESIRS beamline [4] at the new french synchrotron, SOLEIL. The second one is the VUV laser developped at the Centre Laser de l'Université Paris-Sud (CLUPS) [5]. At SOLEIL, a photoelectron-photoion coincidence spectrometer is used to monitor the photoionisation on a large photon energy range. At the CLUPS, a pulsedfield ionisation (PFI-ZEKE) spectrometer allows studies at higher resolution on selected photon energies. The first results obtained with these new setups will be presented. References [1] Fischer, I., Schussler, T., Deyerl, H.J., Elhanine, M. & Alcaraz, C., Photoionization and dissociative photoionization of the allyl radical, C3H5. Int. J. Mass Spectrom., 261 (2-3), 227-233 (2007) [2] Schüßler, T., Roth, W., Gerber, T., Alcaraz, C. & Fischer, I., The vacuum ultraviolet photochemistry of radicals: C3H3 and C2H5. Phys. Chem. Chem. Phys., 7 (5), 819-825 (2005) [3] Schüßler, T., Deyerl, H. J., Dummler, S., Fischer, I., Alcaraz, C. & Elhanine, M., The vacuum ultraviolet photochemistry of the allyl radical investigated using synchrotron radiation J. Chem. Phys., 118 (20), 9077-80 (2003) [4] DESIRS, http://www.synchrotronsoleil. fr/portal/page/portal/Recherche/LignesLumiere/ DESIRS [5] CLUPS, http://www.clups.u-psud.fr/

System and method of applying energetic ions for sterilization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, John A.

2003-12-23

A method of sterilization of a container is provided whereby a cold plasma is caused to be disposed near a surface to be sterilized, and the cold plasma is then subjected to a pulsed voltage differential for producing energized ions in the plasma. Those energized ions then operate to achieve spore destruction on the surface to be sterilized. Further, a system for sterilization of a container which includes a conductive or non-conductive container, a cold plasma in proximity to the container, and a high voltage source for delivering a pulsed voltage differential between an electrode and the container and acrossmore » the cold plasma, is provided.« less

ChemRad Sample Form Instructions

EPA Pesticide Factsheets

These instructons are intended to assist registered users of the EPA Region 8 Drinking Water Watch website who would like to create ChemRad Sample Forms for monitoring that is required during the current year.

Soil diversity and hydration as observed by ChemCam at Gale crater, Mars

USGS Publications Warehouse

Meslin, P.-Y.; Gasnault, O.; Forni, O.; Schroder, S.; Cousin, A.; Berger, G.; Clegg, S.M.; Lasue, J.; Maurice, S.; Sautter, V.; Le Mouélic, S.; Wiens, R.C.; Fabre, C.; Goetz, W.; Bish, D.L.; Mangold, N.; Ehlmann, B.; Lanza, N.; Harri, A.-M.; Anderson, Ryan Bradley; Rampe, E.; McConnochie, T.H.; Pinet, P.; Blaney, D.; ,; Archer, D.; Barraclough, B.; Bender, S.; Blake, D.; Blank, J.G.; Bridges, N.; Clark, B. C.; DeFlores, L.; Delapp, D.; Dromart, G.; Dyar, M.D.; Fisk, M. R.; Gondet, B.; Grotzinger, J.; Herkenhoff, K.; Johnson, J.; Lacour, J.-L.; Langevin, Y.; Leshin, L.; Lewin, E.; Madsen, M.B.; Melikechi, N.; Mezzacappa, Alissa; Mischna, M.A.; Moores, J.E.; Newsom, H.; Ollila, A.; ,; Renno, N.; Sirven, J.B.; Tokar, R.; de la Torre, M.; d'Uston, L.; Vaniman, D.; Yingst, A.

2013-01-01

The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Soil diversity and hydration as observed by ChemCam at Gale crater, Mars.

PubMed

Meslin, P-Y; Gasnault, O; Forni, O; Schröder, S; Cousin, A; Berger, G; Clegg, S M; Lasue, J; Maurice, S; Sautter, V; Le Mouélic, S; Wiens, R C; Fabre, C; Goetz, W; Bish, D; Mangold, N; Ehlmann, B; Lanza, N; Harri, A-M; Anderson, R; Rampe, E; McConnochie, T H; Pinet, P; Blaney, D; Léveillé, R; Archer, D; Barraclough, B; Bender, S; Blake, D; Blank, J G; Bridges, N; Clark, B C; DeFlores, L; Delapp, D; Dromart, G; Dyar, M D; Fisk, M; Gondet, B; Grotzinger, J; Herkenhoff, K; Johnson, J; Lacour, J-L; Langevin, Y; Leshin, L; Lewin, E; Madsen, M B; Melikechi, N; Mezzacappa, A; Mischna, M A; Moores, J E; Newsom, H; Ollila, A; Perez, R; Renno, N; Sirven, J-B; Tokar, R; de la Torre, M; d'Uston, L; Vaniman, D; Yingst, A

2013-09-27

The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Improving integrative searching of systems chemical biology data using semantic annotation.

PubMed

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Are Lithium Ion Cells Intrinsically Safe?

PubMed Central

Dubaniewicz, Thomas H.; DuCarme, Joseph P.

2015-01-01

National Institute for Occupational Safety and Health researchers are studying the potential for Li-ion-battery thermal runaway from an internal short circuit in equipment approved as permissible for use in underground coal mines. Researchers used a plastic wedge to induce internal short circuits for thermal runaway susceptibility evaluation purposes, which proved to be a more severe test than the flat plate method for selected Li-ion cells. Researchers conducted cell crush tests within a 20-L chamber filled with 6.5% CH4–air to simulate the mining hazard. Results indicate that LG Chem ICR18650S2 LiCoO2 cells pose a CH4 explosion hazard from a cell internal short circuit. Under specified test conditions, A123 Systems 26650 LiFePO4 cells were safer than the LG Chem ICR18650S2 LiCoO2 cells at a conservative statistical significance level. PMID:26166911

Prediction of drug transport processes using simple parameters and PLS statistics. The use of ACD/logP and ACD/ChemSketch descriptors.

PubMed

Osterberg, T; Norinder, U

2001-01-01

A method of modelling and predicting biopharmaceutical properties using simple theoretically computed molecular descriptors and multivariate statistics has been investigated for several data sets related to solubility, IAM chromatography, permeability across Caco-2 cell monolayers, human intestinal perfusion, brain-blood partitioning, and P-glycoprotein ATPase activity. The molecular descriptors (e.g. molar refractivity, molar volume, index of refraction, surface tension and density) and logP were computed with ACD/ChemSketch and ACD/logP, respectively. Good statistical models were derived that permit simple computational prediction of biopharmaceutical properties. All final models derived had R(2) values ranging from 0.73 to 0.95 and Q(2) values ranging from 0.69 to 0.86. The RMSEP values for the external test sets ranged from 0.24 to 0.85 (log scale).

From the one-bead-one-compound concept to one-bead-one-reactor.

PubMed

Marani, Mariela M; Paradís-Bas, Marta; Tulla-Puche, Judit; Côté, Simón; Camperi, Silvia A; Cascone, Osvaldo; Albericio, Fernando

2007-01-01

The one-bead-one-compound method gives access to millions of compounds that can be screened directly on the bead. Although characterization techniques are increasingly potent and reliable, problems can still be encountered in deciphering the sequence of the active compound because of sensitiveness or manipulation of the bead. ChemMatrix, a totally PEG-based resin, has resolved the synthesis of peptides of outstanding difficulty. Like other PEG-based resins, it permits on-bead screening because of its compatibility in aqueous media and has the further advantage of having a high loading, comparable to polystyrene resins. ChemMatrix beads previously swelled in water can be nicely divided into four parts that can be characterized using different analytical techniques or just stored for safety or for further testing. The four bead parts show high homogeneity and can thus be considered to be replicas.

Effect of Intramolecular Dispersion Interactions on the Conformational Preferences of Monoterpenoids

NASA Astrophysics Data System (ADS)

Loru, Donatella; Vigorito, Annalisa; Santos, Andreia; Tang, Jackson; Sanz, M. Eugenia

2017-06-01

The rotational spectra of several monoterpenoids have been reinvestigated with a 2-8 GHz chirped pulse FTMW spectrometer. Axial conformers, in addition to previously reported equatorial conformers, have been detected for carvone, perillaldehyde, and limonene. Observation of the ^{13}C isotopologues of these monoterpenoids in their natural abundances allowed the determination of r_s and r_0 structures. Axial conformers are stabilised by dispersion interactions between the six-membered ring of the monoterpenoids and the isopropenyl group. Comparison of experimental data with ab initio and density functional calculations shows that an accurate description of dispersion interactions is still a challenge for theoretical methods. J. R. Avilés Moreno, F. Partal Ureña, J. J. López González and T. R. Huet, Chem. Phys. Lett., 2009, 473, 17-20. J. R. Avilés Moreno, T. R. Huet and J. J. López González, Struct. Chem., 2013, 24, 1163-1170.

State-specific tunneling lifetimes from classical trajectories: H-atom dissociation in electronically excited pyrrole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Weiwei; Domcke, Wolfgang; Farantos, Stavros C.

A trajectory method of calculating tunneling probabilities from phase integrals along straight line tunneling paths, originally suggested by Makri and Miller [J. Chem. Phys. 91, 4026 (1989)] and recently implemented by Truhlar and co-workers [Chem. Sci. 5, 2091 (2014)], is tested for one- and two-dimensional ab initio based potentials describing hydrogen dissociation in the {sup 1}B{sub 1} excited electronic state of pyrrole. The primary observables are the tunneling rates in a progression of bending vibrational states lying below the dissociation barrier and their isotope dependences. Several initial ensembles of classical trajectories have been considered, corresponding to the quasiclassical and themore » quantum mechanical samplings of the initial conditions. It is found that the sampling based on the fixed energy Wigner density gives the best agreement with the quantum mechanical dissociation rates.« less

Quantum dynamics study of H+NH3-->H2+NH2 reaction.

PubMed

Zhang, Xu Qiang; Cui, Qian; Zhang, John Z H; Han, Ke Li

2007-06-21

We report in this paper a quantum dynamics study for the reaction H+NH3-->NH2+H2 on the potential energy surface of Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The quantum dynamics calculation employs the semirigid vibrating rotor target model [J. Z. H. Zhang, J. Chem. Phys. 111, 3929 (1999)] and time-dependent wave packet method to propagate the wave function. Initial state-specific reaction probabilities are obtained, and an energy correction scheme is employed to account for zero point energy changes for the neglected degrees of freedom in the dynamics treatment. Tunneling effect is observed in the energy dependency of reaction probability, similar to those found in H+CH4 reaction. The influence of rovibrational excitation on reaction probability and stereodynamical effect are investigated. Reaction rate constants from the initial ground state are calculated and are compared to those from the transition state theory and experimental measurement.

Thermodynamics and kinetics of graphene chemistry: a graphene hydrogenation prototype study.

PubMed

Pham, Buu Q; Gordon, Mark S

2016-12-07

The thermodynamic and kinetic controls of graphene chemistry are studied computationally using a graphene hydrogenation reaction and polyaromatic hydrocarbons to represent the graphene surface. Hydrogen atoms are concertedly chemisorped onto the surface of graphene models of different shapes (i.e., all-zigzag, all-armchair, zigzag-armchair mixed edges) and sizes (i.e., from 16-42 carbon atoms). The second-order Z-averaged perturbation theory (ZAPT2) method combined with Pople double and triple zeta basis sets are used for all calculations. It is found that both the net enthalpy change and the barrier height of graphene hydrogenation at graphene edges are lower than at their interior surfaces. While the thermodynamic product distribution is mainly determined by the remaining π-islands of functionalized graphenes (Phys. Chem. Chem. Phys., 2013, 15, 3725-3735), the kinetics of the reaction is primarily correlated with the localization of the electrostatic potential of the graphene surface.

Is the common cold a clinical entity or a cultural concept?

PubMed

Eccles, R

2013-03-01

Common cold is the most common infectious disease of mankind and the term is widely used in the clinical literature as though it were a defined clinical syndrome. Clinical studies on this syndrome often use elaborate symptom scoring systems to diagnose a common cold. The symptom scores are based on a study conducted over 50 years ago to retrospectively diagnose experimental cold and this method cannot be applied to diagnosis of common cold in the community. Diagnosis of the common cold by virology is not feasible because of the number of viruses and the variability in the disease states caused by the viruses. Because of the familiarity of subjects with common cold and the variability in symptomatology it seems a more reasonable approach to use self-diagnosis of common cold for clinical research studies and accept that the common cold is a cultural concept and not a clinical entity.

PubChem3D: conformer ensemble accuracy

PubMed Central

2013-01-01

Background PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules. Results The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (STST-opt) and combo-Tanimoto (ComboTST-opt), and color-optimized color-Tanimoto (CTCT-opt) and combo-Tanimoto (ComboTCT-opt). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 Å), and decreasing the STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively). Conclusion This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D sampling on 3-D similarity measures shows that there is a linear degradation of average accuracy with respect to molecular size and flexibility. Generally speaking, one can likely expect the worst-case minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, and 1.13, in terms of STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt, respectively. This expected accuracy improves linearly as the molecule becomes smaller or less flexible. PMID:23289532

DEVELOPMENT OF IN-PLACE DENSITY METHOD FOR COLD IN-PLACE RECYCLING

DOT National Transportation Integrated Search

2018-01-01

This report presents the results of a research study funded by the Nevada DOT and the SOLARIS University Transportation Center. The research developed a method for measuring the in-place density of the cold in-place recycled (CIR) layer immediately a...

Prevalence of Post-tonsillectomy Bleeding as Day-case Surgery with Combination Method; Cold Dissection Tonsillectomy and Bipolar Diathermy Hemostasis

PubMed Central

Faramarzi, Abolahassan; Heydari, Seyed Taghi

2010-01-01

Objective Post-tonsillectomy hemorrhage remains an important factor in determining the safety of performing tonsillectomy as a day case procedure. The aim of this study was to determine the safety of day case tonsillectomy by using combination method, cold dissection tonsillectomy and bipolar diathermy hemostasis. Methods A prospective randomized clinical study conducted on the patients who had undergone day case tonsillectomy (DCT). There were two groups (DCT and control group) each group consisting of 150 cases. Tonsillectomy was performed by using combination method; cold dissection and hemostasis was achieved by ligation of vessels with bipolar electerocautery. Findings We found 3 cases of post-tonsillectomy bleeding in DCT group and 4 cases in the control group. There was no statistically significant difference in the rate of post-operative hemorrhage between the two groups. Conclusion The findings suggest the safety of the combination of cold dissection tonsillectomy and bipolar diathermy hemostasis as day case tonsillectomy. PMID:23056702

Full Configuration Interaction Quantum Monte Carlo and Diffusion Monte Carlo: A Comparative Study of the 3D Homogeneous Electron Gas

NASA Astrophysics Data System (ADS)

Shepherd, James J.; López Ríos, Pablo; Needs, Richard J.; Drummond, Neil D.; Mohr, Jennifer A.-F.; Booth, George H.; Grüneis, Andreas; Kresse, Georg; Alavi, Ali

2013-03-01

Full configuration interaction quantum Monte Carlo1 (FCIQMC) and its initiator adaptation2 allow for exact solutions to the Schrödinger equation to be obtained within a finite-basis wavefunction ansatz. In this talk, we explore an application of FCIQMC to the homogeneous electron gas (HEG). In particular we use these exact finite-basis energies to compare with approximate quantum chemical calculations from the VASP code3. After removing the basis set incompleteness error by extrapolation4,5, we compare our energies with state-of-the-art diffusion Monte Carlo calculations from the CASINO package6. Using a combined approach of the two quantum Monte Carlo methods, we present the highest-accuracy thermodynamic (infinite-particle) limit energies for the HEG achieved to date. 1 G. H. Booth, A. Thom, and A. Alavi, J. Chem. Phys. 131, 054106 (2009). 2 D. Cleland, G. H. Booth, and A. Alavi, J. Chem. Phys. 132, 041103 (2010). 3 www.vasp.at (2012). 4 J. J. Shepherd, A. Grüneis, G. H. Booth, G. Kresse, and A. Alavi, Phys. Rev. B. 86, 035111 (2012). 5 J. J. Shepherd, G. H. Booth, and A. Alavi, J. Chem. Phys. 136, 244101 (2012). 6 R. Needs, M. Towler, N. Drummond, and P. L. Ríos, J. Phys.: Condensed Matter 22, 023201 (2010).

Detection/classification/quantification of chemical agents using an array of surface acoustic wave (SAW) devices

NASA Astrophysics Data System (ADS)

Milner, G. Martin

2005-05-01

ChemSentry is a portable system used to detect, identify, and quantify chemical warfare (CW) agents. Electro chemical (EC) cell sensor technology is used for blood agents and an array of surface acoustic wave (SAW) sensors is used for nerve and blister agents. The combination of the EC cell and the SAW array provides sufficient sensor information to detect, classify and quantify all CW agents of concern using smaller, lighter, lower cost units. Initial development of the SAW array and processing was a key challenge for ChemSentry requiring several years of fundamental testing of polymers and coating methods to finalize the sensor array design in 2001. Following the finalization of the SAW array, nearly three (3) years of intensive testing in both laboratory and field environments were required in order to gather sufficient data to fully understand the response characteristics. Virtually unbounded permutations of agent characteristics and environmental characteristics must be considered in order to operate against all agents and all environments of interest to the U.S. military and other potential users of ChemSentry. The resulting signal processing design matched to this extensive body of measured data (over 8,000 agent challenges and 10,000 hours of ambient data) is considered to be a significant advance in state-of-the-art for CW agent detection.

Effectiveness of two commercial rotenone formulations in the eradication of virile crayfish Orconectes virillis

USGS Publications Warehouse

Recsetar, Matthew S.; Bonar, Scott A.

2015-01-01

The virile or northern crayfish Orconectes virilis is an invasive species throughout much of the USA, damaging aquatic communities where it is introduced. Therefore, identification of effective methods for its eradication from areas in which it is unwanted is important. We studied the effectiveness of two commercial formulations of rotenone, Chem Fish Regular and CFT Legumine, for virile crayfish control. Although both formulations were effective for fish eradication, earlier observations by fisheries managers suggested that the relative effectiveness of the two formulations differs for crayfish. The only noteworthy difference between the formulations is that the former contains a synergist. In our first experiment, we tested each toxicant at the maximum labeled dosage (5 ppm) and found CFT Legumine to be 100% ineffective (0% mortality), while the Chem Fish Regular treatment resulted in 12.5% mortality. After we deemed Chem Fish Regular to be the only toxicant with any effectiveness against virile crayfish, we tested concentrations from 5 to 50 ppm and found 10 times the maximum labeled dosage (50 ppm rotenone) was needed to kill all virile crayfish. Because crayfish burrow and can leave water, and because 100% eradication is usually desired, rotenone applied at the labeled rates will not be effective for crayfish control. However, treating a body of water with CFT Legumine to eradicate invasive fish while leaving desirable crayfish unharmed is possible.

Top-down Estimate of Dust Emissions Through Integration of MODIS and MISR Aerosol Retrievals With the Geos-chem Adjoint Model

NASA Technical Reports Server (NTRS)

Wang, Jun; Xu, Xiaoguang; Henze, Daven K.; Zeng, Jing; Ji, Qiang; Tsay, Si-Chee; Huang, Jianping

2012-01-01

Predicting the influences of dust on atmospheric composition, climate, and human health requires accurate knowledge of dust emissions, but large uncertainties persist in quantifying mineral sources. This study presents a new method for combined use of satellite-measured radiances and inverse modeling to spatially constrain the amount and location of dust emissions. The technique is illustrated with a case study in May 2008; the dust emissions in Taklimakan and Gobi deserts are spatially optimized using the GEOSChem chemical transport model and its adjoint constrained by aerosol optical depth (AOD) that are derived over the downwind dark-surface region in China from MODIS (Moderate Resolution Imaging Spectroradiometer) reflectance with the aerosol single scattering properties consistent with GEOS-chem. The adjoint inverse modeling yields an overall 51% decrease in prior dust emissions estimated by GEOS-Chem over the Taklimakan-Gobi area, with more significant reductions south of the Gobi Desert. The model simulation with optimized dust emissions shows much better agreement with independent observations from MISR (Multi-angle Imaging SpectroRadiometer) AOD and MODIS Deep Blue AOD over the dust source region and surface PM10 concentrations. The technique of this study can be applied to global multi-sensor remote sensing data for constraining dust emissions at various temporal and spatial scales, and hence improving the quantification of dust effects on climate, air quality, and human health.

Chem/bio sensing with non-classical light and integrated photonics.

PubMed

Haas, J; Schwartz, M; Rengstl, U; Jetter, M; Michler, P; Mizaikoff, B

2018-01-29

Modern quantum technology currently experiences extensive advances in applicability in communications, cryptography, computing, metrology and lithography. Harnessing this technology platform for chem/bio sensing scenarios is an appealing opportunity enabling ultra-sensitive detection schemes. This is further facilliated by the progress in fabrication, miniaturization and integration of visible and infrared quantum photonics. Especially, the combination of efficient single-photon sources together with waveguiding/sensing structures, serving as active optical transducer, as well as advanced detector materials is promising integrated quantum photonic chem/bio sensors. Besides the intrinsic molecular selectivity and non-destructive character of visible and infrared light based sensing schemes, chem/bio sensors taking advantage of non-classical light sources promise sensitivities beyond the standard quantum limit. In the present review, recent achievements towards on-chip chem/bio quantum photonic sensing platforms based on N00N states are discussed along with appropriate recognition chemistries, facilitating the detection of relevant (bio)analytes at ultra-trace concentration levels. After evaluating recent developments in this field, a perspective for a potentially promising sensor testbed is discussed for reaching integrated quantum sensing with two fiber-coupled GaAs chips together with semiconductor quantum dots serving as single-photon sources.

Ground-state energy of HeH+

NASA Astrophysics Data System (ADS)

Zhou, Bing-Lu; Zhu, Jiong-Ming; Yan, Zong-Chao

2006-06-01

The nonrelativistic ground-state energy of He4H+ is calculated using a variational method in Hylleraas coordinates. Convergence to a few parts in 1010 is achieved, which improves the best previous result of Pavanello [J. Chem. Phys. 123, 104306 (2005)]. Expectation values of the interparticle distances are evaluated. Similar results for He3H+ are also presented.

First Principles Modeling of the Performance of a Hydrogen-Peroxide-Driven Chem-E-Car

ERIC Educational Resources Information Center

Farhadi, Maryam; Azadi, Pooya; Zarinpanjeh, Nima

2009-01-01

In this study, performance of a hydrogen-peroxide-driven car has been simulated using basic conservation laws and a few numbers of auxiliary equations. A numerical method was implemented to solve sets of highly non-linear ordinary differential equations. Transient pressure and the corresponding traveled distance for three different car weights are…

77 FR 57541 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-18

...-600 series airplanes. This proposed AD was prompted by reports of early fatigue cracks at chem- mill... the fuselage skin at certain locations at chem-mill areas, and repair if necessary. We are proposing...

ChemCam Mast Unit Being Prepared for Laser Firing

NASA Image and Video Library

2010-12-23

Researchers prepare for a test of the Chemistry and Camera ChemCam instrument that will fly on NASA Mars Science Laboratory mission; researchers are preparing the instrument mast unit for a laser firing test.

Readying ChemCam

NASA Image and Video Library

2012-08-17

This image shows the calibration target for the Chemistry and Camera ChemCam instrument on NASA Curiosity rover. The calibration target is one square and a group of nine circles that look dark in the black-and-white image.

System and method for crystalline sheet growth using a cold block and gas jet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kellerman, Peter L.; Mackintosh, Brian; Carlson, Frederick M.

A crystallizer for growing a crystalline sheet from a melt may include a cold block having a cold block surface that faces an exposed surface of the melt, the cold block configured to generate a cold block temperature at the cold block surface that is lower than a melt temperature of the melt at the exposed surface. The system may also include a nozzle disposed within the cold block and configured to deliver a gas jet to the exposed surface, wherein the gas jet and the cold block are interoperative to generate a process zone that removes heat from themore » exposed surface at a first heat removal rate that is greater than a second heat removal rate from the exposed surface in outer regions outside of the process zone.« less

Nanoporous Polymeric Grating-Based Optical Biosensors (Preprint)

DTIC Science & Technology

2007-03-01

Tombelli, S.; Mascini, M.; Bilia, A; Bergonzi, M. C.; Vincieri, F. F. Talanta 2005, 65, 578-585. Haughey, S. A; Baxter, G. A J of AOAC Inter. 2006 , 89, 862...C.; Bowers, M. T. JAm. Chem. Soc 2006 , 128,8484-8492. (6) Wang, l et. al. Anal. Chim. Acta 1997, 347, 1-8. Jena, B. K.; Raj, C. R. Anal. Chem. 2006 ...78, 6332-6339. Hansen, J. A; Wang, l; Kawde, A; Xiang, Y.; Gothelf, K. V.; Collins, G JAm. Chem. Soc 2006 , 128,2228-2229. Huang, T; 14 Liu, M.; Knight

Substituent Effects and Bonding Characteristics in o- Benzoquinonediiminebis(bipyrdine) Ruthenium(II) Complexes

DTIC Science & Technology

1992-10-23

C.; Dei, A.; Gatteschi , D.; Pardi, L Inorg. Chem. 1989, 2L 1476; (b) Benel, C.; Dei, A.; Gatteschi , D.; Ckdel, H. U.; Pardi, L Inorg. Ckem. 1989, 28...3091; (c) Benelli, C.; Dei, A.; Gatteschi , D.; Pardi, L Inorg.Chem. 1990,2& 3409. 16. Bruni, S.; Cariati, F.; Dei, A.; Gatteschi , D. Inog Cbim. Ata...1991, 186 157. 17. Dei, A.; Gatteschi , D.; Pardi, L; Barra, A. L; Brunel, L C. Chem, Py. Lett.. 1990, 175. 589; Dei, A.; Pardi, L Inorg, Chim.Acta

Mechanisms of Laser Induced Reactions in Opaque Heterogeneous Environments

DTIC Science & Technology

1993-11-01

D. Oelkrug, W.P. Hagan, J. Hyslop and F. Wilkinson, Opt. Acta, 1983, 30, 1090. 38. D. Oelkrug, S. Uhl, C.J. Willsher and F. Wilkinson, J. Phys. Chem...Oelkrug D. Hagan W P, Hyslop ]I and Wilkinson F 1983 Opt. Acta 301090 Kessler Rt W and Wilkinson F 1981 J. Chem. Soc.. Fa’aday Trans. 1 77 309 Kossanyi J...under the corrected emission spectrum is a direct evaluation 8 T. Kartens and K. Ki.obs, J. Phys. Chem., 1980 , 84, 1871. of OF. The displacement of the

Calcium Sulfate Characterized by ChemCam/Curiosity at Gale Crater, Mars

NASA Technical Reports Server (NTRS)

Nachon, M.; Clegg, S. N.; Mangold, N.; Schroeder, S.; Kah, L. C.; Dromart, G.; Ollila, A.; Johnson, J. R.; Oehler, D. Z.; Bridges, J. C.;

Compilation of Atomic and Molecular Data Relevant to Gas Lasers. Volume VII.

DTIC Science & Technology

1980-12-01

Schaefer and A. E. Orel, "Potential Energy Curves for Diatomic Zinc and Codmium", J. Chem. Phys. 71, 1122 (1979). 19. M. F. Golde and A. Kuaran...34Chemiluminescence of Argon Bromide. I. The Emission Spectrum of ArBr", J. Chem. Phys. 72, 434 (1980). 20. M. F. Golde and K. Kuaran, "Chemiluminescence of...72, 2469 (1980). (A-4.6 - A-4.17). 3. M. F. Golde and A. Kvaran, "Chemiluminescence of Argon Bromide. I. The Emission Spectrum of Ar Br", J. Chem

BiF/NF2 Kinetics Studies: Mechanism and Conversion Efficiency

DTIC Science & Technology

1990-08-31

68A, 61 (1964) 9. R. F Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 84, 2137 (1986). 10. R. J. Malins and D. W Setser, J...Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 93, 7818 (1989). 15. C. H . Corliss and W R. Bozman, Experimental Transition...MS Informal Report, UC-34a, UC-LASL (July 1980). 18. R. F Heidner III, H . Helvajian , J. S. Holloway, and J. B. Koffend, J. Chem. Phys. 93, 7813 (1989

EQCM Measurements: Redox-Induced Changes in Solvent and Ion Content in Anchored Redox Monolayers of Organosulfur Compounds and Their Electrocatalysis on Gold Electrodes

DTIC Science & Technology

1990-08-01

Langmuir, I. J. Am. Chem. Soc. 1917, 39, 1848-1906. b ) Blodgett, K. B . J. Am. Chem. Soc. 1935, 57, 1007-1022. c) Blinov , L. M. Russ. Chem. Rev. 1988, 52...pressure producing a polarization b ) Converse piezoelectric effect (structural deformation) caused by applying a potential across the crystal...of Ferrocenamide phenyl disulfide in: A) IM HC104, B ) IM HNO 3 , and C) iM H2 SO4 versus SSCE ....... ...... ................ s34 Figure 3.7 Study of

Calculation of Kinetic Data for Processes Leading to UV Signatures

DTIC Science & Technology

1989-03-31

Jv we make use of the numerical algorithm developed by Stodden and Micha 17, extending it to the equations of motion in curvilinear coordinates. To be...in the field of the average potential V(Q). The set of equations (4.13’) have been recently derived by Stodden and Michat 5 in a more tedious.way by...B. Bloom, J. Chem. Phys. 83, 5703 (1985) 5 P. K. Swamninathan, C. D. Stodden , and D. A. Micha, J. Chem. Phys., in press (1989). 6 R. A. Marcus, Chem

Synthesis Laboratory for the U.S. Army Medical Research Institute of Infectious Diseases Selection Panel

DTIC Science & Technology

1991-01-14

McCain 27 1 M. D. Ochs 73.5 4 C Richards 203.25 11 Dr. J. M. Riordan 108.5 6 Glassware Technicians: A. D. Jackson 322 18 W. Johnson 172 10 R...Kissinger. L. W.; Von. 1. / Med. Chem., 1*4*. 68, 1220- 1225. 3. Robins, R. K; Christensen, L. F. /. Med. Chem., 1978, 21, 742 4. Branson , J. (Bristol...Myers), personal communication. 5. Branson , Joanne J.; Ghazzouli, I.; Hitchcock, M. J. M; Webb, R. R.; Martin, J. C, J. Med. Chem., 1989. 32, 1457-1463

Self-Assembled Multi-Component Catenanes: The Effect of Multivalency and Cooperativity on Structure and Stability

DTIC Science & Technology

2012-06-11

12835−12842. (b) Paul, P. K. C.; Sukumar, M.; Bardi , R.; Piazzesi, A . M.; Valle, G.; Toniolo, C.; Balaram, P. J . Am. Chem. Soc. 1986, 108, 6363−6370...dx.doi.org/10.1021/ja302347q | J . Am. Chem. Soc. 2012, 134, 11430−1144311432 3), however, was unexpected, as it led to a large decrease (>1000-fold...Journal of the American Chemical Society Article dx.doi.org/10.1021/ja302347q | J . Am. Chem. Soc. 2012, 134, 11430−1144311439 described by a combination

Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum.

DTIC Science & Technology

1985-12-31

0.33) or a Schwarzschild reflector (N.A. ..- - 1.25, x 36) directly onto the GaAs (100) substrate housed in a stainless steel, 4-window cell. The cell...Department of Energy under contract .. DE-AC-02-78ER04940. (1) G. Karl , P. Kruus and J. Polanyl, J. Chem. Phys. 46,224, (1967). .- (2) G. Karl , P. Kruus, J...Chem. 39, 2244, (1961). (7) G. Karl and J. Polanyl, J. Chem Phys. 38, 271, (1963). (8) H. Okabe, Photochemistrv-of Small Molecules, New York, J

Calibrating the ChemCam LIBS for Carbonate Minerals on Mars

DOE R&D Accomplishments Database

Wiens, Roger C.; Clegg, Samuel M.; Ollila, Ann M.; Barefield, James E.; Lanza, Nina; Newsom, Horton E.

2009-01-01

The ChemCam instrument suite on board the NASA Mars Science Laboratory (MSL) rover includes the first LIBS instrument for extraterrestrial applications. Here we examine carbonate minerals in a simulated martian environment using the LIDS technique in order to better understand the in situ signature of these materials on Mars. Both chemical composition and rock type are determined using multivariate analysis (MVA) techniques. Composition is confirmed using scanning electron microscopy (SEM) techniques. Our initial results suggest that ChemCam can recognize and differentiate between carbonate materials on Mars.

Applications of Scanning Tunneling Microscopy to Electrochemistry

DTIC Science & Technology

1988-10-28

electrochemically pretreated platinum surfaces in air by baro and coworkers (68) and by Fan and bard (Fan, F-R.F.; Bard, A.J. Anl ._Chem,, submitted) have...W.V.; Coleman, R.V.; Drake, B.; Hansma, P.K. MXL. Rev, A 1986 4, 994-1005. 10. Smith, D.P.E.; Kirk, M.D.; Quate, C.F. - 1987, 8, 6034 -38. 11...Electroanal. Chem. 1988, 238, 9-31. 65. Wightman, R.M. Anl hm 1981, U3, lI26A-31A. 66. Gong. L.; Reed, R.A.; Longuire, N.; Murray, R.W. J. Phxs. Chem

Free Energy Barrier for Molecular Motions in Bistable [2]Rotaxane Molecular Electronic Devices

DTIC Science & Technology

2009-04-10

H. R.; Vignon, S . A.; Star, A.; Celestre, P. C.; Stoddart, J. F.; Heath, J. R. ChemPhysChem 2003, 4, 1335–1339. (18) Credi, A.; Balzani, V .; Langford...Chem. Soc. 2004, 126, 3370–3371. (29) Badjic, J. D.; Balzani, V .; Credi, A.; Silvi, S .; Stoddart, J. F. Science 2004, 303, 1845–1849. (30) Tseng, H. R...Tseng, H. R.; Vignon, S . A.; Celestre, P. C.; Perkins, J.; Jeppesen, J. O.; Di Fabio, A.; Ballardini, R.; Gandolfi, M. T.; Venturi, M.; Balzani, V

Method of fabricating a cooled electronic system

DOEpatents

Chainer, Timothy J; Gaynes, Michael A; Graybill, David P; Iyengar, Madhusudan K; Kamath, Vinod; Kochuparambil, Bejoy J; Schmidt, Roger R; Schultz, Mark D; Simco, Daniel P; Steinke, Mark E

2014-02-11

A method of fabricating a liquid-cooled electronic system is provided which includes an electronic assembly having an electronics card and a socket with a latch at one end. The latch facilitates securing of the card within the socket. The method includes providing a liquid-cooled cold rail at the one end of the socket, and a thermal spreader to couple the electronics card to the cold rail. The thermal spreader includes first and second thermal transfer plates coupled to first and second surfaces on opposite sides of the card, and thermally conductive extensions extending from end edges of the plates, which couple the respective transfer plates to the liquid-cooled cold rail. The extensions are disposed to the sides of the latch, and the card is securable within or removable from the socket using the latch without removing the cold rail or the thermal spreader.

Co-amplification at lower denaturation temperature-PCR: methodology and applications.

PubMed

Liang, Hui; Chen, Guo-Jie; Yu, Yan; Xiong, Li-Kuan

2018-03-20

Co-amplification at lower denaturation temperature-polymerase chain reaction (COLD-PCR) is a novel form of PCR that selectively denatures and amplifies low-abundance mutations from mixtures of wild-type and mutation-containing sequences, enriching the mutation 10 to 100 folds. Due to the slightly altered melting temperature (Tm) of the double-stranded DNA and the formation of the mutation/wild-type heteroduplex DNA, COLD-PCR methods are sensitive, specific, accurate, cost-effective and easy to maneuver, and can enrich mutations of any type and at any position, even unknown mutations within amplicons. COLD-PCR and its improved methods are now applied in cancer, microorganisms, prenatal screening, animals and plants. They are extremely useful for early diagnosis, monitoring the prognosis of disease and the efficiency of the treatment, drug selection, prediction of prognosis, plant breeding and etc. In this review, we introduce the principles, key techniques, derived methods and applications of COLD-PCR.

Effects of univariate and multivariate regression on the accuracy of hydrogen quantification with laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Ytsma, Cai R.; Dyar, M. Darby

2018-01-01

Hydrogen (H) is a critical element to measure on the surface of Mars because its presence in mineral structures is indicative of past hydrous conditions. The Curiosity rover uses the laser-induced breakdown spectrometer (LIBS) on the ChemCam instrument to analyze rocks for their H emission signal at 656.6 nm, from which H can be quantified. Previous LIBS calibrations for H used small data sets measured on standards and/or manufactured mixtures of hydrous minerals and rocks and applied univariate regression to spectra normalized in a variety of ways. However, matrix effects common to LIBS make these calibrations of limited usefulness when applied to the broad range of compositions on the Martian surface. In this study, 198 naturally-occurring hydrous geological samples covering a broad range of bulk compositions with directly-measured H content are used to create more robust prediction models for measuring H in LIBS data acquired under Mars conditions. Both univariate and multivariate prediction models, including partial least square (PLS) and the least absolute shrinkage and selection operator (Lasso), are compared using several different methods for normalization of H peak intensities. Data from the ChemLIBS Mars-analog spectrometer at Mount Holyoke College are compared against spectra from the same samples acquired using a ChemCam-like instrument at Los Alamos National Laboratory and the ChemCam instrument on Mars. Results show that all current normalization and data preprocessing variations for quantifying H result in models with statistically indistinguishable prediction errors (accuracies) ca. ± 1.5 weight percent (wt%) H2O, limiting the applications of LIBS in these implementations for geological studies. This error is too large to allow distinctions among the most common hydrous phases (basalts, amphiboles, micas) to be made, though some clays (e.g., chlorites with ≈ 12 wt% H2O, smectites with 15-20 wt% H2O) and hydrated phases (e.g., gypsum with ≈ 20 wt% H2O) may be differentiated from lower-H phases within the known errors. Analyses of the H emission peak in Curiosity calibration targets and rock and soil targets on the Martian surface suggest that shot-to-shot variations of the ChemCam laser on Mars lead to variations in intensity that are comparable to those represented by the breadth of H standards tested in this study.

What the multiline signal (MLS) simulation data with average of weighted computations reveal about the Mn hyperfine interactions and oxidation states of the manganese cluster in OEC?

NASA Astrophysics Data System (ADS)

Baituti, Bernard

2017-11-01

Understanding the structure of oxygen evolving complex (OEC) fully still remains a challenge. Lately computational chemistry with the data from more detailed X-ray diffraction (XRD) OEC structure, has been used extensively in exploring the mechanisms of water oxidation in the OEC (Gatt et al., J. Photochem. Photobiol. B 104(1-2), 80-93 2011). Knowledge of the oxidation states is very crucial for understanding the core principles of catalysis by photosystem II (PSII) and catalytic mechanism of OEC. The present study involves simulation studies of the X-band continuous wave electron-magnetic resonance (CW-EPR) generated S 2 state signals, to investigate whether the data is in agreement with the four manganese ions in the OEC, being organised as a `3 + 1' (trimer plus one) model (Gatt et al., Angew. Chem. Int. Ed. 51, 12025-12028 2012; Petrie et al., Chem. A Eur. J. 21, 6780-6792 2015; Terrett et al., Chem. Commun. (Camb.) 50, 8-11 2014) or `dimer of dimers' model (Terrett et al. 2016). The question that still remains is how much does each Mn ion contribute to the " g2multiline" signal through its hyperfine interactions in OEC also to differentiate between the `high oxidation state (HOS)' and `low oxidation state (LOS)' paradigms? This is revealed in part by the structure of multiline (ML) signal studied in this project. Two possibilities have been proposed for the redox levels of the Mn ions within the catalytic cluster, the so called `HOS' and `LOS' paradigms (Gatt et al., J. Photochem. Photobiol. B 104(1-2), 80-93 2011). The method of data analysis involves numerical simulations of the experimental spectra on relevant models of the OEC cluster. The simulations of the X-band CW-EPR multiline spectra, revealed three manganese ions having hyperfine couplings with large anisotropy. These are most likely Mn III centres and these clearly support the `LOS' OEC paradigm model, with a mean oxidation of 3.25 in the S2 state. This is consistent with the earlier data by Jin et al. (Phys. Chem. Chem. Phys. (PCCP) 16(17), 7799-812 2014), but the present results clearly indicate that heterogeneity in hyperfine couplings exist in samples as typically prepared.

Numeric kinetic energy operators for molecules in polyspherical coordinates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadri, Keyvan; Meyer, Hans-Dieter; Lauvergnat, David

Generalized curvilinear coordinates, as, e.g., polyspherical coordinates, are in general better adapted to the resolution of the nuclear Schroedinger equation than rectilinear ones like the normal mode coordinates. However, analytical expressions of the kinetic energy operators (KEOs) for molecular systems in polyspherical coordinates may be prohibitively complicated for large systems. In this paper we propose a method to generate a KEO numerically and bring it to a form practicable for dynamical calculations. To examine the new method we calculated vibrational spectra and eigenenergies for nitrous acid (HONO) and compare it with results obtained with an exact analytical KEO derived previouslymore » [F. Richter, P. Rosmus, F. Gatti, and H.-D. Meyer, J. Chem. Phys. 120, 6072 (2004)]. In a second example we calculated {pi}{yields}{pi}* photoabsorption spectrum and eigenenergies of ethene (C{sub 2}H{sub 4}) and compared it with previous work [M. R. Brill, F. Gatti, D. Lauvergnat, and H.-D. Meyer, Chem. Phys. 338, 186 (2007)]. In this ethene study the dimensionality was reduced from 12 to 6 by freezing six internal coordinates. Results for both molecules show that the proposed method for obtaining an approximate KEO is reliable for dynamical calculations. The error in eigenenergies was found to be below 1 cm{sup -1} for most states calculated.« less

Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reboredo, Fernando A.; Kim, Jeongnim

A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys. 136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspacemore » of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.« less

A New WRF-Chem Treatment for Studying Regional Scale Impacts of Cloud-Aerosol Interactions in Parameterized Cumuli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berg, Larry K.; Shrivastava, ManishKumar B.; Easter, Richard C.

A new treatment of cloud-aerosol interactions within parameterized shallow and deep convection has been implemented in WRF-Chem that can be used to better understand the aerosol lifecycle over regional to synoptic scales. The modifications to the model to represent cloud-aerosol interactions include treatment of the cloud dropletnumber mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convective cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. Thesechanges have beenmore » implemented in both the WRF-Chem chemistry packages as well as the Kain-Fritsch cumulus parameterization that has been modified to better represent shallow convective clouds. Preliminary testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS) as well as a high-resolution simulation that does not include parameterized convection. The simulation results are used to investigate the impact of cloud-aerosol interactions on the regional scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column integrated BC can be as large as -50% when cloud-aerosol interactions are considered (due largely to wet removal), or as large as +35% for sulfate in non-precipitating conditions due to the sulfate production in the parameterized clouds. The modifications to WRF-Chem version 3.2.1 are found to account for changes in the cloud drop number concentration (CDNC) and changes in the chemical composition of cloud-drop residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to WRF-Chem version 3.5, and it is anticipated that they will be included in a future public release of WRF-Chem.« less

Hydrogen adsorption strength and sites in the metal organic framework MOF5: Comparing experiment and model calculations

NASA Astrophysics Data System (ADS)

Mulder, F. M.; Dingemans, T. J.; Schimmel, H. G.; Ramirez-Cuesta, A. J.; Kearley, G. J.

2008-07-01

Hydrogen adsorption in porous, high surface area, and stable metal organic frameworks (MOF's) appears a novel route towards hydrogen storage materials [N.L. Rosi, J. Eckert, M. Eddaoudi, D.T. Vodak, J. Kim, M. O'Keeffe, O.M. Yaghi, Science 300 (2003) 1127; J.L.C. Rowsell, A.R. Millward, K. Sung Park, O.M. Yaghi, J. Am. Chem. Soc. 126 (2004) 5666; G. Ferey, M. Latroche, C. Serre, F. Millange, T. Loiseau, A. Percheron-Guegan, Chem. Commun. (2003) 2976; T. Loiseau, C. Serre, C. Huguenard, G. Fink, F. Taulelle, M. Henry, T. Bataille, G. Férey, Chem. Eur. J. 10 (2004) 1373]. A prerequisite for such materials is sufficient adsorption interaction strength for hydrogen adsorbed on the adsorption sites of the material because this facilitates successful operation under moderate temperature and pressure conditions. Here we report detailed information on the geometry of the hydrogen adsorption sites, based on the analysis of inelastic neutron spectroscopy (INS). The adsorption energies for the metal organic framework MOF5 equal about 800 K for part of the different sites, which is significantly higher than for nanoporous carbon materials (˜550 K) [H.G. Schimmel, G.J. Kearley, M.G. Nijkamp, C.T. Visser, K.P. de Jong, F.M. Mulder, Chem. Eur. J. 9 (2003) 4764], and is in agreement with what is found in first principles calculations [T. Sagara, J. Klassen, E. Ganz, J. Chem. Phys. 121 (2004) 12543; F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113]. Assignments of the INS spectra is realized using comparison with independently published model calculations [F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113] and structural data [T. Yildirim, M.R. Hartman, Phys. Rev. Lett. 95 (2005) 215504].

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.

PubMed

Jeffryes, James G; Colastani, Ricardo L; Elbadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D; Broadbelt, Linda J; Hanson, Andrew D; Fiehn, Oliver; Tyo, Keith E J; Henry, Christopher S

2015-01-01

In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC-MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures. Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.

The influence of aerosols and land-use type on NO2 satellite retrieval over China

NASA Astrophysics Data System (ADS)

Liu, Mengyao; Lin, Jintai; Boersma, Folkert; Eskes, Henk; Chimot, Julien

2017-04-01

Both aerosols and surface reflectance have a strong influence on the retrieval of NO2 tropospheric vertical column densities (VCDs), especially over China with its heavy aerosol loading and rapid changes in land-use type. However, satellite retrievals of NO2 VCDs usually do not explicitly account for aerosol optical effects and surface reflectance anisotropy (BRDF) that varies in space and time. We develop an improved algorithm to derive tropospheric AMFs and VCDs over China from the OMI instrument - POMINO and DOMINO. This method can also be applied to TropOMI NO2 retrievals in the future. With small pixels of TropOMI and higher probability of encountering clear-sky scenes, the influence of BRDF and aerosol interference becomes more important than for OMI. Daily aerosol information is taken from the GEOS-Chem chemistry transport model and the aerosol optical depth (AOD) is adjusted via MODIS AOD climatology. We take the MODIS MCD43C2 C5 product to account for BRDF effects. The relative altitude of NO2 and aerosols is critical factor influencing the NO2 retrieval. In order to evaluate the aerosol extinction profiles (AEP) of GEOS-Chem improve our algorithm, we compare the GEOS-Chem simulation with CALIOP and develop a CALIOP AEP climatology to regulate the model's AEP. This provides a new way to include aerosol information into the tracer gas retrieval for OMI and TropOMI. Preliminary results indicate that the model performs reasonably well in reproducing the AEP shape. However, it seems to overestimate aerosols under 2km and underestimate above. We find that relative humidity (RH) is an important factor influencing the AEP shape when comparing the model with observations. If we adjust the GEOS-Chem RH to CALIOP's RH, the correlations of their AEPs also improve. Besides, take advantage of our retrieval method, we executed sensitivity tests to analyze their influences on NO2 trend and spatiotemporal variations in retrieval. It' the first time to investigate influence from aerosols and surface reflectance in 10-year period (2005-2015) in the real retrieval. We find their influences are largely time and space dependent, but their effects on trend are small, leading relative 7% differences in different areas.

Precision Spectroscopy in Cold Molecules: the First Rotational Intervals of He_2^+ by High-Resolution Spectroscopy and Rydberg-Series Extrapolation

NASA Astrophysics Data System (ADS)

Jansen, Paul; Semeria, Luca; Scheidegger, Simon; Merkt, Frederic

2015-06-01

Having only three electrons, He_2^+ represents a system for which highly accurate ab initio calculations are possible. The latest calculation of rovibrational energies in He_2^+ do not include relativistic or QED corrections but claim an accuracy of about 120 MHz The available experimental data on He_2^+, though accurate to 300 MHz, are not precise enough to rigorously test these calculations or reveal the magnitude of the relativistic and QED corrections. We have performed high-resolution Rydberg spectroscopy of metastable He_2 molecules and employed multichannel-quantum-defect-theory extrapolation techniques to determine the rotational energy-level structure in the He_2^+ ion. To this end we have produced samples of helium molecules in the a ^3σ_u^+ state in supersonic beams with velocities tunable down to 100 m/s by combining a cryogenic supersonic-beam source with a multistage Zeeman decelerator. The metastable He_2 molecules are excited to np Rydberg states using the frequency doubled output of a pulse-amplified ring dye laser. Although the bandwidth of the laser systems is too large to observe the reduction of the Doppler width resulting from deceleration, the deceleration greatly simplifies the spectral assignments because of its spin-rotational state selectivity. Our approach enabled us to determine the rotational structure of He_2^+ with unprecedented accuracy, to determine the size of the relativistic and QED corrections by comparison with the results of Ref.~a and to precisely measure the rotational structure of the metastable state for comparison with the results of Focsa~et al. W.-C. Tung, M. Pavanello, L. Adamowicz, J. Chem. Phys. 136, 104309 (2012). D. Sprecher, J. Liu, T. Krähenmann, M. Schäfer, and F. Merkt, J. Chem. Phys. 140, 064304 (2014). M. Motsch, P. Jansen, J. A. Agner, H. Schmutz, and F. Merkt, Phys. Rev. A 89, 043420 (2014). C. Focsa, P. F. Bernath, and R. Colin, J. Mol. Spectrosc. 191, 209 (1998).

Electronic Relaxation Processes of Transition Metal Atoms in Helium Nanodroplets

NASA Astrophysics Data System (ADS)

Kautsch, Andreas; Lindebner, Friedrich; Koch, Markus; Ernst, Wolfgang E.

2014-06-01

Spectroscopy of doped superfluid helium nanodroplets (He_N) gives information about the influence of this cold, chemically inert, and least interacting matrix environment on the excitation and relaxation dynamics of dopant atoms and molecules. We present the results from laser induced fluorescence (LIF), photoionization (PI), and mass spectroscopy of Cr and Cu doped He_N. From these results, we can draw a comprehensive picture of the complex behavior of such transition metal atoms in He_N upon photo-excitation. The strong Cr and Cu ground state transitions show an excitation blueshift and broadening with respect to the bare atom transitions which can be taken as indication for the solvation inside the droplet. From the originally excited states the atoms relax to energetically lower states and are ejected from the He_N. The relaxation processes include bare atom spin-forbidden transitions, which clearly bears the signature of the He_N influence. Two-color resonant two-photon ionization (2CR2PI) also shows the formation of bare atoms and small Cr-He_n and Cu-He_n clusters in their ground and metastable states ^c. Currently, Cr dimer excitation studies are in progress and a brief outlook on the available results will be given. C. Callegari and W. E. Ernst, Helium Droplets as Nanocryostats for Molecular Spectroscopy - from the Vacuum Ultraviolet to the Microwave Regime, in Handbook of High-Resolution Spectroscopy, eds. M. Quack and F. Merkt, John Wiley & Sons, Chichester, 2011. A. Kautsch, M. Koch, and W. E. Ernst, J. Phys. Chem. A, 117 (2013) 9621-9625, DOI: 10.1021/jp312336m F. Lindebner, A. Kautsch, M. Koch, and W. E. Ernst, Int. J. Mass Spectrom. (2014) in press, DOI: 10.1016/j.ijms.2013.12.022 M. Koch, A. Kautsch, F. Lackner, and W. E. Ernst, submitted to J. Phys. Chem. A

Mechanisms and Effects of Summertime Transport of African Dust Through the Tokar Mountain Gap to the Red Sea and Arabian Peninsula

NASA Astrophysics Data System (ADS)

Kalenderski, S.; Stenchikov, G. L.

2015-12-01

Very high dust loading over the Red Sea region in summer strongly affects the nutrition balance and thermal and dynamic regimes of the sea. The observations suggest that small-scale local dynamic and orographic effects, from both the Arabian and African sides, strongly contribute to dust plume formation. To better understand and quantify these processes we present here the first high resolution modeling study of the dust outbreak phenomena in June 2012 over East Africa, the Red Sea, and the Arabian Peninsula using the WRF-Chem model. We identified several dust generating dynamical processes that range from convective to synoptic scales, including: synoptic cyclones, nocturnal low-level jets, and cold pools of mesoscale convective systems. The simulations reveal an eastward transport of African dust across the Red Sea. Over the northern part of the Red Sea most of the dust transport occurs beyond 2 km above ground level and is strengthened by a pressure gradient formed by low pressure over the eastern Mediterranean and high pressure over the Arabian Peninsula. Across the central and southern parts of the Red Sea dust is mostly transported below 2 km height. During the study period dust is a dominant contributor (87%) to aerosol optical depth (AOD), producing a domain average cooling effect of -12.1 W m-2 at surface, a warming of 7.1 W m-2 in the atmosphere, and a residual cooling of -4.9 W m-2 at the top of the atmosphere. WRF-Chem simulations demonstrate that both dry and wet deposition processes contribute significantly to dust removal from the atmosphere. During the dust outbreak 49.2 Tg of dust deposits within the calculation domain, which is approximately 90% of the total dust emission of 54.5 Tg. Model results compare well with available ground-based and satellite observations but generally underestimate the observed AOD maximum values.

Tropospheric Emission Spectrometer (TES) for the Earth Observing System (EOS) CHEM Satellite

NASA Technical Reports Server (NTRS)

Beer, R.; Glavich, T.; Rider, D.

2000-01-01

The Tropospheric Emission Spectrometer (TES) is an imaging infrared Fourier transform spectrometer scheduled to be launched into polar sun-synchronous orbit on the Earth Observing System (EOS) CHEM satellite in December 2002.

Curiosity ChemCam Analyzes Rocks, Soils and Dust

NASA Image and Video Library

2013-04-08

This diagram shows how materials analyzed by the ChemCam instrument on NASA Curiosity Mars rover during the first 100 Martian days of the mission differed with regard to hydrogen content horizontal axis and alkali vertical axis.

Drilled Hole and ChemCam Marks at Cumberland

NASA Image and Video Library

2013-06-05

The Chemistry and Camera ChemCam instrument on NASA Mars rover Curiosity was used to check the composition of gray tailings from the hole in rock target Cumberland that the rover drilled on May 19, 2013.

Evaluation of Chem-Crete : final report.

DOT National Transportation Integrated Search

1982-01-01

Two test sections, one on new construction and the other on a maintenance resurfacing project, were installed in the fall of 1980 to evaluate the proprietary product Chem-Crete. Laboratory tests and dynaflect and density measurements were performed o...

Interactive Gaussian Graphical Models for Discovering Depth Trends in ChemCam Data

NASA Astrophysics Data System (ADS)

Oyen, D. A.; Komurlu, C.; Lanza, N. L.

2018-04-01

Interactive Gaussian graphical models discover surface compositional features on rocks in ChemCam targets. Our approach visualizes shot-to-shot relationships among LIBS observations, and identifies the wavelengths involved in the trend.

HExpoChem: a systems biology resource to explore human exposure to chemicals.

PubMed

Taboureau, Olivier; Jacobsen, Ulrik Plesner; Kalhauge, Christian; Edsgärd, Daniel; Rigina, Olga; Gupta, Ramneek; Audouze, Karine

2013-05-01

Humans are exposed to diverse hazardous chemicals daily. Although an exposure to these chemicals is suspected to have adverse effects on human health, mechanistic insights into how they interact with the human body are still limited. Therefore, acquisition of curated data and development of computational biology approaches are needed to assess the health risks of chemical exposure. Here we present HExpoChem, a tool based on environmental chemicals and their bioactivities on human proteins with the objective of aiding the qualitative exploration of human exposure to chemicals. The chemical-protein interactions have been enriched with a quality-scored human protein-protein interaction network, a protein-protein association network and a chemical-chemical interaction network, thus allowing the study of environmental chemicals through formation of protein complexes and phenotypic outcomes enrichment. HExpoChem is available at http://www.cbs.dtu.dk/services/HExpoChem-1.0/.

Stereomicroscopic imaging technique for the quantification of cold flow in drug-in-adhesive type of transdermal drug delivery systems.

PubMed

Krishnaiah, Yellela S R; Katragadda, Usha; Khan, Mansoor A

2014-05-01

Cold flow is a phenomenon occurring in drug-in-adhesive type of transdermal drug delivery systems (DIA-TDDS) because of the migration of DIA coat beyond the edge. Excessive cold flow can affect their therapeutic effectiveness, make removal of DIA-TDDS difficult from the pouch, and potentially decrease available dose if any drug remains adhered to pouch. There are no compendial or noncompendial methods available for quantification of this critical quality attribute. The objective was to develop a method for quantification of cold flow using stereomicroscopic imaging technique. Cold flow was induced by applying 1 kg force on punched-out samples of marketed estradiol DIA-TDDS (model product) stored at 25°C, 32°C, and 40°C/60% relative humidity (RH) for 1, 2, or 3 days. At the end of testing period, dimensional change in the area of DIA-TDDS samples was measured using image analysis software, and expressed as percent of cold flow. The percent of cold flow significantly decreased (p < 0.001) with increase in size of punched-out DIA-TDDS samples and increased (p < 0.001) with increase in cold flow induction temperature and time. This first ever report suggests that dimensional change in the area of punched-out samples stored at 32°C/60%RH for 2 days applied with 1 kg force could be used for quantification of cold flow in DIA-TDDS. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Science Underlying 2008 Nobel Prizes

NASA Astrophysics Data System (ADS)

Caldwell, Bernadette A.

2009-01-01

JCE offers a wealth of materials for teaching and learning chemistry that you can explore online. In the list below, Bernadette Caldwell of the Editorial Staff suggests additional resources that are available through JCE for teaching the science behind some of the 2008 Nobel Prizes . Discovering and Applying the Chemistry of GFP The Royal Swedish Academy of Sciences awarded the 2008 Nobel Prize in Chemistry for the discovery and development of the green fluorescent protein, GFP to three scientists: Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien. These scientists led the field in discovering and introducing a fluorescing protein from jellyfish into cells and genes under study, which allows researchers to witness biochemistry in action. Now tags are available that emit light in different colors, revealing myriad biological processes and their interactions simultaneously. Identifying HPV and HIV, HIV's Replication Cycle, and HIV Virus-Host Interactions The Nobel Assembly at Karolinska Institutet awarded the 2008 Nobel Prize in Medicine or Physiology for their discovery of human immunodeficiency virus (HIV) to two scientists: Françoise Barré-Sinoussi and Luc Montagnier; and for his discovery of human papilloma viruses [HPV] causing cervical cancer to one scientist, Harald zur Hausen. Diseases caused by these infectious agents significantly affect global health. While isolating and studying the virus, researchers discovered HIV is an uncommon retrovirus that infects humans and relies on the host to make its viral DNA, infecting and killing the host's white blood cells, ultimately destroying the immune systems of infected humans. Related Resources at JCE Online The Journal has published articles relating to GFP specifically, and more generally to fluorescing compounds applied to biochemistry. The Journal has also published an article and a video on protease inhibition—a strategy to suppress HIV's biological processes. With the video clips, an accompanying guide for teachers includes instructions for three student activities that use enzymes. The resources below may help introduce students to the science behind some of these Nobel Prizes. Turning on the Light: Lessons from Luminescence. O'Hara, P. B.; Engelson, C.; St. Peter, W. J. Chem. Educ. 2005, 82, 49 . (See especially the bioluminescence section on page 51 that concisely explains GFP.) JCE Classroom Activity #68: Turning on the Light. O'Hara, P. B.; Engelson, C.; St. Peter, W. J. Chem. Educ. 2005, 82, 48A . JCE Classroom Activity #81: pHantastic Fluorescence. Muyskens, M. J. Chem. Educ. 2006, 83, 768A . Recombinant Green Fluorescent Protein Isoforms: Exercises To Integrate Molecular Biology, Biochemistry, and Biophysical Chemistry. Hicks, B. W. J. Chem. Educ. 1999, 76, 409 . C-SNARF-1 as a Fluorescent Probe for pH Measurements in Living Cells: Two-Wavelength-Ratio Method versus Whole-Spectral-Resolution Method. Ribou, A-C.; Vigo, J.; Salmon, J-M. J. Chem. Educ. 2002, 79, 1471 . An Attack on the AIDS Virus: Inhibition of the HIV-1 Protease: New Drug Development Based on the Structure and Activity of the Protease and Its Role in the Replication and Maturation of the Virus. Volker, E. J. J. Chem. Educ. 1993, 70, 3 . From Chemistry Comes Alive!, five video clips demonstrate properties and mechanisms involved in the chemistry of HIV. HIV-1 Protease: An Enzyme at Work . All articles from Volume 1 to the current issue are available in full-text PDF at JCE Online : Browse by year, month, and page , or choose title and author searching of all issues of JCE.

Freeze drying method

DOEpatents

Coppa, Nicholas V.; Stewart, Paul; Renzi, Ernesto

1999-01-01

The present invention provides methods and apparatus for freeze drying in which a solution, which can be a radioactive salt dissolved within an acid, is frozen into a solid on vertical plates provided within a freeze drying chamber. The solid is sublimated into vapor and condensed in a cold condenser positioned above the freeze drying chamber and connected thereto by a conduit. The vertical positioning of the cold condenser relative to the freeze dryer helps to help prevent substances such as radioactive materials separated from the solution from contaminating the cold condenser. Additionally, the system can be charged with an inert gas to produce a down rush of gas into the freeze drying chamber to also help prevent such substances from contaminating the cold condenser.

Optimization of laser cladding of cold spray coatings with B4C and Ni powders

NASA Astrophysics Data System (ADS)

Fomin, V. M.; Golyshev, A. A.; Malikov, A. G.; Orishich, A. M.; Filippov, A. A.; Ryashin, N. S.

2017-12-01

In the present work, a combined method is considered for the production of a metal-matrix composite coating based on Ni and B4C. The coating is created by consistently applied methods: cold spray and laser cladding. The conditions of obtaining cermet layers are investigated depending on the parameters of laser cladding and cold spray. It is shown that the laser track structure significantly changes in accordance to the size of ceramic particles ranging 3-75 µm and its concentration. It is shown that the most perspective layers for additive manufacturing could be obtain from cold spray coatings with ceramic concentrations more than 50% by weight treated in the heat-conductivity laser mode.

RATIONAL DETERMINATION METHOD OF PROBABLE FREEZING INDEX FOR n-YEARS CONSIDERING THE REGIONAL CHARACTERISTICS

NASA Astrophysics Data System (ADS)

Kawabata, Shinichiro; Hayashi, Keiji; Kameyama, Shuichi

This paper investigates a method for ob taining the probable freezing index for n -years from past frostaction damage and meteorological data. From investigati on of Japanese cold winter data from the areas of Hokkaido, Tohoku and south of Tohoku, it was found that the extent of cold winter had regularity by location south or north. Also, after obtaining return periods of cold winters by area, obvious regional characteristics were found. Mild winters are rare in Hokkaido. However, it was clarified that when Hokkaido had cold winters, its size increased. It wa s effective to determine the probable freezing indices as 20-, 15- and 10-year return periods for Hokkaido, Tohoku and south of Tohoku, respectively.

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

PubMed

Roh, Min K; Gillespie, Dan T; Petzold, Linda R

2010-11-07

The weighted stochastic simulation algorithm (wSSA) was developed by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] to efficiently estimate the probabilities of rare events in discrete stochastic systems. The wSSA uses importance sampling to enhance the statistical accuracy in the estimation of the probability of the rare event. The original algorithm biases the reaction selection step with a fixed importance sampling parameter. In this paper, we introduce a novel method where the biasing parameter is state-dependent. The new method features improved accuracy, efficiency, and robustness.

Methods to Estimate Acclimatization to Urban Heat Island Effects on Heat- and Cold-Related Mortality

PubMed Central

Milojevic, Ai; Armstrong, Ben G.; Gasparrini, Antonio; Bohnenstengel, Sylvia I.; Barratt, Benjamin; Wilkinson, Paul

2016-01-01

Background: Investigators have examined whether heat mortality risk is increased in neighborhoods subject to the urban heat island (UHI) effect but have not identified degrees of difference in susceptibility to heat and cold between cool and hot areas, which we call acclimatization to the UHI. Objectives: We developed methods to examine and quantify the degree of acclimatization to heat- and cold-related mortality in relation to UHI anomalies and applied these methods to London, UK. Methods: Case–crossover analyses were undertaken on 1993–2006 mortality data from London UHI decile groups defined by anomalies from the London average of modeled air temperature at a 1-km grid resolution. We estimated how UHI anomalies modified excess mortality on cold and hot days for London overall and displaced a fixed-shape temperature-mortality function (“shifted spline” model). We also compared the observed associations with those expected under no or full acclimatization to the UHI. Results: The relative risk of death on hot versus normal days differed very little across UHI decile groups. A 1°C UHI anomaly multiplied the risk of heat death by 1.004 (95% CI: 0.950, 1.061) (interaction rate ratio) compared with the expected value of 1.070 (1.057, 1.082) if there were no acclimatization. The corresponding UHI interaction for cold was 1.020 (0.979, 1.063) versus 1.030 (1.026, 1.034) (actual versus expected under no acclimatization, respectively). Fitted splines for heat shifted little across UHI decile groups, again suggesting acclimatization. For cold, the splines shifted somewhat in the direction of no acclimatization, but did not exclude acclimatization. Conclusions: We have proposed two analytical methods for estimating the degree of acclimatization to the heat- and cold-related mortality burdens associated with UHIs. The results for London suggest relatively complete acclimatization to the UHI effect on summer heat–related mortality, but less clear evidence for cold–related mortality. Citation: Milojevic A, Armstrong BG, Gasparrini A, Bohnenstengel SI, Barratt B, Wilkinson P. 2016. Methods to estimate acclimatization to urban heat island effects on heat- and cold-related mortality. Environ Health Perspect 124:1016–1022; http://dx.doi.org/10.1289/ehp.1510109 PMID:26859738

Arctic chlorine activation and ozone depletion: Comparison of chemistry transport models with satellite observations.

NASA Astrophysics Data System (ADS)

Grooß, J.-U.; Wegner, T.; Müller, R.; Chipperfield, M. P.; Feng, W.; Santee, M. L.

2009-04-01

The accurate simulation of Arctic stratospheric ozone depletion has been an issue for two decades. However, there are still notable quantitative discrepancies between the models and observations. We show results from the SLIMCAT and CLaMS 3D chemistry-transport models that differ in some aspects of simulated chlorine activation and descent in the polar vortex. Consequently, the estimates of accumulated ozone depletion in the polar vortex for these two models in cold Arctic winters still largely disagree. As shown recently by Santee et al. (JGR, 2008) using MLS and ACE data, the extent of chlorine activation for the cold Arctic winter of 2004/2005 within the basic SLIMCAT model is overestimated with the likely consequence of too much simulated ozone depletion. In contrast, the CLaMS simulation for the same winter shows too little chlorine activation compared to observations, and therefore likely too little loss. For SLIMCAT the version used by Santee et al. has been updated to replace the equilibrium treatment of NAT PSCs with a Lagrangian microphysical scheme. This leads to smaller regions of NAT particles and less denitrification, in better agreement with observations. The impact of this on the modeled extent of chlorine activation will be discussed. For CLaMS we have changed the parameterization of heterogeneous reactions on liquid aerosols from Carslaw et al. to that of Shi et al. (2001), with which chlorine activation on liquid aerosol becomes more efficient. In turn, the simulated chlorine activation agrees better with the observations. The impact of these model changes on chlorine activation and ozone loss will be assessed and remaining model-observation discrepancies will be discussed in terms of different model formulations. We will also show the impact of recent lab measurements of Cl2O2 absorption cross sections by von Hobe et al. (2009) on the simulated ozone depletion. References: von Hobe, M., F. Stroh, H. Beckers, T. Benter, and H. Willner, The UV/Vis absorption spectrum of matrix isolated dichlorine peroxide, ClOOCl, Phys. Chem. Chem. Phys. , doi:10.1039/B814373K, 2009. Santee M. L., I. A. MacKenzie, G. L. Manney, M. P. Chipperfield, P. F. Bernath, K. A. Walker, C. D. Boone, L. Froidevaux, N. J. Livesey, J. W. Waters, A study of stratospheric chlorine partitioning based on new satellite measurements and modeling, J. Geophys. Res., 113, D12307, doi:10.1029/2007JD009057, 2008. Shi, Q., J. Jayne, C. Kolb, D. Worsnop, and P. Davidovits, Kinetic model for reaction of ClONO2 with H2O and HCl and HOCl with HCl in sulfuric acid solutions, J. Geophys. Res., 106, 24259-24274, 2001.

Secondary organic aerosol formation from road vehicle emissions

NASA Astrophysics Data System (ADS)

Pieber, Simone M.; Platt, Stephen M.; El Haddad, Imad; Zardini, Alessandro A.; Suarez-Bertoa, Ricardo; Slowik, Jay G.; Huang, Ru-Jin; Hellebust, Stig; Temime-Roussel, Brice; Marchand, Nicolas; Drinovec, Luca; Mocnik, Grisa; Baltensperger, Urs; Astorga, Covadogna; Prévôt, André S. H.

2014-05-01

Organic aerosol particles (OA) are a major fraction of the submicron particulate matter. OA consists of directly emitted primary (POA) and secondary OA (SOA). SOA is formed in-situ in the atmosphere via the reaction of volatile organic precursors. The partitioning of SOA species depends not only on the exposure to oxidants, but for instance also on temperature, relative humidity (RH), and the absorptive mass chemical composition (presence of inorganics) and concentration. Vehicle exhaust is a known source of POA and likely contributes to SOA formation in urban areas [1;2]. This has recently been estimated by (i) analyzing ambient data from urban areas combined with fuel consumption data [3], (ii) by examining the chemical composition of raw fuels [4], or (iii) smog chamber studies [5, 6]. Contradictory and thus somewhat controversial results in the relative quantity of SOA from diesel vs. gasoline vehicle exhaust were observed. In order to elucidate the impact of variable ambient conditions on the potential SOA formation of vehicle exhaust, and its relation to the emitted gas phase species, we studied SOA formed from the exhaust of passenger cars and trucks as a function of fuel and engine type (gasoline, diesel) at different temperatures (T 22 vs. -7oC) and RH (40 vs. 90%), as well as with different levels of inorganic salt concentrations. The exhaust was sampled at the tailpipe during regulatory driving cycles on chassis dynamometers, diluted (200 - 400x) and introduced into the PSI mobile smog chamber [6], where the emissions were subjected to simulated atmospheric ageing. Particle phase instruments (HR-ToF-AMS, aethalometers, CPC, SMPS) and gas phase instruments (PTR-TOF-MS, CO, CO2, CH4, THC, NH3 and other gases) were used online during the experiments. We found that gasoline emissions, because of cold starts, were generally larger than diesel, especially during cold temperatures driving cycles. Gasoline vehicles also showed the highest SOA formation. Furthermore, we observed that vehicle emissions and SOA are significantly affected by temperature and RH: doubling the RH in the chamber resulted in significantly increased SOA formation. Primary emissions and secondary aerosol formation from diesel and gasoline vehicles will be compared at different temperature and RH. Also the interaction and influence of inorganics on organics will be discussed. References: [1] Robinson, A.L., et al. (2007) Science 315, 1259. [2] Weitkamp, E.A., et al. (2007) Environ. Sci. Technol. 41, 6969. [3] Bahreini, R., et al. (2012) Geophys. Res. Lett. 39, L06805. [4] Gentner, D.R. et al. (2012) PNAS 109, 18318. [5] Gordon, T.D. et al. (2013) Atmos. Chem. Phys. Discuss 13, 23173. [6] Platt, S.M., et al. (2013) Atmos. Chem. Phys. Discuss. 12, 28343.

INTERLABORATORY STUDY OF THE COLD VAPOR TECHNIQUE FOR TOTAL MERCURY IN WATER

EPA Science Inventory

The American Society for Testing and Materials (ASTM) and the U.S. Environmental Protection Agency (EPA) conducted a joint study of the cold vapor technique for total mercury in water, before formal acceptance of the method by each organization. The method employs an acid-permang...

Critical temperature: A quantitative method of assessing cold tolerance

Treesearch

D.H. DeHayes; M.W., Jr. Williams

1989-01-01

Critical temperature (Tc), defined as the highest temperature at which freezing injury to plant tissues can be detected, provides a biologically meaningful and statistically defined assessment of the relative cold tolerance of plant tissues. A method is described for calculating critical temperatures in laboratory freezing studies that use...

Pre-flight calibration and initial data processing for the ChemCam laser-induced breakdown spectroscopy instrument on the Mars Science Laboratory rover

USGS Publications Warehouse

Wiens, R.C.; Maurice, S.; Lasue, J.; Forni, O.; Anderson, R.B.; Clegg, S.; Bender, S.; Blaney, D.; Barraclough, B.L.; Cousin, A.; DeFlores, L.; Delapp, D.; Dyar, M.D.; Fabre, C.; Gasnault, O.; Lanza, N.; Mazoyer, J.; Melikechi, N.; Meslin, P.-Y.; Newsom, H.; Ollila, A.; Perez, R.; Tokar, R.; Vaniman, D.

2013-01-01

The ChemCam instrument package on the Mars Science Laboratory rover, Curiosity, is the first planetary science instrument to employ laser-induced breakdown spectroscopy (LIBS) to determine the compositions of geological samples on another planet. Pre-processing of the spectra involves subtracting the ambient light background, removing noise, removing the electron continuum, calibrating for the wavelength, correcting for the variable distance to the target, and applying a wavelength-dependent correction for the instrument response. Further processing of the data uses multivariate and univariate comparisons with a LIBS spectral library developed prior to launch as well as comparisons with several on-board standards post-landing. The level-2 data products include semi-quantitative abundances derived from partial least squares regression. A LIBS spectral library was developed using 69 rock standards in the form of pressed powder disks, glasses, and ceramics to minimize heterogeneity on the scale of the observation (350–550 μm dia.). The standards covered typical compositional ranges of igneous materials and also included sulfates, carbonates, and phyllosilicates. The provenance and elemental and mineralogical compositions of these standards are described. Spectral characteristics of this data set are presented, including the size distribution and integrated irradiances of the plasmas, and a proxy for plasma temperature as a function of distance from the instrument. Two laboratory-based clones of ChemCam reside in Los Alamos and Toulouse for the purpose of adding new spectra to the database as the need arises. Sensitivity to differences in wavelength correlation to spectral channels and spectral resolution has been investigated, indicating that spectral registration needs to be within half a pixel and resolution needs to match within 1.5 to 2.6 pixels. Absolute errors are tabulated for derived compositions of each major element in each standard using PLS regression. Sources of errors are investigated and discussed, and methods for improving the analytical accuracy of compositions derived from ChemCam spectra are discussed.

Monitoring Air Quality over China: Evaluation of the modeling system of the PANDA project

NASA Astrophysics Data System (ADS)

Bouarar, Idir; Katinka Petersen, Anna; Brasseur, Guy; Granier, Claire; Xie, Ying; Wang, Xuemei; Fan, Qi; Wang, Lili

2015-04-01

Air pollution has become a pressing problem in Asia and specifically in China due to rapid increase in anthropogenic emissions related to growth of China's economic activity and increasing demand for energy in the past decade. Observed levels of particulate matter and ozone regularly exceed World Health Organization (WHO) air quality guidelines in many parts of the country leading to increased risk of respiratory illnesses and other health problems. The EU-funded project PANDA aims to establish a team of European and Chinese scientists to monitor air pollution over China and elaborate air quality indicators in support of European and Chinese policies. PANDA combines state-of-the-art air pollution modeling with space and surface observations of chemical species to improve methods for monitoring air quality. The modeling system of the PANDA project follows a downscaling approach: global models such as MOZART and MACC system provide initial and boundary conditions to regional WRF-Chem and EMEP simulations over East Asia. WRF-Chem simulations at higher resolution (e.g. 20km) are then performed over a smaller domain covering East China and initial and boundary conditions from this run are used to perform simulations at a finer resolution (e.g. 5km) over specific megacities like Shanghai. Here we present results of model simulations for January and July 2010 performed during the first year of the project. We show an intercomparison of the global (MACC, EMEP) and regional (WRF-Chem) simulations and a comprehensive evaluation with satellite measurements (NO2, CO) and in-situ data (O3, CO, NOx, PM10 and PM2.5) at several surface stations. Using the WRF-Chem model, we demonstrate that model performance is influenced not only by the resolution (e.g. 60km, 20km) but also the emission inventories used (MACCity, HTAPv2), their resolution and diurnal variation, and the choice of initial and boundary conditions (e.g. MOZART, MACC analysis).

Chemical Reactions of Molecules Promoted and Simultaneously Imaged by the Electron Beam in Transmission Electron Microscopy.

PubMed

Skowron, Stephen T; Chamberlain, Thomas W; Biskupek, Johannes; Kaiser, Ute; Besley, Elena; Khlobystov, Andrei N

2017-08-15

The main objective of this Account is to assess the challenges of transmission electron microscopy (TEM) of molecules, based on over 15 years of our work in this field, and to outline the opportunities in studying chemical reactions under the electron beam (e-beam). During TEM imaging of an individual molecule adsorbed on an atomically thin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule, displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactions which can be imaged concurrently with their activation by the e-beam and can be presented as stop-frame movies. This experimental approach, which we term ChemTEM, harnesses energy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictions of bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of the reactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the product formed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM acts simultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM reveals atomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time; structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed with atomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating the potential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discovery of materials that can be synthesized on preparative scale.

A full-dimensional multilayer multiconfiguration time-dependent Hartree study on the ultraviolet absorption spectrum of formaldehyde oxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn; Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de

2014-09-28

Employing the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method in conjunction with the multistate multimode vibronic coupling Hamiltonian (MMVCH) model, we perform a full dimensional (9D) quantum dynamical study on the simplest Criegee intermediate, formaldehyde oxide, in five lower-lying singlet electronic states. The ultraviolet (UV) spectrum is then simulated by a Fourier transform of the auto-correlation function. The MMVCH model is built based on extensive MRCI(8e,8o)/aug-cc-pVTZ calculations. To ensure a fast convergence of the final calculations, a large number of ML-MCTDH test calculations is performed to find an appropriate multilayer separations (ML-trees) of the ML-MCTDH nuclear wave functions, and the dynamicalmore » calculations are carefully checked to ensure that the calculations are well converged. To compare the computational efficiency, standard MCTDH simulations using the same Hamiltonian are also performed. A comparison of the MCTDH and ML-MCTDH calculations shows that even for the present not-too-large system (9D here) the ML-MCTDH calculations can save a considerable amount of computational resources while producing identical spectra as the MCTDH calculations. Furthermore, the present theoretical B{sup ~} {sup 1}A{sup ′}←X{sup ~} {sup 1}A{sup ′} UV spectral band and the corresponding experimental measurements [J. M. Beames, F. Liu, L. Lu, and M. I. Lester, J. Am. Chem. Soc. 134, 20045–20048 (2012); L. Sheps, J. Phys. Chem. Lett. 4, 4201–4205 (2013); W.-L. Ting, Y.-H. Chen, W. Chao, M. C. Smith, and J. J.-M. Lin, Phys. Chem. Chem. Phys. 16, 10438–10443 (2014)] are discussed. To the best of our knowledge, this is the first theoretical UV spectrum simulated for this molecule including nuclear motion beyond an adiabatic harmonic approximation.« less

Symmetrical windowing for quantum states in quasi-classical trajectory simulations: Application to electron transfer

NASA Astrophysics Data System (ADS)

Cotton, Stephen J.; Igumenshchev, Kirill; Miller, William H.

2014-08-01

It has recently been shown [S. J. Cotton and W. H. Miller, J. Chem. Phys. 139, 234112 (2013)] that a symmetrical windowing quasi-classical (SQC) approach [S. J. Cotton and W. H. Miller, J. Phys. Chem. A 117, 7190 (2013)] applied to the Meyer-Miller model [H.-D. Meyer and W. H. Miller, J. Chem. Phys. 70, 3214 (1979)] for the electronic degrees of freedom in electronically non-adiabatic dynamics is capable of quantitatively reproducing quantum mechanical results for a variety of test applications, including cases where "quantum" coherence effects are significant. Here we apply this same SQC methodology, within a flux-side correlation function framework, to calculate thermal rate constants corresponding to several proposed models of electron transfer processes [P. Huo, T. F. Miller III, and D. F. Coker, J. Chem. Phys. 139, 151103 (2013); A. R. Menzeleev, N. Ananth, and T. F. Miller III, J. Chem. Phys. 135, 074106 (2011)]. Good quantitative agreement with Marcus Theory is obtained over several orders of magnitude variation in non-adiabatic coupling. Moreover, the "inverted regime" in thermal rate constants (with increasing bias) known from Marcus Theory is also reproduced with good accuracy by this very simple classical approach. The SQC treatment is also applied to a recent model of photoinduced proton coupled electron transfer [C. Venkataraman, A. V. Soudackov, and S. Hammes-Schiffer, J. Chem. Phys. 131, 154502 (2009)] and population decay of the photoexcited donor state is found to be in reasonable agreement with results calculated via reduced density matrix theory.

Symmetrical windowing for quantum states in quasi-classical trajectory simulations: Application to electron transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cotton, Stephen J.; Igumenshchev, Kirill; Miller, William H., E-mail: millerwh@berkeley.edu

It has recently been shown [S. J. Cotton and W. H. Miller, J. Chem. Phys. 139, 234112 (2013)] that a symmetrical windowing quasi-classical (SQC) approach [S. J. Cotton and W. H. Miller, J. Phys. Chem. A 117, 7190 (2013)] applied to the Meyer-Miller model [H.-D. Meyer and W. H. Miller, J. Chem. Phys. 70, 3214 (1979)] for the electronic degrees of freedom in electronically non-adiabatic dynamics is capable of quantitatively reproducing quantum mechanical results for a variety of test applications, including cases where “quantum” coherence effects are significant. Here we apply this same SQC methodology, within a flux-side correlation functionmore » framework, to calculate thermal rate constants corresponding to several proposed models of electron transfer processes [P. Huo, T. F. Miller III, and D. F. Coker, J. Chem. Phys. 139, 151103 (2013); A. R. Menzeleev, N. Ananth, and T. F. Miller III, J. Chem. Phys. 135, 074106 (2011)]. Good quantitative agreement with Marcus Theory is obtained over several orders of magnitude variation in non-adiabatic coupling. Moreover, the “inverted regime” in thermal rate constants (with increasing bias) known from Marcus Theory is also reproduced with good accuracy by this very simple classical approach. The SQC treatment is also applied to a recent model of photoinduced proton coupled electron transfer [C. Venkataraman, A. V. Soudackov, and S. Hammes-Schiffer, J. Chem. Phys. 131, 154502 (2009)] and population decay of the photoexcited donor state is found to be in reasonable agreement with results calculated via reduced density matrix theory.« less

Correction: Assembly and relaxation behaviours of phosphatidylethanolamine monolayers investigated by polarization and frequency resolved SFG-VS.

PubMed

Wei, Feng; Xiong, Wei; Li, Wenhui; Lu, Wangting; Allen, Heather C; Zheng, Wanquan

2016-06-14

Correction for 'Assembly and relaxation behaviours of phosphatidylethanolamine monolayers investigated by polarization and frequency resolved SFG-VS' by Feng Wei et al., Phys. Chem. Chem. Phys., 2015, 17, 25114-25122.

Chem-E-Car Downunder.

ERIC Educational Resources Information Center

Rhodes, Martin

2002-01-01

Presents the Chem-E-Car competition in which students build a small car powered by a chemical reaction. Focuses on a controlled chemical reaction in which the car travels a required specific distance and stops. Requires participants to prepare poster presentations. (YDS)

Curiosity First Rock Star

NASA Image and Video Library

2012-08-17

This mosaic image shows the first target NASA Curiosity rover aims to zap ChemCam instrument. ChemCam will be firing a laser at this rock, provisionally named N165, and analyzing the glowing, ionized gas, called plasma, that the laser excites.

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface tomore » be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

DOEpatents

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.; Kamath, Vinod; Kochuparambil, Bejoy J.; Schmidt, Roger R.; Steinke, Mark E.

2016-08-09

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

DOEpatents

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.; Kamath, Vinod; Kochuparambil, Bejoy J.; Schmidt, Roger R.; Steinke, Mark E.

2016-04-05

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.

Cold Cook Methods: An Ethnographic Exploration on the Myths of Methamphetamine Production and Policy Implications

PubMed Central

Boeri, Miriam W.; Gibson, David; Harbry, Liam

2011-01-01

Background Urban legends and myths are prevalent in drug-use environments. However, the distinction between myth and fact is not always clear. We found contradictory claims regarding the emergence of cold cook methods for producing methamphetamine when contrasting user-generated reports with official reports repudiating such methods as myths. Our aim is to open the topic for more academic discussion. Methods We examine cold cook methods of methamphetamine production revealed in our ethnographic study and interviews with former (n=50) and current (n=48) methamphetamine users. Data were collected in the suburbs of a large southeastern city in the United States. We compare the data with reports from law enforcement professionals and public health officials. Results Official reports claim the cold cook method described by users in our study is a myth and does not produce methamphetamine. Small-scale producers sell it as methamphetamine and users claim it has the same effect as methamphetamine. They are charged for possession and distribution of methamphetamine when caught with this drug. It appears the unintended consequences of recent policy aimed to reduce production and use of methamphetamine may be a user-friendly production method. We do not know the health implications at this time. Conclusion We do not make any definitive conclusions on the legitimacy of the stories or myths discussed here but instead suggest that labeling drug stories as myths might lead to dismissing facts that hold partial truth. The subsequent dismissal of cold cook methods among policy and public health officials risks a range of unintended consequences among vulnerable populations. We present our case for more research attention on the myths of methamphetamine production. PMID:19195870

The impact of cold spells on mortality and effect modification by cold spell characteristics

NASA Astrophysics Data System (ADS)

Wang, Lijun; Liu, Tao; Hu, Mengjue; Zeng, Weilin; Zhang, Yonghui; Rutherford, Shannon; Lin, Hualiang; Xiao, Jianpeng; Yin, Peng; Liu, Jiangmei; Chu, Cordia; Tong, Shilu; Ma, Wenjun; Zhou, Maigeng

2016-12-01

In China, the health impact of cold weather has received little attention, which limits our understanding of the health impacts of climate change. We collected daily mortality and meteorological data in 66 communities across China from 2006 to 2011. Within each community, we estimated the effect of cold spell exposure on mortality using a Distributed Lag Nonlinear Model (DLNM). We also examined the modification effect of cold spell characteristics (intensity, duration, and timing) and individual-specific factors (causes of death, age, gender and education). Meta-analysis method was finally used to estimate the overall effects. The overall cumulative excess risk (CER) of non-accidental mortality during cold spell days was 28.2% (95% CI: 21.4%, 35.3%) compared with non-cold spell days. There was a significant increase in mortality when the cold spell duration and intensity increased or occurred earlier in the season. Cold spell effects and effect modification by cold spell characteristics were more pronounced in south China. The elderly, people with low education level and those with respiratory diseases were generally more vulnerable to cold spells. Cold spells statistically significantly increase mortality risk in China, with greater effects in southern China. This effect is modified by cold spell characteristics and individual-level factors.

Simple, reliable, and nondestructive method for the measurement of vacuum pressure without specialized equipment.

PubMed

Yuan, Jin-Peng; Ji, Zhong-Hua; Zhao, Yan-Ting; Chang, Xue-Fang; Xiao, Lian-Tuan; Jia, Suo-Tang

2013-09-01

We present a simple, reliable, and nondestructive method for the measurement of vacuum pressure in a magneto-optical trap. The vacuum pressure is verified to be proportional to the collision rate constant between cold atoms and the background gas with a coefficient k, which can be calculated by means of the simple ideal gas law. The rate constant for loss due to collisions with all background gases can be derived from the total collision loss rate by a series of loading curves of cold atoms under different trapping laser intensities. The presented method is also applicable for other cold atomic systems and meets the miniaturization requirement of commercial applications.

Dust Detection by Curiosity ChemCam

NASA Image and Video Library

2013-04-08

The ChemCam instrument on NASA Curiosity Mars rover fired its laser 50 times at its onboard graphite target showing spectral measurements from the first shot, which hit dust on the target, compared to spectral measurements of from the 50th shot.

FastChem: An ultra-fast equilibrium chemistry

NASA Astrophysics Data System (ADS)

Kitzmann, Daniel; Stock, Joachim

2018-04-01

FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.

Picosecond Studies of Condensed-Phase Energetic Materials

DTIC Science & Technology

1987-01-21

population is zero before the pump pulse arrives. In other words, for t< 0, fo O [>Z In 4t - En IRn -t In D’(t) - E In D(t) (3.11). 104 The order of...Inorg. Chem. 104 (1984) 2596-2597; Re-PTZ is [((2,2’- bpy)Re1(CO)3(PY-PT)]"’ where bpy is bipyridine, and py-PT is a methyl pyridine substituted...phenothiazine. 12. S. M. Beck and L. E. Brus, J. Amer. Chem. Soc. 104 (1982) 1805-1808. 13. S. M. Beck and L. E. Brus, J. Chem. Phys. 75 (1981) 4934-4940

Synthetic chemerin-derived peptides suppress inflammation through ChemR23

PubMed Central

Cash, Jenna L.; Hart, Rosie; Russ, Andreas; Dixon, John P.C.; Colledge, William H.; Doran, Joanne; Hendrick, Alan G.; Carlton, Mark B.L.; Greaves, David R.

2008-01-01

Chemerin is a chemotactic protein that binds to the G protein–coupled receptor, ChemR23. We demonstrate that murine chemerin possesses potent antiinflammatory properties that are absolutely dependent on proteolytic processing. A series of peptides was designed, and only those identical to specific C-terminal chemerin sequences exerted antiinflammatory effects at picomolar concentrations in vitro. One of these, chemerin15 (C15; A140-A154), inhibited macrophage (MΦ) activation to a similar extent as proteolyzed chemerin, but exhibited reduced activity as a MΦ chemoattractant. Intraperitoneal administration of C15 (0.32 ng/kg) to mice before zymosan challenge conferred significant protection against zymosan-induced peritonitis, suppressing neutrophil (63%) and monocyte (62%) recruitment with a concomitant reduction in proinflammatory mediator expression. Importantly, C15 was unable to ameliorate zymosan-induced peritonitis in ChemR23−/− mice, demonstrating that C15's antiinflammatory effects are entirely ChemR23 dependent. In addition, administration of neutralizing anti-chemerin antibody before zymosan challenge resulted in a significant exacerbation of peritoneal inflammation (up to 170%), suggesting an important endogenous antiinflammatory role for chemerin-derived species. Collectively, these results show that chemerin-derived peptides may represent a novel therapeutic strategy for the treatment of inflammatory diseases through ChemR23. PMID:18391062

Details on Silica-Rich Elk Target near Marias Pass

NASA Image and Video Library

2015-12-17

This image from the Chemistry and Camera (ChemCam) instrument on NASA's Curiosity Mars rover shows detailed texture of a rock target called "Elk" on Mars' Mount Sharp, revealing laminations that are present in much of the Murray Formation geological unit of lower Mount Sharp. Researchers also used ChemCam's laser and spectrometers to assess Elk's composition and found it to be rich in silica. The image covers a patch of rock surface about 2.8 inches (7 centimeters) across. It was taken on May 22, 2015, during the mission's 992nd Martian day, or sol. ChemCam's Remote Micro-Imager camera, on top of Curiosity's mast, captured the image from a distance of about 9 feet (2.75 meters). Annotations in red identify five points on Elk that were hit with ChemCam's laser. Each of the highlighted points is a location where ChemCam fired its laser 30 times to ablate a tiny amount of target material. By analyzing the light emitted from this laser-ablation, researchers can deduce the composition of that point. For some purposes, composition is presented as a combination of the information from multiple points on the same rock. However, using the points individually can track fine-scale variations in targets. http://photojournal.jpl.nasa.gov/catalog/PIA20267

Effect of MERRA-2 initial and boundary conditions on WRF-Chem aerosol simulations over the Arabian Peninsula

NASA Astrophysics Data System (ADS)

Ukhov, Alexander; Stenchikov, Georgiy

2017-04-01

In this study, we test the sensitivity of the horizontal and vertical distributions of aerosols to the initial and boundary conditions (IC&BC) of the aerosol/chemistry. We use the WRF-Chem model configured over the Arabian Peninsula to study both dust and anthropogenic aerosols. Currently, in the WRF-Chem the aerosol/chemistry IC&BC are constructed using either default aerosol/chemistry profiles with no inflow of aerosols and chemicals through the lateral boundaries or using the aerosol/chemistry fields from MOZART, the model for ozone and related chemical tracers from the NCAR. Here, we construct aerosol/chemistry IC&BC using MERRA-2 output. MERRA-2 is a recently developed reanalysis that assimilates ground-based and satellite observations to provide the improved distributions of aerosols and chemical species. We ran WRF-Chem simulations for July-August 2015 using GOCART/AFWA dust emission and GOCART aerosol schemes. We used the EDGAR HTAP V4 dataset to calculate SO2 emissions. Comparison of three runs initiated using the same ERA-Interim reanalysis fields but different aerosol/chemistry IC&BC (default WRF-Chem, MOZART, and MERRA-2) with AERONET, Micropulse Lidar, Balloon, and satellite observations shows that the MERRA-2 IC&BC are superior.

Characterising Brazilian biomass burning emissions using WRF-Chem with MOSAIC sectional aerosol

NASA Astrophysics Data System (ADS)

Archer-Nicholls, S.; Lowe, D.; Darbyshire, E.; Morgan, W. T.; Bela, M. M.; Pereira, G.; Trembath, J.; Kaiser, J. W.; Longo, K. M.; Freitas, S. R.; Coe, H.; McFiggans, G.

2014-09-01

The South American Biomass Burning Analysis (SAMBBA) field campaign took detailed in-situ flight measurements of aerosol during the 2012 dry season to characterise biomass burning aerosol and improve understanding of its impacts on weather and climate. Developments have been made to the Weather research and Forecast model with chemistry (WRF-Chem) model to improve the representation of biomass burning aerosol in the region by coupling a sectional aerosol scheme to the plume rise parameterisation. Brazilian Biomass Burning Emissions Model (3BEM) fire emissions are used, prepared using PREP-CHEM-SRC, and mapped to CBM-Z and MOSAIC species. Model results have been evaluated against remote sensing products, AERONET sites, and four case studies of flight measurements from the SAMBBA campaign. WRF-Chem predicted layers of elevated aerosol loadings (5-20 μg sm-3) of particulate organic matter at high altitude (6-8 km) over tropical forest regions, while flight measurements showed a sharp decrease above 2-4 km altitude. This difference was attributed to the plume-rise parameterisation overestimating injection height. The 3BEM emissions product was modified using estimates of active fire size and burned area for the 2012 fire season, which reduced the fire size. The enhancement factor for fire emissions was increased from 1.3 to 5 to retain reasonable aerosol optical depths (AOD). The smaller fire size lowered the injection height of the emissions, but WRF-Chem still showed elevated aerosol loadings between 4-5 km altitude. Over eastern Cerrado (savannah-like) regions, both modelled and measured aerosol loadings decreased above approximately 4 km altitude. Compared with MODIS satellite data and AERONET sites, WRF-Chem represented AOD magnitude well (between 0.3-1.5) over western tropical forest fire regions in the first half of the campaign, but tended to over-predict them in the second half, when precipitation was more significant. Over eastern Cerrado regions, WRF-Chem tended to under-predict AOD. Modeled aerosol loadings in the east were higher in the modified emission scenario. The primary organic matter to black carbon ratio was typically between 8-10 in WRF-Chem. This was lower than western flights measurements (interquartile range of 11.6-15.7 in B734, 14.7-24.0 in B739), but similar to the eastern flight B742 (8.1-10.4). However, single scattering albedo was close to measured over the western flights (0.87-0.89 in model; 0.88-0.91 in flight B734, and 0.86-0.95 in flight B739 measurements) but too high over the eastern flight B742 (0.86-0.87 in model, 0.81-0.84 in measurements). This suggests that improvements are needed to both modeled aerosol composition and optical properties calculations in WRF-Chem.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eggeman, Tim; O'Neill, Brian

2016-08-17

ZeaChem Inc. and US DOE successfully demonstrated the ZeaChem process for producing sugars and ethanol from high-impact biomass feedstocks. The project was executed over a 5-year period under a $31.25 million cooperative agreement (80:20 Federal:ZeaChem cost share). The project was managed by dividing it into three budget periods. Activities during Budget Period 1 were limited to planning, permitting, and other pre-construction planning. Budget Period 2 activities included engineering, procurement, construction, commissioning, start-up and initial operations through the Independent Engineer Test Runs. The scope of construction was limited to the Chem Frac and Hydrogenolysis units, as the Core Facility was alreadymore » in place. Construction was complete in December 2012, and the first cellulosic ethanol was produced in February 2013. Additional operational test runs were conducted during Budget Period 3 (completed June 2015) using hybrid poplar, corn stover, and wheat straw feedstocks, resulting in the production of cellulosic ethanol and various other biorefinery intermediates. The research adds to the understanding of the Chem Frac and Hydrogenolysis technologies in that the technical performance of each unit was measured, and the resulting data and operational experience can be used as the basis for engineering designs, thus mitigating risks for deployment in future commercial facilities. The Chem Frac unit was initially designed to be operated as two-stage dilute acid hydrolysis, with first stage conditions selected to remove the hemicellulose fraction of the feedstock, and the second stage conditions selected to remove the cellulose fraction. While the Chem Frac unit met or exceeded the design capacity of 10 ton(dry)/day, the technical effectiveness of the Chem Frac unit was below expectations in its initial two-stage dilute acid configuration. The sugars yields were low, the sugars were dilute, and the sugars had poor fermentability caused by excessive inhibitors from wood breakdown products, resulting in a non-viable process from an economic point of view. Later runs with the Chem Frac unit switched to a configuration that used dilute acid pretreatment followed by enzymatic hydrolysis. This change improved yield, increased sugar concentrations, and improved fermentability of sugars. The Hydrogenolysis unit met or exceeded all expectations with respect to unit capacity, technical performance, and economic performance. The US DOE funds for the project were provided through the American Recovery and Reinvestment Act of 2009. In addition to the scientific/technical merit of the project, this project benefited the public through the creation of approximately 75 onsite direct construction-related jobs, 25 direct on-going operations-related jobs, plus numerous indirect jobs, and thus was well aligned with the goals of the American Recovery and Reinvestment Act of 2009.« less

Results of the Second U.S. Manned Suborbital Space Flight, July 21, 1961

DTIC Science & Technology

1961-07-21

Alpha - ketoglutaric ...... Neg. Neg. Neg. Neg . .............................. Isocitric ............... 0 to 10...M.: An Accurate Method for the Determination of Blood Urea Nitrogen by Direct Nesslerization. Jour. Biol. Chem., vol. 143, 1942, pp. 531-544. Calcium ...DIEHL, H., and FI.LINGBOE, J. L.: Indicator for Titration of Calcium in Presence of Magnesium With Disodium. Dihy- drogen Ethylene

Comment on {open_quotes}Local frequency analysis and the structure of classical phase space of the LiNC/LiCN molecular system{close_quotes} [J. Chem. Phys. {bold 108}, 63 (1998)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martens, C.C.; Davis, M.J.; Ezra, G.S.

In this Comment, we correct a misunderstanding in the title paper concerning the accuracy of the fast Fourier transform method of local frequency analysis of Martens, Davis, and Ezra. We also discuss the application of the Martens{endash}Davis{endash}Ezra method to a two degree of freedom model of OSC. {copyright} {ital 1998 American Institute of Physics.}

Methods for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds

DTIC Science & Technology

2007-04-04

contains color images. 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 12 19a...Opterons with 4 GB of memory . We used the descriptor- spaces GF, ECZ3, and ErG (described in Section 4) for the evaluating the methods introduced in...screening: Use of data fusion and machine learning to enchance the effectiveness of sim- ilarity searching. J. Chem. Info. Model., (46):462–470, 2006. [18] J

Decadal evaluation of regional climate, air quality, and their interactions over the continental US and their interactions using WRF/Chem version 3.6.1

NASA Astrophysics Data System (ADS)

Yahya, Khairunnisa; Wang, Kai; Campbell, Patrick; Glotfelty, Timothy; He, Jian; Zhang, Yang

2016-02-01

The Weather Research and Forecasting model with Chemistry (WRF/Chem) v3.6.1 with the Carbon Bond 2005 (CB05) gas-phase mechanism is evaluated for its first decadal application during 2001-2010 using the Representative Concentration Pathway 8.5 (RCP 8.5) emissions to assess its capability and appropriateness for long-term climatological simulations. The initial and boundary conditions are downscaled from the modified Community Earth System Model/Community Atmosphere Model (CESM/CAM5) v1.2.2. The meteorological initial and boundary conditions are bias-corrected using the National Center for Environmental Protection's Final (FNL) Operational Global Analysis data. Climatological evaluations are carried out for meteorological, chemical, and aerosol-cloud-radiation variables against data from surface networks and satellite retrievals. The model performs very well for the 2 m temperature (T2) for the 10-year period, with only a small cold bias of -0.3 °C. Biases in other meteorological variables including relative humidity at 2 m, wind speed at 10 m, and precipitation tend to be site- and season-specific; however, with the exception of T2, consistent annual biases exist for most of the years from 2001 to 2010. Ozone mixing ratios are slightly overpredicted at both urban and rural locations with a normalized mean bias (NMB) of 9.7 % but underpredicted at rural locations with an NMB of -8.8 %. PM2.5 concentrations are moderately overpredicted with an NMB of 23.3 % at rural sites but slightly underpredicted with an NMB of -10.8 % at urban/suburban sites. In general, the model performs relatively well for chemical and meteorological variables, and not as well for aerosol-cloud-radiation variables. Cloud-aerosol variables including aerosol optical depth, cloud water path, cloud optical thickness, and cloud droplet number concentration are generally underpredicted on average across the continental US. Overpredictions of several cloud variables over the eastern US result in underpredictions of radiation variables (such as net shortwave radiation - GSW - with a mean bias - MB - of -5.7 W m-2) and overpredictions of shortwave and longwave cloud forcing (MBs of ˜ 7 to 8 W m-2), which are important climate variables. While the current performance is deemed to be acceptable, improvements to the bias-correction method for CESM downscaling and the model parameterizations of cloud dynamics and thermodynamics, as well as aerosol-cloud interactions, can potentially improve model performance for long-term climate simulations.

How good are publicly available web services that predict bioactivity profiles for drug repurposing?

PubMed

Murtazalieva, K A; Druzhilovskiy, D S; Goel, R K; Sastry, G N; Poroikov, V V

2017-10-01

Drug repurposing provides a non-laborious and less expensive way for finding new human medicines. Computational assessment of bioactivity profiles shed light on the hidden pharmacological potential of the launched drugs. Currently, several freely available computational tools are available via the Internet, which predict multitarget profiles of drug-like compounds. They are based on chemical similarity assessment (ChemProt, SuperPred, SEA, SwissTargetPrediction and TargetHunter) or machine learning methods (ChemProt and PASS). To compare their performance, this study has created two evaluation sets, consisting of (1) 50 well-known repositioned drugs and (2) 12 drugs recently patented for new indications. In the first set, sensitivity values varied from 0.64 (TarPred) to 1.00 (PASS Online) for the initial indications and from 0.64 (TarPred) to 0.98 (PASS Online) for the repurposed indications. In the second set, sensitivity values varied from 0.08 (SuperPred) to 1.00 (PASS Online) for the initial indications and from 0.00 (SuperPred) to 1.00 (PASS Online) for the repurposed indications. Thus, this analysis demonstrated that the performance of machine learning methods surpassed those of chemical similarity assessments, particularly in the case of novel repurposed indications.

Combined quantum mechanics and molecular mechanics simulation of Ca2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology

NASA Astrophysics Data System (ADS)

Kerdcharoen, Teerakiat; Morokuma, Keiji

2003-05-01

An extension of the ONIOM (Own N-layered Integrated molecular Orbital and molecular Mechanics) method [M. Svensson, S. Humbel, R. D. J. Froese, T. Mutsubara, S. Sieber, and K. Morokuma, J. Phys. Chem. 100, 19357 (1996)] for simulation in the condensed phase, called ONIOM-XS (XS=eXtension to Solvation) [T. Kerdcharoen and K. Morokuma, Chem. Phys. Lett. 355, 257 (2002)], was applied to investigate the coordination of Ca2+ in liquid ammonia. A coordination number of 6 is found. Previous simulations based on pair potential or pair potential plus three-body correction gave values of 9 and 8.2, respectively. The new value is the same as the coordination number most frequently listed in the Cambridge Structural Database (CSD) and Protein Data Bank (PDB). N-Ca-N angular distribution reveals a near-octahedral coordination structure. Inclusion of many-body interactions (which amounts to 25% of the pair interactions) into the potential energy surface is essential for obtaining reasonable coordination number. Analyses of the metal coordination in water, water-ammonia mixture, and in proteins reveals that cation/ammonia solution can be used to approximate the coordination environment in proteins.

FTIR spectroscopy and thermodynamics of hydrogen adsorbed in a cross-linked polymer.

PubMed

Spoto, Giuseppe; Vitillo, Jenny G; Cocina, Donato; Damin, Alessandro; Bonino, Francesca; Zecchina, Adriano

2007-09-28

The adsorption of H(2) in a cross-linked poly(styrene-co-divinylbenzene) (St-DVB) microporous polymer (BET surface area 920 m(2) g(-1)) is studied by volumetric and gravimetric methods, FTIR spectroscopy at variable temperature (300-14 K) and ab initio calculations. At 77 K the polymer reversibly stores up to 1.3 mass% H(2) at a pressure of 1 bar and 1.8 mass% at 10 bar. The adsorption process involves the specific interaction of H(2) with the structural phenyl rings through weak dispersive forces. The interacting molecules become IR active and give rise to vibrational and rotational-vibrational manifestations which are affected by the temperature, the contact time and the H(2) equilibrium pressure. The spectra of the H(2)/St-DVB system reported here represent the first IR evidence of the adsorption of hydrogen on unsaturated molecules. The adsorption enthalpy is evaluated by the VTIR (variable temperature IR spectroscopy) method (C. Otero Areán et al., Phys. Chem. Chem. Phys., 2007, DOI: 10.1039/b615535a) and compared with the results of ab initio calculations for the H(2)/benzene interaction and with literature data.

Numerical study of the effects of surface topography and chemistry on the wetting transition using the string method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanan, E-mail: ynzhang@suda.edu.cn; Ren, Weiqing, E-mail: matrw@nus.edu.sg; Institute of High Performance Computing, Singapore 138632

2014-12-28

Droplets on a solid surface patterned with microstructures can exhibit the composite Cassie-Baxter (CB) state or the wetted Wenzel state. The stability of the CB state is determined by the energy barrier separating it from the wetted state. In this work, we study the CB to Wenzel transition using the string method [E et al., J. Chem. Phys. 126, 164103 (2007); W. Ren and E. Vanden-Eijnden, J. Chem. Phys. 138, 134105 (2013)]. We compute the transition states and energy barriers for a three-dimensional droplet on patterned surfaces. The liquid-vapor coexistence is modeled using the mean field theory. Numerical results aremore » obtained for surfaces patterned with straight pillars and nails, respectively. It is found that on both type of surfaces, wetting occurs via infiltration of the liquid in a single groove. The reentrant geometry of nails creates large energy barrier for the wetting of the solid surface compared to straight pillars. We also study the effect of surface chemistry, pillar height, and inter-pillar spacing on the energy barrier and compare it with nails.« less

Physical Activity and the Common Cold in Undergraduate University Students: Implications for Health Professionals

ERIC Educational Resources Information Center

Vossen, Deborah P.; McArel, Heather; Vossen, Jeffery F.; Thompson, Angela M.

2004-01-01

Objective: The common cold, known as upper respiratory tract infection (URTI), is the world's most prevalent illness. The purpose of this study was to determine if physical activity is linked to the incidence and/or duration of the common cold. Method: Undergraduate university students (n=200) were asked to complete two questionnaires. The…

COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications.

PubMed

Mauger, Florence; How-Kit, Alexandre; Tost, Jörg

2017-06-01

Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.

Narrowing the surface temperature range in CMIP5 simulations over the Arctic

NASA Astrophysics Data System (ADS)

Hao, Mingju; Huang, Jianbin; Luo, Yong; Chen, Xin; Lin, Yanluan; Zhao, Zongci; Xu, Ying

2018-05-01

Much uncertainty exists in reproducing Arctic temperature using different general circulation models (GCMs). Therefore, evaluating the performance of GCMs in reproducing Arctic temperature is critically important. In our study, 32 GCMs in the fifth phase of the Coupled Model Intercomparison Project (CMIP5) during the period 1900-2005 are used, and several metrics, i.e., bias, correlation coefficient ( R), and root mean square error (RMSE), are applied. The Cowtan data set is adopted as the reference data. The results suggest that the GCMs used can reasonably reproduce the Arctic warming trend during the period 1900-2005, as observed in the observational data, whereas a large variation of inter-model differences exists in modeling the Arctic warming magnitude. With respect to the reference data, most GCMs have large cold biases, whereas others have weak warm biases. Additionally, based on statistical thresholds, the models MIROC-ESM, CSIRO-Mk3-6-0, HadGEM2-AO, and MIROC-ESM-CHEM (bias ≤ ±0.10 °C, R ≥ 0.50, and RMSE ≤ 0.60 °C) are identified as well-performing GCMs. The ensemble of the four best-performing GCMs (ES4), with bias, R, and RMSE values of -0.03 °C, 0.72, and 0.39 °C, respectively, performs better than the ensemble with all 32 members, with bias, R, and RMSE values of -0.04 °C, 0.64, and 0.43 °C, respectively. Finally, ES4 is used to produce projections for the next century under the scenarios of RCP2.6, RCP4.5, and RCP8.0. The uncertainty in the projected temperature is greater in the higher emissions scenarios. Additionally, the projected temperature in the cold half year has larger variations than that in the warm half year.

Quantum dynamics of the reaction H((2)S) + HeH(+)(X(1)Σ(+)) → H2(+)(X(2)Σg(+)) + He((1)S) from cold to hyperthermal energies: time-dependent wavepacket study and comparison with time-independent calculations.

PubMed

Gamallo, Pablo; Akpinar, Sinan; Defazio, Paolo; Petrongolo, Carlo

2014-08-21

We present the adiabatic quantum dynamics of the proton-transfer reaction H((2)S) + HeH(+)(X(1)Σ(+)) → H2(+)(X(2)Σg(+)) + He((1)S) on the HeH2(+) X̃(2)Σ(+) RMRCI6 (M = 6) PES of C. N. Ramachandran et al. ( Chem. Phys. Lett. 2009, 469, 26). We consider the HeH(+) molecule in the ground vibrational–rotational state and obtain initial-state-resolved reaction probabilities and the ground-state cross section σ0 and rate constant k0 by propagating time-dependent, coupled-channel, real wavepackets (RWPs) and performing a flux analysis. Three different wavepackets are propagated to describe the wide range of energies explored, from cold (0.0001 meV) to hyperthermal (1000 meV) collision energies, and in a temperature range from 0.01 to 2000 K. We compare our time-dependent results with the time-independent ones by D. De Fazio and S. Bovino et al., where De Fazio carried out benchmark coupled-channel calculations whereas Bovino et al. employed the negative imaginary potential and the centrifugal-sudden approximations. The RWP cross section is in good agreement with that by De Fazio, except at the lowest collision energies below ∼0.01 meV, where the former is larger than the latter. However, neither the RWP and De Fazio results possess the huge resonance in probability and cross section at 0.01 meV, found by Bovino et al., who also obtained a too low σ0 at high energies. Therefore, the RWP and De Fazio rate constants compare quite well, whereas that by Bovino et al. is in general lower.

Weighted ssGBLUP improves genomic selection accuracy for bacterial cold water disease resistance in a rainbow trout population

USDA-ARS?s Scientific Manuscript database

The objective of this study was to compare methods for genomic evaluation in a Rainbow Trout (Oncorhynchus mykiss) population for survival when challenged by Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). The used methods were: 1)regular ssGBLUP that assume...

Analyzing carbon dioxide and methane emissions in California using airborne measurements and model simulations

NASA Astrophysics Data System (ADS)

Johnson, M. S.; Yates, E. L.; Iraci, L. T.; Jeong, S.; Fischer, M. L.

2013-12-01

Greenhouse gas (GHG) concentrations have increased over the past decades and are linked to global temperature increases and climate change. These changes in climate have been suggested to have varying effects, and uncertain consequences, on agriculture, water supply, weather, sea-level rise, the economy, and energy. To counteract the trend of increasing atmospheric concentrations of GHGs, the state of California has passed the California Global Warming Act of 2006 (AB-32). This requires that by the year 2020, GHG (e.g., carbon dioxide (CO2) and methane (CH4)) emissions will be reduced to 1990 levels. To quantify GHG fluxes, emission inventories are routinely compiled for the State of California (e.g., CH4 emissions from the California Greenhouse Gas Emissions Measurement (CALGEM) Project). The major sources of CO2 and CH4 in the state of California are: transportation, electricity production, oil and gas extraction, cement plants, agriculture, landfills/waste, livestock, and wetlands. However, uncertainties remain in these emission inventories because many factors contributing to these processes are poorly quantified. To alleviate these uncertainties, a synergistic approach of applying air-borne measurements and chemical transport modeling (CTM) efforts to provide a method of quantifying local and regional GHG emissions will be performed during this study. Additionally, in order to further understand the temporal and spatial distributions of GHG fluxes in California and the impact these species have on regional climate, CTM simulations of daily variations and seasonality of total column CO2 and CH4 will be analyzed. To assess the magnitude and spatial variation of GHG emissions and to identify local 'hot spots', airborne measurements of CH4 and CO2 were made by the Alpha Jet Atmospheric eXperiment (AJAX) over the San Francisco Bay Area (SFBA) and San Joaquin Valley (SJV) in January and February 2013 during the Discover-AQ-CA study. High mixing ratios of GHGs were observed in-flight with a high degree of spatial variability. To provide an additional method to quantify GHG emissions, and analyze AJAX measurement data, the GEOS-Chem CTM is used to simulate SFBA/SJV GHG measurements. A nested-grid version of GEOS-Chem will be applied and utilizes varying emission inventories and model parameterizations to simulate GHG fluxes/emissions. The model considers CO2 fluxes from fossil fuel use, biomass/biofuel burning, terrestrial and oceanic biosphere exchanges, shipping and aviation, and production from the oxidation of carbon monoxide, CH4, and non-methane volatile organic carbons. The major sources of CH4 simulated in GEOS-Chem are domesticated animals, rice fields, natural gas leakage, natural gas venting/flaring (oil production), coal mining, wetlands, and biomass burning. Preliminary results from the comparison between available observations (e.g., AJAX and CALGEM CH4 emission maps) and GEOS-Chem results will be presented, along with a discussion of CO2 and CH4 source apportionment and the use of the GEOS-Chem-adjoint to perform inverse GHG modeling.

Correction: Influence of particle size and dielectric environment on the dispersion behaviour and surface plasmon in nickel nanoparticles.

PubMed

Sharma, Vikash; Chotia, Chanderbhan; Tarachand; Ganesan, Vedachalaiyer; Okram, Gunadhor S

2017-07-21

Correction for 'Influence of particle size and dielectric environment on the dispersion behaviour and surface plasmon in nickel nanoparticles' by Vikash Sharma et al., Phys. Chem. Chem. Phys., 2017, 19, 14096-14106.

Spark Generated by ChemCam Laser During Tests

NASA Image and Video Library

2010-09-21

The ChemCam instrument for NASA Mars Science Laboratory mission uses a pulsed laser beam to vaporize a pinhead-size target, producing a flash of light from the ionized material plasma that can be analyzed to identify chemical elements in the target.

Curiosity ChemCam Removes Dust

NASA Image and Video Library

2013-04-08

This pair of images taken a few minutes apart show how laser firing by NASA Mars rover Curiosity removes dust from the surface of a rock. The images were taken by the remote micro-imager camera in the laser-firing Chemistry and Camera ChemCam.

Correction: Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source.

PubMed

Telling, Mark T F; Campbell, Stuart I; Engberg, Dennis; Martín Y Marero, David; Andersen, Ken H

2016-03-21

Correction for 'Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source' by Mark T. F. Telling et al., Phys. Chem. Chem. Phys., 2005, 7, 1255-1261.

Effects of Melatonin on Anti-oxidative Systems and Photosystem II in Cold-Stressed Rice Seedlings

PubMed Central

Han, Qiao-Hong; Huang, Bo; Ding, Chun-Bang; Zhang, Zhong-Wei; Chen, Yang-Er; Hu, Chao; Zhou, Li-Jun; Huang, Yan; Liao, Jin-Qiu; Yuan, Shu; Yuan, Ming

2017-01-01

Melatonin (N-acetyl-5-methoxytryptamine) plays important role in multiple plant developmental processes and stress responses. We investigated the possible mediatory role of melatonin in growth, photosynthesis, and the response to cold stress in rice by using three different experiments: soaking seed; immersing roots, and spraying to leaves with 0, 20, or 100 μM melatonin. After 6 days of cold stress, the growth of rice seedlings was significantly inhibited, but this inhibition was alleviated by exogenous melatonin. Furthermore, exogenous melatonin pretreatment alleviated the accumulation of reactive oxygen species, malondialdehyde and cell death induced by cold stress. Melatonin pretreatment also relieved the stress-induced inhibitions to photosynthesis and photosystem II activities. Further investigations showed that, antioxidant enzyme activities and non-enzymatic antioxidant levels were increased by melatonin pretreatments. The treatment methods of seed soaking and root immersion were more effective in improving cold stress resistance than the spraying method. The results also indicated the dose-dependent response of melatonin on rice physiological, biochemical, and photosynthetic parameters. PMID:28553310

Assessing the CAM5 Physics Suite in the WRF-Chem Model: Implementation, Resolution Sensitivity, and a First Evaluation for a Regional Case Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Po-Lun; Rasch, Philip J.; Fast, Jerome D.

A suite of physical parameterizations (deep and shallow convection, turbulent boundary layer, aerosols, cloud microphysics, and cloud fraction) from the global climate model Community Atmosphere Model version 5.1 (CAM5) has been implemented in the regional model Weather Research and Forecasting with chemistry (WRF-Chem). A downscaling modeling framework with consistent physics has also been established in which both global and regional simulations use the same emissions and surface fluxes. The WRF-Chem model with the CAM5 physics suite is run at multiple horizontal resolutions over a domain encompassing the northern Pacific Ocean, northeast Asia, and northwest North America for April 2008 whenmore » the ARCTAS, ARCPAC, and ISDAC field campaigns took place. These simulations are evaluated against field campaign measurements, satellite retrievals, and ground-based observations, and are compared with simulations that use a set of common WRF-Chem Parameterizations. This manuscript describes the implementation of the CAM5 physics suite in WRF-Chem provides an overview of the modeling framework and an initial evaluation of the simulated meteorology, clouds, and aerosols, and quantifies the resolution dependence of the cloud and aerosol parameterizations. We demonstrate that some of the CAM5 biases, such as high estimates of cloud susceptibility to aerosols and the underestimation of aerosol concentrations in the Arctic, can be reduced simply by increasing horizontal resolution. We also show that the CAM5 physics suite performs similarly to a set of parameterizations commonly used in WRF-Chem, but produces higher ice and liquid water condensate amounts and near-surface black carbon concentration. Further evaluations that use other mesoscale model parameterizations and perform other case studies are needed to infer whether one parameterization consistently produces results more consistent with observations.« less

Characterization of LIBS emission lines for the identification of chlorides, carbonates, and sulfates in salt/basalt mixtures for the application to MSL ChemCam data: LIBS OF CL, C, S IN SALT-BASALT MIXTURES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, D. E.; Ehlmann, B. L.; Forni, O.

Ancient environmental conditions on Mars can be probed through the identification of minerals on its surface, including water-deposited salts and cements dispersed in the pore space of sedimentary rocks. Laser-induced breakdown spectroscopy (LIBS) analyses by the Martian rover Curiosity's ChemCam instrument can indicate salts, and ChemCam surveys aid in identifying and selecting sites for further, detailed in situ analyses. Here, we performed laboratory LIBS experiments under simulated Mars conditions with a ChemCam-like instrument on a series of mixtures containing increasing concentrations of salt in a basaltic background to investigate the potential for identifying and quantifying chloride, carbonate, and sulfate saltsmore » found only in small amounts, dispersed in bulk rock with ChemCam, rather than concentrated in veins. The data then indicate that the presence of emission lines from the basalt matrix limited the number of Cl, C, and S emission lines found to be useful for quantitative analysis; nevertheless, several lines with intensities sensitive to salt concentration were identified. Detection limits for the elements based on individual emission lines ranged from ~20 wt % carbonate (2 wt % C), ~5–30 wt % sulfate (1–8 wt % S), and ~5–10 wt % chloride (3–6 wt % Cl) depending on the basaltic matrix and/or salt cation. Absolute quantification of Cl, C, and S in the samples via univariate analysis depends on the cation-anion pairing in the salt but appears relatively independent of matrices tested, following normalization. Our results are promising for tracking relative changes in the salt content of bulk rock on the Martian surface with ChemCam.« less

Characterization of LIBS emission lines for the identification of chlorides, carbonates, and sulfates in salt/basalt mixtures for the application to MSL ChemCam data: LIBS OF CL, C, S IN SALT-BASALT MIXTURES

DOE PAGES

Anderson, D. E.; Ehlmann, B. L.; Forni, O.; ...

2017-04-24

Ancient environmental conditions on Mars can be probed through the identification of minerals on its surface, including water-deposited salts and cements dispersed in the pore space of sedimentary rocks. Laser-induced breakdown spectroscopy (LIBS) analyses by the Martian rover Curiosity's ChemCam instrument can indicate salts, and ChemCam surveys aid in identifying and selecting sites for further, detailed in situ analyses. Here, we performed laboratory LIBS experiments under simulated Mars conditions with a ChemCam-like instrument on a series of mixtures containing increasing concentrations of salt in a basaltic background to investigate the potential for identifying and quantifying chloride, carbonate, and sulfate saltsmore » found only in small amounts, dispersed in bulk rock with ChemCam, rather than concentrated in veins. The data then indicate that the presence of emission lines from the basalt matrix limited the number of Cl, C, and S emission lines found to be useful for quantitative analysis; nevertheless, several lines with intensities sensitive to salt concentration were identified. Detection limits for the elements based on individual emission lines ranged from ~20 wt % carbonate (2 wt % C), ~5–30 wt % sulfate (1–8 wt % S), and ~5–10 wt % chloride (3–6 wt % Cl) depending on the basaltic matrix and/or salt cation. Absolute quantification of Cl, C, and S in the samples via univariate analysis depends on the cation-anion pairing in the salt but appears relatively independent of matrices tested, following normalization. Our results are promising for tracking relative changes in the salt content of bulk rock on the Martian surface with ChemCam.« less

iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties

PubMed Central

Feng, Peng-Mian; Ding, Chen; Zuo, Yong-Chun; Chou, Kuo-Chen

2012-01-01

Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional) feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection) procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96% in identifying nucleosomal or linker sequences. As a web-server, iNuc-PhysChem is freely accessible to the public at http://lin.uestc.edu.cn/server/iNuc-PhysChem. For the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented just for the integrity in developing the predictor. Meanwhile, for those who prefer to run predictions in their own computers, the predictor's code can be easily downloaded from the web-server. It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design. PMID:23144709

Thick, Dark Veins at Garden City, Mars

NASA Image and Video Library

2015-11-11

These images from the Chemistry and Camera (ChemCam) instrument on NASA's Curiosity Mars rover indicate similarly dark material, but with very different chemistries, in mineral veins at "Garden City." Each of the side-by-side circular images covers an area about 2 inches (5 centimeters) in diameter. The images were taken by ChemCam's Remote Micro-Imager. Researchers used ChemCam's laser, telescope and spectrometers to examine the chemistry of material in these veins. While both of these veins are dark, their chemistries are very different, indicating that they were formed by different fluids. One common aspect of the chemistry in the dark material is an iron content higher than nearby bedrock. Thus the dark appearance may be result of similar iron content. The dark maerial in the vein on the left is enriched in calcium and contains calcium fluorine. The dark material in the vein on the right is enriched in magnesium, but not in calcium or calcium fluorine. Thus, the veins were formed by different fluids that deposited minerals in rock fractures. The Remote Micro-Imager took the image on the left on March 27, 2015, during the 938th Martian day, or sol, of Curiosity's work on Mars. The next day, it took the image on the right. A broader view of the prominent mineral veins at Garden City is at PIA19161. ChemCam is one of 10 instruments in Curiosity's science payload. The U.S. Department of Energy's Los Alamos National Laboratory, in Los Alamos, New Mexico, developed ChemCam in partnership with scientists and engineers funded by the French national space agency (CNES), the University of Toulouse and the French national research agency (CNRS). More information about ChemCam is available at http://www.msl-chemcam.com. http://photojournal.jpl.nasa.gov/catalog/PIA19924

Fit Point-Wise AB Initio Calculation Potential Energies to a Multi-Dimension Long-Range Model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2016-06-01

A potential energy surface (PES) is a fundamental tool and source of understanding for theoretical spectroscopy and for dynamical simulations. Making correct assignments for high-resolution rovibrational spectra of floppy polyatomic and van der Waals molecules often relies heavily on predictions generated from a high quality ab initio potential energy surface. Moreover, having an effective analytic model to represent such surfaces can be as important as the ab initio results themselves. For the one-dimensional potentials of diatomic molecules, the most successful such model to date is arguably the ``Morse/Long-Range'' (MLR) function developed by R. J. Le Roy and coworkers. It is very flexible, is everywhere differentiable to all orders. It incorporates correct predicted long-range behaviour, extrapolates sensibly at both large and small distances, and two of its defining parameters are always the physically meaningful well depth {D}_e and equilibrium distance r_e. Extensions of this model, called the Multi-Dimension Morse/Long-Range (MD-MLR) function, linear molecule-linear molecule systems and atom-non-linear molecule system. have been applied successfully to atom-plus-linear molecule, linear molecule-linear molecule and atom-non-linear molecule systems. However, there are several technical challenges faced in modelling the interactions of general molecule-molecule systems, such as the absence of radial minima for some relative alignments, difficulties in fitting short-range potential energies, and challenges in determining relative-orientation dependent long-range coefficients. This talk will illustrate some of these challenges and describe our ongoing work in addressing them. Mol. Phys. 105, 663 (2007); J. Chem. Phys. 131, 204309 (2009); Mol. Phys. 109, 435 (2011). Phys. Chem. Chem. Phys. 10, 4128 (2008); J. Chem. Phys. 130, 144305 (2009) J. Chem. Phys. 132, 214309 (2010) J. Chem. Phys. 140, 214309 (2010)

Mw Systematic Study of Alkaloids: the Distorted Tropane of Scopoline

NASA Astrophysics Data System (ADS)

Ecija, Patricia; Cocinero, Emilio J.; Basterretxea, Francisco J.; Fernandez, Jose A.; Castano, Fernando; Lesarri, Alberto

2013-06-01

Tropane alkaloids have diverse pharmacological uses and are well-known for their neurostimulant activity. Previous structure-activity-relationship established correlations between bioactivity and several aspects of ligand conformation and stereochemistry, including delicate intramolecular effects like nitrogen inversion^{a}. We have initiated a series of structural studies on tropane alkaloids^{b}, aimed to discerning their intrinsic stereochemical properties using rotational spectroscopy in supersonic jets^{c}. Here we extend these studies to the epoxytropanes, initially motivated to interrogate the influence of the epoxy group on nitrogen inversion and ring conformation. The rotational spectrum evidences a single structure in the gas phase, providing a first description of the (three ring) structurally-distorted tropane in scopoline. The determined rotational parameters of scopoline reveal the structural consequences of the intramolecular cyclation of scopine, which breaks the original epoxy group and creates a new ether bridge and a 7β-hydroxytropane configuration. The hydroxyl group further stabilizes the molecule by an O-H \\cdots N intramolecular hydrogen bond, which, in turn, forces the N-methyl group to the less stable axial form^{b}. The experimental work was supported by ab initio and DFT calculations. ^{a} i) S.Singh, Chem. Rev. 100, 925 (2000); ii) A. Krunic, D. Pan, W.J. Dunn III, S.V.S. Miariappan, Bioorg. & Med. Chem. 17, 811 (2009). ^{b} E.J. Cocinero, A. Lesarri, P. écija, J.-U. Grabow, J.A. Fernández, F. Castaño, Phys. Chem. Chem. Phys. 12, 6076 (2010). ^{c} E.J. Cocinero, A. Lesarri, P. écija, J.-U. Grabow, J.A. Fernández, F. Castaño, Phys. Chem. Chem. Phys. 12, 12486 (2010).

Weak Hydrogen Bonds from Aliphatic and Fluorinated Alocohols to Molecular Nitrogen Detected by Supersonic Jet FTIR Spectroscopy

NASA Astrophysics Data System (ADS)

Oswald, Soenke; Suhm, Martin A.

2017-06-01

Complexes of organic molecules with the main component of earth's atmosphere are of interest, also for a stepwise understanding of the phenomenon of matrix isolation. Via its large quadrupole moment, nitrogen binds strongly to polarized OH groups in hydrogen-bonded dimers. Further complexation leads to a smooth spectral transition from free to embedded molecules which we probe in supersonic jets. Results for 1,1,1,3,3,3-hexafluoro-2-propanol, methanol, t-butyl alcohol, and the conformationally more complex ethanol are presented and assigned with the help of quantum chemical calculations. Kuma, S., Slipchenko, M. N., Kuyanov, K. E., Momose, T., Vilesov, A. F., Infrared Spectra and Intensities of the H_2O and N_2 Complexes in the Range of the ν_1- and ν_3-Bands of Water, J. Phys. Chem. A, 2006, 110, 10046-10052. Coussan, S., Bouteiller, Y., Perchard, J. P., Zheng, W. Q., Rotational Isomerism of Ethanol and Matrix Isolation Infrared Spectroscopy, J. Phys. Chem. A, 1998, 102, 5789-5793. Suhm, M. A., Kollipost, F., Femtisecond single-mole infrared spectroscopy of molecular clusters, Phys. Chem. Chem. Phys., 2013, 15, 10702-10721. Larsen, R. W., Zielke, P., Suhm, M. A., Hydrogen bonded OH stretching modes of methanol clusters: a combined IR and Raman isotopomer study, J. Chem. Phys., 2007, 126, 194307. Zimmermann, D., Häber, T., Schaal, H., Suhm, M. A., Hydrogen bonded rings, chains and lassos: The case of t-butyl alcohol clusters, Mol. Phys., 2001, 99, 413-425. Wassermann, T. N., Suhm, M. A., Ethanol Monomers and Dimers Revisited: A Raman Study of Conformational Preferences and Argon Nanocoating Effects, J. Phys. Chem. A, 2010, 114, 8223-8233.

The Discrepant and Similar Responses of Genome-Wide Transcriptional Profiles between Drought and Cold Stresses in Cassava.

PubMed

Zeng, Changying; Ding, Zehong; Zhou, Fang; Zhou, Yufei; Yang, Ruiju; Yang, Zi; Wang, Wenquan; Peng, Ming

2017-12-12

Background : Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods : To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq. Results : Many genes specifically and commonly responsive to cold and drought were revealed: genes related to basic cellular metabolism, tetrapyrrole synthesis, and brassinosteroid metabolism exclusively responded to cold; genes related to abiotic stress and ethylene metabolism exclusively responded to drought; and genes related to cell wall, photosynthesis, and carbohydrate metabolism, DNA synthesis/chromatic structure, abscisic acid and salicylic acid metabolism, and calcium signaling commonly responded to both cold and drought. Discussion : Combined with cold- and/or drought-responsive transcription factors, the regulatory networks responding to cold and drought in cassava were constructed. All these findings will improve our understanding of the specific and common responses to cold and drought in cassava, and shed light on genetic improvement of cold and drought tolerance in cassava.

Cold cook methods: an ethnographic exploration on the myths of methamphetamine production and policy implications.

PubMed

Boeri, Miriam W; Gibson, David; Harbry, Liam

2009-09-01

Urban legends and myths are prevalent in drug-use environments. However, the distinction between myth and fact is not always clear. We found contradictory claims regarding the emergence of cold cook methods for producing methamphetamine when contrasting user-generated reports with official reports repudiating such methods as myths. Our aim is to open the topic for more academic discussion. We examine cold cook methods of methamphetamine production revealed in our ethnographic study and interviews with former (n=50) and current (n=48) methamphetamine users. Data were collected in the suburbs of a large southeastern city in the United States. We compare the data with reports from law enforcement professionals and public health officials. Official reports claim the cold cook method described by users in our study is a myth and does not produce methamphetamine. Small-scale producers sell it as methamphetamine and users claim it has the same effect as methamphetamine. They are charged for possession and distribution of methamphetamine when caught with this drug. It appears the unintended consequences of recent policy aimed to reduce production and use of methamphetamine may be a user-friendly production method. We do not know the health implications at this time. We do not make any definitive conclusions on the legitimacy of the stories or myths discussed here but instead suggest that labelling drug stories as myths might lead to dismissing facts that hold partial truth. The subsequent dismissal of cold cook methods among policy and public health officials risks a range of unintended consequences among vulnerable populations. We present our case for more research attention on the myths of methamphetamine production.

First High Resolution IR Spectra of 2,2-D_{2}-PROPANE. the νb{15} (B_{1}) A-Type Band Near 954.709 \\wn. Determination of Ground and Upper State Constants.

NASA Astrophysics Data System (ADS)

Gjuraj, Daniel; Daunt, S. J.; Grzywacz, Robert; Lafferty, Walter; Flaud, Jean-Marie; Billinghurst, Brant E.

2017-06-01

As part of our project on the study of isotopologues of propane we have taken the spectra of the 2-D and 2,2-D_2 substituted species. There have been no studies of these species since the early IR studies. We recorded high resolution (Δν = 0.0009 \\wn) FTS data on the Canadian Light Source Far-IR beamline. The spectra of all bands of both species in the region examined (500 - 1250 \\wn) show torsionally perturbed lines, all but one band appearing globally perturbed. Virtually all bands were not amenable to analysis at present except for the νb{15} (B_{1}) A-type band centered at 954.709 \\wn. One can still see a few perturbed lines with torsional components but overall most lines were single and could be readily assigned using traditional methods. The spectrum is modelled well using PGOPHER. No MW determined GS constants were available so we have analyzed about 3500 levels to determine both ground state and upper state rotational constants. Friedman & Turkevich, J. Chem. Phys. 17, 1012 ff. (1949) McMurry, Thornton & Condon, J. Chem. Phys. 17, 918 ff. (1949) McMurry & Thornton, J. Chem. Phys. 19, 1014 ff.(1951) Gayles & King, Spectrochim. Acta 21, 543 ff.(1965) Kondo & Saeki, Spectrochim. Acta 29A, 735 ff. (1973) Western, J. Quant. Spectrosc. Rad. Transf. 186, 221 ff. (2017).

Accuracy Quantification of the Loci-CHEM Code for Chamber Wall Heat Transfer in a GO2/GH2 Single Element Injector Model Problem

NASA Technical Reports Server (NTRS)

West, Jeff; Westra, Doug; Lin, Jeff; Tucker, Kevin

2006-01-01

A robust rocket engine combustor design and development process must include tools which can accurately predict the multi-dimensional thermal environments imposed on solid surfaces by the hot combustion products. Currently, empirical methods used in the design process are typically one dimensional and do not adequately account for the heat flux rise rate in the near-injector region of the chamber. Computational Fluid Dynamics holds promise to meet the design tool requirement, but requires accuracy quantification, or validation, before it can be confidently applied in the design process. This effort presents the beginning of such a validation process for the Loci-CHEM CFD code. The model problem examined here is a gaseous oxygen (GO2)/gaseous hydrogen (GH2) shear coaxial single element injector operating at a chamber pressure of 5.42 MPa. The GO2/GH2 propellant combination in this geometry represents one the simplest rocket model problems and is thus foundational to subsequent validation efforts for more complex injectors. Multiple steady state solutions have been produced with Loci-CHEM employing different hybrid grids and two-equation turbulence models. Iterative convergence for each solution is demonstrated via mass conservation, flow variable monitoring at discrete flow field locations as a function of solution iteration and overall residual performance. A baseline hybrid was used and then locally refined to demonstrate grid convergence. Solutions were obtained with three variations of the k-omega turbulence model.

Biaxial Flexural Strength of High-Viscosity Glass-Ionomer Cements Heat-Cured with an LED Lamp during Setting

PubMed Central

Fabián Molina, Gustavo; Cabral, Ricardo Juan; Mazzola, Ignacio; Brain Lascano, Laura; Frencken, Jo E.

2013-01-01

Adding heat to glass ionomers during setting might improve mechanical properties. The aim was to compare the biaxial flexural strength (BFS) between and within four glass ionomers, by time of exposure to a high-intensity LED light-curing unit. Materials and methods. Samples of Fuji 9 Gold Label, Ketac Molar Easymix, ChemFil Rock, and the EQUIA system were divided into three treatment groups (n = 30): without heating (Group 1), heated with LED lamp of 1400 mW/cm2 for 30 s while setting (Group 2), and heated with LED lamp of 1400 mW/cm2 for 60 s while setting (Group 3). Samples were stored for 48 hours in distilled water at 37°C until tested. BFS was tested, using a universal testing machine at a crosshead speed of 1 mm/min. Data were analyzed, using ANOVA test with the Bonferroni correction (α = 0.05). Heating the glass-ionomer cements with an LED curing light of 1400 mW/cm2 during setting for 30 s increased the BFS value of all GICs. No statistically significant difference in mean BFS scores was found between the EQUIA system and ChemFil Rock at 30 s and 60 s. The mean BFS value was statistically significantly higher for the EQUIA system and ChemFil Rock than for Fuji 9 Gold Label and Ketac Molar Easymix at all exposure times. PMID:23841095

Biaxial flexural strength of high-viscosity glass-ionomer cements heat-cured with an LED lamp during setting.

PubMed

Fabián Molina, Gustavo; Cabral, Ricardo Juan; Mazzola, Ignacio; Brain Lascano, Laura; Frencken, Jo E

2013-01-01

Adding heat to glass ionomers during setting might improve mechanical properties. The aim was to compare the biaxial flexural strength (BFS) between and within four glass ionomers, by time of exposure to a high-intensity LED light-curing unit. Materials and methods. Samples of Fuji 9 Gold Label, Ketac Molar Easymix, ChemFil Rock, and the EQUIA system were divided into three treatment groups (n = 30): without heating (Group 1), heated with LED lamp of 1400 mW/cm(2) for 30 s while setting (Group 2), and heated with LED lamp of 1400 mW/cm(2) for 60 s while setting (Group 3). Samples were stored for 48 hours in distilled water at 37°C until tested. BFS was tested, using a universal testing machine at a crosshead speed of 1 mm/min. Data were analyzed, using ANOVA test with the Bonferroni correction (α = 0.05). Heating the glass-ionomer cements with an LED curing light of 1400 mW/cm(2) during setting for 30 s increased the BFS value of all GICs. No statistically significant difference in mean BFS scores was found between the EQUIA system and ChemFil Rock at 30 s and 60 s. The mean BFS value was statistically significantly higher for the EQUIA system and ChemFil Rock than for Fuji 9 Gold Label and Ketac Molar Easymix at all exposure times.

Accuracy Quantification of the Loci-CHEM Code for Chamber Wall Heat Fluxes in a G02/GH2 Single Element Injector Model Problem

NASA Technical Reports Server (NTRS)

West, Jeff; Westra, Doug; Lin, Jeff; Tucker, Kevin

2006-01-01

A robust rocket engine combustor design and development process must include tools which can accurately predict the multi-dimensional thermal environments imposed on solid surfaces by the hot combustion products. Currently, empirical methods used in the design process are typically one dimensional and do not adequately account for the heat flux rise rate in the near-injector region of the chamber. Computational Fluid Dynamics holds promise to meet the design tool requirement, but requires accuracy quantification, or validation, before it can be confidently applied in the design process. This effort presents the beginning of such a validation process for the Loci- CHEM CPD code. The model problem examined here is a gaseous oxygen (GO2)/gaseous hydrogen (GH2) shear coaxial single element injector operating at a chamber pressure of 5.42 MPa. The GO2/GH2 propellant combination in this geometry represents one the simplest rocket model problems and is thus foundational to subsequent validation efforts for more complex injectors. Multiple steady state solutions have been produced with Loci-CHEM employing different hybrid grids and two-equation turbulence models. Iterative convergence for each solution is demonstrated via mass conservation, flow variable monitoring at discrete flow field locations as a function of solution iteration and overall residual performance. A baseline hybrid grid was used and then locally refined to demonstrate grid convergence. Solutions were also obtained with three variations of the k-omega turbulence model.

The CHEM Study Story.

ERIC Educational Resources Information Center

Merrill, Richard J.; Ridgway, David W.

The history of the planning, funding, preparation of preliminary materials, teacher preparation, trial teaching, evaluation, revision and final publication of the CHEM Study materials is presented. The anecdotal account points out the difficulties encountered, the solutions found and the pitfalls avoided so that the experience gained may be useful…

Correction: The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes.

PubMed

Villanueva-Cab, J; Anta, J A; Oskam, G

2016-05-28

Correction for 'The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes' by J. Villanueva-Cab et al., Phys. Chem. Chem. Phys., 2016, 18, 2303-2308.

Viewing Spark Generated by ChemCam Laser for Mars Rover

NASA Image and Video Library

2010-09-21

The ChemCam instrument for NASA Mars Science Laboratory mission uses a pulsed laser beam to vaporize a pinhead-size target, producing a flash of light from the ionized material plasma that can be analyzed to identify chemical elements in the target.

76 FR 74667 - Airworthiness Directives; The Boeing Company Model 737-200, -200C, -300, -400, and -500 Series...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-01

... at the chem-milled steps, which could result in sudden fracture and failure of the fuselage skin... chem-milled steps, which could result in sudden fracture and failure of the fuselage skin panels, and...

Fuel Cells for Society

NASA Technical Reports Server (NTRS)

1999-01-01

Through a SBIR contract with Lewis Research Center, ElectroChem, Inc. developed a hydrogen/oxygen fuel cell. The objective for Lewis Research Center's collaboration with ElectroChem was to develop a fuel cell system that could deliver 200-W (minimum) approximately to 10kWh of electrical energy.

Incorporating New Technologies for 21st Century Toxicity ...

EPA Pesticide Factsheets

Presentation at the GlobalChem conference in Washington, DC on Incorporating New Technologies for 21st Century Toxicity Testing and Risk Assessment Presentation at the GlobalChem conference in Washington, DC on Incorporating New Technologies for 21st Century Toxicity Testing and Risk Assessment

Atmospheric cold plasma inactivation of Escherichia coli 0157:H7 and aerobic microorganisms in cold-stored romaine lettuce packaged in a commerical polyethylene terephthalate container

USDA-ARS?s Scientific Manuscript database

Leafy greens continue to be a significant vector for foodborne pathogens, including Escherichia coli O157:H7. Dielectric barrier discharge atmospheric cold plasma (ACP) treatment is a promising method for microbial decontamination of produce. An important aspect of this technology is the potential f...

Boron in Calcium Sulfate Vein at Catabola, Mars

NASA Image and Video Library

2016-12-13

The highest concentration of boron measured on Mars, as of late 2016, is in this mineral vein, called "Catabola," examined with the Chemistry and Camera (ChemCam) instrument on NASA's Curiosity rover on Aug, 25, 2016, during Sol 1441 of the mission. This two-part illustration shows the context of the erosion-resistant, raised vein, in an image from Curiosity's Mast Camera (Mastcam), and a detailed inset image from ChemCam's remote micro-imager. The inset includes indicators of the boron content measured at 10 points along the vein that were analyzed with ChemCam's laser-firing spectrometer. The vein's main component is calcium sulfate. The highest boron content identified is less than one-tenth of one percent. The heights of the orange bars at each point indicate relative abundance of boron, compared with boron content at other points. The scale bar for the inset is 9.2 millimeters, or about 0.36 inch. The ChemCam image is enhanced with color information from Mastcam. http://photojournal.jpl.nasa.gov/catalog/PIA21251

Reliability of the method of levels for determining cutaneous temperature sensitivity

NASA Astrophysics Data System (ADS)

Jakovljević, Miroljub; Mekjavić, Igor B.

2012-09-01

Determination of the thermal thresholds is used clinically for evaluation of peripheral nervous system function. The aim of this study was to evaluate reliability of the method of levels performed with a new, low cost device for determining cutaneous temperature sensitivity. Nineteen male subjects were included in the study. Thermal thresholds were tested on the right side at the volar surface of mid-forearm, lateral surface of mid-upper arm and front area of mid-thigh. Thermal testing was carried out by the method of levels with an initial temperature step of 2°C. Variability of thermal thresholds was expressed by means of the ratio between the second and the first testing, coefficient of variation (CV), coefficient of repeatability (CR), intraclass correlation coefficient (ICC), mean difference between sessions (S1-S2diff), standard error of measurement (SEM) and minimally detectable change (MDC). There were no statistically significant changes between sessions for warm or cold thresholds, or between warm and cold thresholds. Within-subject CVs were acceptable. The CR estimates for warm thresholds ranged from 0.74°C to 1.06°C and from 0.67°C to 1.07°C for cold thresholds. The ICC values for intra-rater reliability ranged from 0.41 to 0.72 for warm thresholds and from 0.67 to 0.84 for cold thresholds. S1-S2diff ranged from -0.15°C to 0.07°C for warm thresholds, and from -0.08°C to 0.07°C for cold thresholds. SEM ranged from 0.26°C to 0.38°C for warm thresholds, and from 0.23°C to 0.38°C for cold thresholds. Estimated MDC values were between 0.60°C and 0.88°C for warm thresholds, and 0.53°C and 0.88°C for cold thresholds. The method of levels for determining cutaneous temperature sensitivity has acceptable reliability.

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.

PubMed

Hettne, Kristina M; Williams, Antony J; van Mulligen, Erik M; Kleinjans, Jos; Tkachenko, Valery; Kors, Jan A

2010-03-23

Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus. To achieve an acceptable recall and precision we used a number of automatic and semi-automatic processing steps together with disambiguation rules. However, it remained to be investigated which impact an extensive manual curation of a multi-source chemical dictionary would have on chemical term identification in text. ChemSpider is a chemical database that has undergone extensive manual curation aimed at establishing valid chemical name-to-structure relationships. We acquired the component of ChemSpider containing only manually curated names and synonyms. Rule-based term filtering, semi-automatic manual curation, and disambiguation rules were applied. We tested the dictionary from ChemSpider on an annotated corpus and compared the results with those for the Chemlist dictionary. The ChemSpider dictionary of ca. 80 k names was only a 1/3 to a 1/4 the size of Chemlist at around 300 k. The ChemSpider dictionary had a precision of 0.43 and a recall of 0.19 before the application of filtering and disambiguation and a precision of 0.87 and a recall of 0.19 after filtering and disambiguation. The Chemlist dictionary had a precision of 0.20 and a recall of 0.47 before the application of filtering and disambiguation and a precision of 0.67 and a recall of 0.40 after filtering and disambiguation. We conclude the following: (1) The ChemSpider dictionary achieved the best precision but the Chemlist dictionary had a higher recall and the best F-score; (2) Rule-based filtering and disambiguation is necessary to achieve a high precision for both the automatically generated and the manually curated dictionary. ChemSpider is available as a web service at http://www.chemspider.com/ and the Chemlist dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web at http://www.biosemantics.org/chemlist.

A new WRF-Chem treatment for studying regional-scale impacts of cloud processes on aerosol and trace gases in parameterized cumuli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berg, L. K.; Shrivastava, M.; Easter, R. C.

A new treatment of cloud effects on aerosol and trace gases within parameterized shallow and deep convection, and aerosol effects on cloud droplet number, has been implemented in the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) version 3.2.1 that can be used to better understand the aerosol life cycle over regional to synoptic scales. The modifications to the model include treatment of the cloud droplet number mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convectivemore » cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. These changes have been implemented in both the WRF-Chem chemistry packages as well as the Kain–Fritsch (KF) cumulus parameterization that has been modified to better represent shallow convective clouds. Testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS). The simulation results are used to investigate the impact of cloud–aerosol interactions on regional-scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column-integrated BC can be as large as –50% when cloud–aerosol interactions are considered (due largely to wet removal), or as large as +40% for sulfate under non-precipitating conditions due to sulfate production in the parameterized clouds. The modifications to WRF-Chem are found to account for changes in the cloud droplet number concentration (CDNC) and changes in the chemical composition of cloud droplet residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to the latest version of WRF-Chem, and it is anticipated that they will be included in a future public release of WRF-Chem.« less

iNR-PhysChem: A Sequence-Based Predictor for Identifying Nuclear Receptors and Their Subfamilies via Physical-Chemical Property Matrix

PubMed Central

Xiao, Xuan; Wang, Pu; Chou, Kuo-Chen

2012-01-01

Nuclear receptors (NRs) form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC) whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1thyroid hormone like, NR2HNF4-like, NR3estrogen like, NR4nerve growth factor IB-like, NR5fushi tarazu-F1 like, NR6germ cell nuclear factor like, and NR0knirps like. These rates were derived by the jackknife tests on a stringent benchmark dataset in which none of protein sequences included has pairwise sequence identity to any other in a same subset. As a user-friendly web-server, iNR-PhysChem is freely accessible to the public at either http://www.jci-bioinfo.cn/iNR-PhysChem or http://icpr.jci.edu.cn/bioinfo/iNR-PhysChem. Also a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics involved in developing the predictor. It is anticipated that iNR-PhysChem may become a useful high throughput tool for both basic research and drug design. PMID:22363503

A new WRF-Chem treatment for studying regional-scale impacts of cloud processes on aerosol and trace gases in parameterized cumuli

DOE PAGES

Berg, L. K.; Shrivastava, M.; Easter, R. C.; ...

2015-02-24

A new treatment of cloud effects on aerosol and trace gases within parameterized shallow and deep convection, and aerosol effects on cloud droplet number, has been implemented in the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) version 3.2.1 that can be used to better understand the aerosol life cycle over regional to synoptic scales. The modifications to the model include treatment of the cloud droplet number mixing ratio; key cloud microphysical and macrophysical parameters (including the updraft fractional area, updraft and downdraft mass fluxes, and entrainment) averaged over the population of shallow clouds, or a single deep convectivemore » cloud; and vertical transport, activation/resuspension, aqueous chemistry, and wet removal of aerosol and trace gases in warm clouds. These changes have been implemented in both the WRF-Chem chemistry packages as well as the Kain–Fritsch (KF) cumulus parameterization that has been modified to better represent shallow convective clouds. Testing of the modified WRF-Chem has been completed using observations from the Cumulus Humilis Aerosol Processing Study (CHAPS). The simulation results are used to investigate the impact of cloud–aerosol interactions on regional-scale transport of black carbon (BC), organic aerosol (OA), and sulfate aerosol. Based on the simulations presented here, changes in the column-integrated BC can be as large as –50% when cloud–aerosol interactions are considered (due largely to wet removal), or as large as +40% for sulfate under non-precipitating conditions due to sulfate production in the parameterized clouds. The modifications to WRF-Chem are found to account for changes in the cloud droplet number concentration (CDNC) and changes in the chemical composition of cloud droplet residuals in a way that is consistent with observations collected during CHAPS. Efforts are currently underway to port the changes described here to the latest version of WRF-Chem, and it is anticipated that they will be included in a future public release of WRF-Chem.« less

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining

PubMed Central

2010-01-01

Background Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus. To achieve an acceptable recall and precision we used a number of automatic and semi-automatic processing steps together with disambiguation rules. However, it remained to be investigated which impact an extensive manual curation of a multi-source chemical dictionary would have on chemical term identification in text. ChemSpider is a chemical database that has undergone extensive manual curation aimed at establishing valid chemical name-to-structure relationships. Results We acquired the component of ChemSpider containing only manually curated names and synonyms. Rule-based term filtering, semi-automatic manual curation, and disambiguation rules were applied. We tested the dictionary from ChemSpider on an annotated corpus and compared the results with those for the Chemlist dictionary. The ChemSpider dictionary of ca. 80 k names was only a 1/3 to a 1/4 the size of Chemlist at around 300 k. The ChemSpider dictionary had a precision of 0.43 and a recall of 0.19 before the application of filtering and disambiguation and a precision of 0.87 and a recall of 0.19 after filtering and disambiguation. The Chemlist dictionary had a precision of 0.20 and a recall of 0.47 before the application of filtering and disambiguation and a precision of 0.67 and a recall of 0.40 after filtering and disambiguation. Conclusions We conclude the following: (1) The ChemSpider dictionary achieved the best precision but the Chemlist dictionary had a higher recall and the best F-score; (2) Rule-based filtering and disambiguation is necessary to achieve a high precision for both the automatically generated and the manually curated dictionary. ChemSpider is available as a web service at http://www.chemspider.com/ and the Chemlist dictionary is freely available as an XML file in Simple Knowledge Organization System format on the web at http://www.biosemantics.org/chemlist. PMID:20331846

Cold plate

DOEpatents

Marroquin, Christopher M.; O'Connell, Kevin M.; Schultz, Mark D.; Tian, Shurong

2018-02-13

A cold plate, an electronic assembly including a cold plate, and a method for forming a cold plate are provided. The cold plate includes an interface plate and an opposing plate that form a plenum. The cold plate includes a plurality of active areas arranged for alignment over respective heat generating portions of an electronic assembly, and non-active areas between the active areas. A cooling fluid flows through the plenum. The plenum, at the non-active areas, has a reduced width and/or reduced height relative to the plenum at the active areas. The reduced width and/or height of the plenum, and exterior dimensions of cold plate, at the non-active areas allow the non-active areas to flex to accommodate surface variations of the electronics assembly. The reduced width and/or height non-active areas can be specifically shaped to fit between physical features of the electronics assembly.

Memantine effects on liver and adrenal gland of rats exposed to cold stress

PubMed Central

2011-01-01

Background Memantine attenuates heart stress due cold stress, however, no study focused its effects on liver and adrenal gland. We evaluated its effects on lipid depletion in adrenal gland and glycogen depletion in liver of rats exposed to cold stress. Methods Male rats divided into 4 groups: 1)Control (CON); 2)Memantine (MEM); 3)Induced cold stress (IH) and; 4)Induced cold stress memantine (IHF). Memantine were administrated by gavage (20 mg/kg/day) during eight days. Cold stress were performed during 4 hours once at - 8°C. Lipid and glycogen depletion were presented as its intensity levels. Results Rats exposed to cold stress presented the highest glycogen (p < 0.001) and lipid depletion (p < 0.001) in liver and adrenal gland, respectively. We noted that memantine significantly reduced lipid depletion in adrenal gland and glycogen depletion in liver. Conclusion Memantine prevented glycogen depletion in liver and lipid depletion in adrenal gland of rats under a cold stress condition. PMID:21255456

Chemical Technology Division: Progress report, January 1, 1987--June 30, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1989-02-01

This progress report summarizes the research and development efforts conducted in the Chemical Technology Division (Chem Tech) during the period January 1, 1987, to June 30, 1988. The following major areas are covered: waste management and environmental programs, radiochemical and reactor engineering programs, basic science and technology, Nuclear Regulatory Commission programs, and administrative resources and facilities. The Administrative Summary, an appendix, presents a comprehensive listing of publications, oral presentations, awards and recognitions, and patents of Chem Tech staff members during this period. A staffing level and financial summary and lists of seminars and Chem Tech consultants for the period aremore » also included.« less

Application of ChemDraw NMR Tool: Correlation of Program-Generated 13C Chemical Shifts and pKa Values of para-Substituted Benzoic Acids

NASA Astrophysics Data System (ADS)

Wang, Hongyi

2005-09-01

An application of ChemDraw NMR Tool was demonstrated by correlation of program-generated 13 C NMR chemical shifts and p K a values of para-substituted benzoic acids. Experimental 13 C NMR chemical shifts were analyzed in the same way for comparison. The project can be used as an assignment at the end of the first-year organic chemistry course to review topics or explore new techniques: Hammett equation, acid base equilibrium theory, electronic nature of functional groups, inductive and resonance effects, structure reactivity relationship, NMR spectroscopy, literature search, database search, and ChemDraw software.

Nonequilibrium umbrella sampling in spaces of many order parameters

NASA Astrophysics Data System (ADS)

Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.

2009-02-01

We recently introduced an umbrella sampling method for obtaining nonequilibrium steady-state probability distributions projected onto an arbitrary number of coordinates that characterize a system (order parameters) [A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys. 127, 154112 (2007)]. Here, we show how our algorithm can be combined with the image update procedure from the finite-temperature string method for reversible processes [E. Vanden-Eijnden and M. Venturoli, "Revisiting the finite temperature string method for calculation of reaction tubes and free energies," J. Chem. Phys. (in press)] to enable restricted sampling of a nonequilibrium steady state in the vicinity of a path in a many-dimensional space of order parameters. For the study of transitions between stable states, the adapted algorithm results in improved scaling with the number of order parameters and the ability to progressively refine the regions of enforced sampling. We demonstrate the algorithm by applying it to a two-dimensional model of driven Brownian motion and a coarse-grained (Ising) model for nucleation under shear. It is found that the choice of order parameters can significantly affect the convergence of the simulation; local magnetization variables other than those used previously for sampling transition paths in Ising systems are needed to ensure that the reactive flux is primarily contained within a tube in the space of order parameters. The relation of this method to other algorithms that sample the statistics of path ensembles is discussed.

Local unitary transformation method toward practical electron correlation calculations with scalar relativistic effect in large-scale molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seino, Junji; Nakai, Hiromi, E-mail: nakai@waseda.jp; Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555

In order to perform practical electron correlation calculations, the local unitary transformation (LUT) scheme at the spin-free infinite-order Douglas–Kroll–Hess (IODKH) level [J. Seino and H. Nakai, J. Chem. Phys.136, 244102 (2012); J. Seino and H. Nakai, J. Chem. Phys.137, 144101 (2012)], which is based on the locality of relativistic effects, has been combined with the linear-scaling divide-and-conquer (DC)-based Hartree–Fock (HF) and electron correlation methods, such as the second-order Møller–Plesset (MP2) and the coupled cluster theories with single and double excitations (CCSD). Numerical applications in hydrogen halide molecules, (HX){sub n} (X = F, Cl, Br, and I), coinage metal chain systems,more » M{sub n} (M = Cu and Ag), and platinum-terminated polyynediyl chain, trans,trans-((p-CH{sub 3}C{sub 6}H{sub 4}){sub 3}P){sub 2}(C{sub 6}H{sub 5})Pt(C≡C){sub 4}Pt(C{sub 6}H{sub 5})((p-CH{sub 3}C{sub 6}H{sub 4}){sub 3}P){sub 2}, clarified that the present methods, namely DC-HF, MP2, and CCSD with the LUT-IODKH Hamiltonian, reproduce the results obtained using conventional methods with small computational costs. The combination of both LUT and DC techniques could be the first approach that achieves overall quasi-linear-scaling with a small prefactor for relativistic electron correlation calculations.« less

Diagnostic Analysis of Ozone Concentrations Simulated by Two Regional-Scale Air Quality Models

EPA Science Inventory

Since the Community Multiscale Air Quality modeling system (CMAQ) and the Weather Research and Forecasting with Chemistry model (WRF/Chem) use different approaches to simulate the interaction of meteorology and chemistry, this study compares the CMAQ and WRF/Chem air quality simu...

"CHEM"opera for Chemistry Education

ERIC Educational Resources Information Center

Chung, Yong Hee

2013-01-01

"CHEM"opera is an opera blended with demonstrations of chemical reactions. It has been produced and performed twice by chemistry undergraduate students at Hallym University in South Korea. It aims to demonstrate interesting chemical reactions to chemistry students, children and the public and to facilitate their understanding of the role…

Correction: Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities.

PubMed

Belosludov, Rodion V; Rhoda, Hannah M; Zhdanov, Ravil K; Belosludov, Vladimir R; Kawazoe, Yoshiyuki; Nemykin, Victor N

2017-08-02

Correction for 'Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities' by Rodion V. Belosludov et al., Phys. Chem. Chem. Phys., 2016, 18, 13503-13518.

Different methods of hilar clamping during partial nephrectomy: Impact on renal function.

PubMed

Lee, Jeong Woo; Kim, Hwanik; Choo, Minsoo; Park, Yong Hyun; Ku, Ja Hyeon; Kim, Hyeon Hoe; Kwak, Cheol

2014-03-01

To evaluate the impact of different hilar clamping methods on changes in renal function after partial nephrectomy. We analyzed the clinical data of 369 patients who underwent partial nephrectomy for a single renal tumor of size ≤4.0 cm and a normal contralateral kidney. Patients were separated into three groups depending on hilar clamping method: non-clamping, cold ischemia and warm ischemia. Estimated glomerular filtration rate was examined at preoperative, nadir and 1 year postoperatively. Percent change in estimated glomerular filtration rate was used as the parameter to assess the renal functional outcome. Percent change in nadir estimated glomerular filtration rate in the non-clamping group was significantly less compared with the cold ischemia and warm ischemia groups (P < 0.001). However, no significant differences among the groups were noted in percent change of estimated glomerular filtration rate at 1 year (P = 0.348). The cold ischemia group had a similar serial change of postoperative renal function compared with the warm ischemia group. Percent change in 1-year estimated glomerular filtration rate increased with increasing ischemia time in the cold ischemia (P for trend = 0.073) and warm ischemia groups (P for trend = 0.010). On multivariate analysis, hilar clamping (both warm ischemia and cold ischemia) were significantly associated with percent change in nadir estimated glomerular filtration rate, but not in 1-year estimated glomerular filtration rate. Non-clamping partial nephrectomy results in a lower percent change in nadir estimated glomerular filtration rate, whereas it carries an estimated glomerular filtration rate change at 1 year that is similar to partial nephrectomy with cold ischemia and warm ischemia. Cold ischemia and warm ischemia provide a similar effect on renal function. Therefore, when hilar clamping is required, minimization of ischemia time is necessary. © 2013 The Japanese Urological Association.

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools.

PubMed

Koo, Hyunmin; Hakim, Joseph A; Fisher, Phillip R E; Grueneberg, Alexander; Andersen, Dale T; Bej, Asim K

2016-01-01

In this study, we report the distribution and abundance of cold-adaptation proteins in microbial mat communities in the perennially ice-covered Lake Joyce, located in the McMurdo Dry Valleys, Antarctica. We have used MG-RAST and R code bioinformatics tools on Illumina HiSeq2000 shotgun metagenomic data and compared the filtering efficacy of these two methods on cold-adaptation proteins. Overall, the abundance of cold-shock DEAD-box protein A (CSDA), antifreeze proteins (AFPs), fatty acid desaturase (FAD), trehalose synthase (TS), and cold-shock family of proteins (CSPs) were present in all mat samples at high, moderate, or low levels, whereas the ice nucleation protein (INP) was present only in the ice and bulbous mat samples at insignificant levels. Considering the near homogeneous temperature profile of Lake Joyce (0.08-0.29 °C), the distribution and abundance of these proteins across various mat samples predictively correlated with known functional attributes necessary for microbial communities to thrive in this ecosystem. The comparison of the MG-RAST and the R code methods showed dissimilar occurrences of the cold-adaptation protein sequences, though with insignificant ANOSIM (R = 0.357; p-value = 0.012), ADONIS (R(2) = 0.274; p-value = 0.03) and STAMP (p-values = 0.521-0.984) statistical analyses. Furthermore, filtering targeted sequences using the R code accounted for taxonomic groups by avoiding sequence redundancies, whereas the MG-RAST provided total counts resulting in a higher sequence output. The results from this study revealed for the first time the distribution of cold-adaptation proteins in six different types of microbial mats in Lake Joyce, while suggesting a simpler and more manageable user-defined method of R code, as compared to a web-based MG-RAST pipeline.

A molecular theory of cartilage viscoelasticity.

PubMed

Kovach, I S

1996-03-07

Recent work on the subject of cartilage mechanics has begun to focus on the relationship between the microscopic structure of cartilage and its macroscopic mechanical properties (Bader et al., Biochem. Biophys. Acta, 1116 (1992) 147-154; Buschmann, PhD Thesis, Massachusetts Institute of Technology, 1992; Kovach, Biophys. Chem., 53 (1995) 181-187; Lai et al., J. Biochem. Eng., 113 (1991) 245-248; Armstrong and Mow, J. Bone Jt. Surg., 64A (1982) 88; Jackson and James, Biorheology, 19 (1982) 317-330). This paper reviews recent theoretical developments and presents a comprehensive explanation of the viscoelastic properties of cartilage in terms of molecular structure. In doing this, a closed form hybrid solution to the non-linear, cylindrical Poisson-Boltzmann equation is developed to describe the charge-dependent component of the equilibrium elasticity arising from polysaccharide charge (Benham, J. Chem. Phys., 79 (4) (1983) 1969-1973; Einevoll and Hemmer, J. Phys. Chem., 89 (1) (1988) 474-484; Fixman, J. Chem. Phys., 70 (11) (1979) 4995-5001; Ramanathan and Woodburg, J. Chem. Phys., 82 (3) (1985) 1482-1491; Wennerstrom et al., J. Chem. Phys., 76 (9) (1982) 4665-4670). This solution agrees with numerical solutions found in the literature (Buschmann, PhD Thesis, Massachusetts Institute of Technology, 1992). The charge-independent, entropic contribution to the equilibrium elasticity is explained in a manner similar to that recently presented for concentrated proteoglycan solution (Kovach, Biophys. Chem., 53 (1995) 181-187). This approach exploits a lattice model of the solution, subject to a Bragg-Williams type approximation to derive the volume dependence of polysaccharide configuration entropy (Flory, Principles of Polymer Chemistry, Cornell University Press, Ithaca, NY, 1953; Huggins, Some properties of Solutions of Long-chain Compounds, 1941, pp. 151-157; Stanley, Introduction to Phase Transitions and Critical Phenomena, Oxford University Press, Oxford, 1971). Together, these two contributions accurately reproduce the experimentally determined osmotic pressure of cartilage as previously determined by Maroudas (Maroudas and Bannon, Biorheology, 18 (1981) 619-632). The time-dependent, or creep, phenomena which cartilage exhibits when subject to mechanical load is explained in terms of frictional drag on the polysaccharide chain monomers in terms of a Kirkwood-Riseman type model (Kirkwood and Riseman, J. Chem. Phys., 16 (6) (1948) 573-579). This approach is shown to accurately predict the hydraulic permeability of cartilage as previously determined by Maroudas (Madouras, Ann. Rheum. Dis., 34 (suppl. 3) (1975) 77). By use of a quasi-static approximation (neglecting inertial effects) the time-dependent response to a uniform compressive force is determined and also found to be in good agreement with experimental values from the literature.

40 CFR Appendix C to Part 136 - Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma...

Code of Federal Regulations, 2014 CFR

2014-07-01

... comparative data to other methods and SRM materials are presented in Reference 23 of Section 16.0. 13... Plasma, Anal. Chem. 52:1965, 1980. 20. Deming, S.N. and S.L. Morgan. Experimental Design for Quality and... Statistical Designs, 9941 Rowlett, Suite 6, Houston, TX 77075, 1989. 21. Winefordner, J.D., Trace Analysis...

40 CFR Appendix C to Part 136 - Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma...

Code of Federal Regulations, 2013 CFR

2013-07-01

... comparative data to other methods and SRM materials are presented in Reference 23 of Section 16.0. 13... Plasma, Anal. Chem. 52:1965, 1980. 20. Deming, S.N. and S.L. Morgan. Experimental Design for Quality and... Statistical Designs, 9941 Rowlett, Suite 6, Houston, TX 77075, 1989. 21. Winefordner, J.D., Trace Analysis...

40 CFR Appendix C to Part 136 - Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma...

Code of Federal Regulations, 2012 CFR

2012-07-01

... comparative data to other methods and SRM materials are presented in Reference 23 of Section 16.0. 13... Plasma, Anal. Chem. 52:1965, 1980. 20. Deming, S.N. and S.L. Morgan. Experimental Design for Quality and... Statistical Designs, 9941 Rowlett, Suite 6, Houston, TX 77075, 1989. 21. Winefordner, J.D., Trace Analysis...

Ground-state energy of HeH{sup +}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou Binglu; Zhu Jiongming; Yan Zongchao

2006-06-15

The nonrelativistic ground-state energy of {sup 4}HeH{sup +} is calculated using a variational method in Hylleraas coordinates. Convergence to a few parts in 10{sup 10} is achieved, which improves the best previous result of Pavanello et al. [J. Chem. Phys. 123, 104306 (2005)]. Expectation values of the interparticle distances are evaluated. Similar results for {sup 3}HeH{sup +} are also presented.

Functional Analysis of the Beclin-1 Tumor Suppressor Interaction with hVps34 (Type-III P13’-kinase) in Breast Cancer Cells

DTIC Science & Technology

2008-06-01

Methods for monitoring autophagy. Int.J Biochem.Cell Biol., 36: 2491-2502, 2004. 13. Scarlatti , F., Bauvy, C., Ventruti, A., Sala, G., Cluzeaud, F...J.Biol.Chem., 279: 18384-18391, 2004. 14. Scarlatti , F., Maffei, R., Beau, I., Codogno, P., and Ghidoni, R. Role of non-canonical Beclin 1- independent

Evaluation of Lateral-Flow Clostridium botulinum Neurotoxin Detection Kits for Food Analysis

DTIC Science & Technology

2005-02-08

toxic proteins. Annu. Rev. Microbiol. 53:551–575. 19. Ketema, F., C. Zeh, D. C. Edelman, R. Saville, and N. T. Constantine. 2001. Assessment of the...H. H., and F. Sun. 2001. Assessing cyanogen content in cassava -based food using the enzyme-dipstick method. Food Chem. Toxicol. 39:649–653. VOL. 71, 2005 RAPID DETECTION OF C. BOTULINUM NEUROTOXIN 3941

Direct observation of the protonation of acetone ketyl radical by conductometric pulse radiolysis. [8-MeV electrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janata, E.; Schuler, R.H.

1980-12-11

Improvements in conductometric pulse radiolysis methods allow direct observation of the protonation of the acetone ketyl radical anion on the 10-ns time scale. The protonation period of 9.7 +- 0.5 ns determined here is in good agreement with that estimated from the ESR line broadening studies of Laroff and Fessenden, (J. Phys. Chem., 77, 1283(1973)).

Assessing the thermal dissipation sap flux density method for monitoring cold season water transport in seasonally snow-covered forests

DOE PAGES

Chan, Allison M.; Bowling, David R.

2017-05-26

Productivity of conifers in seasonally snow-covered forests is high before and during snowmelt when environmental conditions are optimal for photosynthesis. Climate change is altering the timing of spring in many locations, and changes in the date of transition from winter dormancy can have large impacts on annual productivity. Sap flow methods provide a promising approach to monitor tree activity during the cold season and the winter–spring and fall–winter transitions. Although sap flow techniques have been widely used, cold season results are generally not reported. Here we examine the feasibility of using the Granier thermal dissipation (TD) sap flux density methodmore » to monitor transpiration and dormancy of evergreen conifers during the cold season. We conducted a laboratory experiment which demonstrated that the TD method reliably detects xylem water transport (when it occurs) both at near freezing temperature and at low flow rate, and that the sensors can withstand repeated freeze–thaw events. However, the dependence between sensor output and water transport rate in these experiments differed from the established TD relation. In field experiments, sensors installed in two Abies forests lasted through two winters and a summer with low failure. The baseline (no-flow) sensor output varied considerably with temperature during the cold season, and a new baseline algorithm was developed to accommodate this variation. The Abies forests differed in elevation (2070 and 2620 m), and there was a clear difference in timing of initiation and cessation of transpiration between them. We conclude that the TD method can be reliably used to examine water transport during cold periods with associated low flow conditions« less

Assessing the thermal dissipation sap flux density method for monitoring cold season water transport in seasonally snow-covered forests

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Allison M.; Bowling, David R.

Productivity of conifers in seasonally snow-covered forests is high before and during snowmelt when environmental conditions are optimal for photosynthesis. Climate change is altering the timing of spring in many locations, and changes in the date of transition from winter dormancy can have large impacts on annual productivity. Sap flow methods provide a promising approach to monitor tree activity during the cold season and the winter–spring and fall–winter transitions. Although sap flow techniques have been widely used, cold season results are generally not reported. Here we examine the feasibility of using the Granier thermal dissipation (TD) sap flux density methodmore » to monitor transpiration and dormancy of evergreen conifers during the cold season. We conducted a laboratory experiment which demonstrated that the TD method reliably detects xylem water transport (when it occurs) both at near freezing temperature and at low flow rate, and that the sensors can withstand repeated freeze–thaw events. However, the dependence between sensor output and water transport rate in these experiments differed from the established TD relation. In field experiments, sensors installed in two Abies forests lasted through two winters and a summer with low failure. The baseline (no-flow) sensor output varied considerably with temperature during the cold season, and a new baseline algorithm was developed to accommodate this variation. The Abies forests differed in elevation (2070 and 2620 m), and there was a clear difference in timing of initiation and cessation of transpiration between them. We conclude that the TD method can be reliably used to examine water transport during cold periods with associated low flow conditions« less

Generalized method calculating the effective diffusion coefficient in periodic channels.

PubMed

Kalinay, Pavol

2015-01-07

The method calculating the effective diffusion coefficient in an arbitrary periodic two-dimensional channel, presented in our previous paper [P. Kalinay, J. Chem. Phys. 141, 144101 (2014)], is generalized to 3D channels of cylindrical symmetry, as well as to 2D or 3D channels with particles driven by a constant longitudinal external driving force. The next possible extensions are also indicated. The former calculation was based on calculus in the complex plane, suitable for the stationary diffusion in 2D domains. The method is reformulated here using standard tools of functional analysis, enabling the generalization.

AutoClickChem: click chemistry in silico.

PubMed

Durrant, Jacob D; McCammon, J Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in "big pharma." High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu.

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

ChemNet: A Transferable and Generalizable Deep Neural Network for Small-Molecule Property Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goh, Garrett B.; Siegel, Charles M.; Vishnu, Abhinav

With access to large datasets, deep neural networks through representation learning have been able to identify patterns from raw data, achieving human-level accuracy in image and speech recognition tasks. However, in chemistry, availability of large standardized and labelled datasets is scarce, and with a multitude of chemical properties of interest, chemical data is inherently small and fragmented. In this work, we explore transfer learning techniques in conjunction with the existing Chemception CNN model, to create a transferable and generalizable deep neural network for small-molecule property prediction. Our latest model, ChemNet learns in a semi-supervised manner from inexpensive labels computed frommore » the ChEMBL database. When fine-tuned to the Tox21, HIV and FreeSolv dataset, which are 3 separate chemical tasks that ChemNet was not originally trained on, we demonstrate that ChemNet exceeds the performance of existing Chemception models, contemporary MLP models that trains on molecular fingerprints, and it matches the performance of the ConvGraph algorithm, the current state-of-the-art. Furthermore, as ChemNet has been pre-trained on a large diverse chemical database, it can be used as a universal “plug-and-play” deep neural network, which accelerates the deployment of deep neural networks for the prediction of novel small-molecule chemical properties.« less

Response to ``Comment on `Slow Debye-type peak observed in the dielectric response of polyalcohols' '' [J. Chem. Phys. 134, 037101 (2011)

NASA Astrophysics Data System (ADS)

Bergman, R.; Jansson, H.; Swenson, J.

2011-01-01

In our recent article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)] we investigated some polyalcohols, i.e., glycerol, xylitol, and sorbitol by dielectric spectroscopy. In the study, a low-frequency peak of Debye character that normally is hidden by the large low-frequency dispersion due to conductivity was revealed by analyzing the real part of the permittivity and by using a thin Teflon film to suppress the low-frequency dispersion. We agree with the comment by Paluch et al. [J. Chem. Phys. 134, 037101 (2011)] that the Teflon film setup will indeed create a peak due to the dc conductivity. However, due to the fact that the location of the peak was almost identical in measurement with and without Teflon, we unfortunately mainly showed the data measured with Teflon, despite that it could also be observed in the real part of the permittivity without using the Teflon setup, as shown in our original article [R. Bergman et al., J. Chem. Phys. 132, 044504 (2010)]. Here, we show that the low-frequency peak of Debye character can also be observed by subtracting the dc conductivity. Furthermore, we show that the modulus representation used in Paluch et al. [J. Chem. Phys. 134, 037101 (2011).] is also not suitable for detecting processes hidden by the conductivity.

AutoClickChem: Click Chemistry in Silico

PubMed Central

Durrant, Jacob D.; McCammon, J. Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu. PMID:22438795

Dust Removal on Mars Using Laser-Induced Breakdown Spectroscopy

NASA Technical Reports Server (NTRS)

Graff, T. G.; Morris, R. V.; Clegg, S. M.; Wiens, R. C.; Anderson, R. B.

2011-01-01

Dust coatings on the surface of Mars complicate and, if sufficiently thick, mask the spectral characteristics and compositional determination of underlying material from in situ and remote sensing instrumentation. The Laser-Induced Breakdown Spectroscopy (LIBS) portion of the Chemistry & Camera (ChemCam) instrument, aboard the Mars Science Laboratory (MSL) rover, will be the first active remote sensing technique deployed on Mars able to remove dust. ChemCam utilizes a 5 ns pulsed 1067 nm high-powered laser focused to less than 400 m diameter on targets at distances up to 7 m [1,2]. With multiple laser pulses, dust and weathering coatings can be remotely analyzed and potentially removed using this technique [2,3]. A typical LIBS measurement during MSL surface operations is planned to consist of 50 laser pulses at 14 mJ, with the first 5 to 10 pulses used to analyze as well as remove any surface coating. Additionally, ChemCam's Remote Micro-Imager (RMI) is capable of resolving 200 m details at a distance of 2 m, or 1 mm at 10 m [1,4]. In this study, we report on initial laboratory experiments conducted to characterize the removal of dust coatings using similar LIBS parameters as ChemCam under Mars-like conditions. These experiments serve to better understand the removal of surface dust using LIBS and to facilitate the analysis of ChemCam LIBS spectral data and RMI images.

Simulation of the single-vibronic-level emission spectrum of HPS.

PubMed

Mok, Daniel K W; Lee, Edmond P F; Chau, Foo-tim; Dyke, John M

2014-05-21

We have computed the potential energy surfaces of the X¹A' and ùA" states of HPS using the explicitly correlated multi-reference configuration interaction (MRCI-F12) method, and Franck-Condon factors between the two states, which include anharmonicity and Duschinsky rotation, with the aim of testing the assignment of the recently reported single-vibronic-level (SVL) emission spectrum of HPS [R. Grimminger, D. J. Clouthier, R. Tarroni, Z. Wang, and T. J. Sears, J. Chem. Phys. 139, 174306 (2013)]. These are the highest level calculations on these states yet reported. It is concluded that our spectral simulation supports the assignments of the molecular carrier, the electronic states involved and the vibrational structure of the experimental laser induced fluorescence, and SVL emission spectra proposed by Grimminger et al. [J. Chem. Phys. 139, 174306 (2013)]. However, there remain questions unanswered regarding the relative electronic energies of the two states and the geometry of the excited state of HPS.

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

Excited state electron affinity calculations for aluminum

NASA Astrophysics Data System (ADS)

Hussein, Adnan Yousif

2017-08-01

Excited states of negative aluminum ion are reviewed, and calculations of electron affinities of the states (3s^23p^2)^1D and (3s3p^3){^5}{S}° relative to the (3s^23p)^2P° and (3s3p^2)^4P respectively of the neutral aluminum atom are reported in the framework of nonrelativistic configuration interaction (CI) method. A priori selected CI (SCI) with truncation energy error (Bunge in J Chem Phys 125:014107, 2006) and CI by parts (Bunge and Carbó-Dorca in J Chem Phys 125:014108, 2006) are used to approximate the valence nonrelativistic energy. Systematic studies of convergence of electron affinity with respect to the CI excitation level are reported. The calculated value of the electron affinity for ^1D state is 78.675(3) meV. Detailed Calculations on the ^5S°c state reveals that is 1216.8166(3) meV below the ^4P state.

Comment on “Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set” [J. Chem. Phys. 139, 114104 (2013)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandbyge, Mads, E-mail: mads.brandbyge@nanotech.dtu.dk

2014-05-07

In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, andmore » that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.« less

Quantum dynamics calculations using symmetrized, orthogonal Weyl-Heisenberg wavelets with a phase space truncation scheme. III. Representations and calculations.

PubMed

Poirier, Bill; Salam, A

2004-07-22

In a previous paper [J. Theo. Comput. Chem. 2, 65 (2003)], one of the authors (B.P.) presented a method for solving the multidimensional Schrodinger equation, using modified Wilson-Daubechies wavelets, and a simple phase space truncation scheme. Unprecedented numerical efficiency was achieved, enabling a ten-dimensional calculation of nearly 600 eigenvalues to be performed using direct matrix diagonalization techniques. In a second paper [J. Chem. Phys. 121, 1690 (2004)], and in this paper, we extend and elaborate upon the previous work in several important ways. The second paper focuses on construction and optimization of the wavelength functions, from theoretical and numerical viewpoints, and also examines their localization. This paper deals with their use in representations and eigenproblem calculations, which are extended to 15-dimensional systems. Even higher dimensionalities are possible using more sophisticated linear algebra techniques. This approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where differential equations are involved.

Wetting transition on patterned surfaces: transition states and energy barriers.

PubMed

Ren, Weiqing

2014-03-18

We study the wetting transition on microstructured hydrophobic surfaces. We use the string method [J. Chem. Phys. 2007, 126, 164103; J. Chem. Phys. 2013, 138, 134105] to accurately compute the transition states, the energy barriers, and the minimum energy paths for the wetting transition from the Cassie-Baxter state to the Wenzel state. Numerical results are obtained for the wetting of a hydrophobic surface textured with a square lattice of pillars. It is found that the wetting of the solid substrate occurs via infiltration of the liquid in a single groove, followed by lateral propagation of the liquid front. The propagation of the liquid front proceeds in a stepwise manner, and a zipping mechanism is observed during the infiltration of each layer. The minimum energy path for the wetting transition goes through a sequence of intermediate metastable states, whose wetted areas reflect the microstructure of the patterned surface. We also study the dependence of the energy barrier on the drop size and the gap between the pillars.

Comment on "Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature" by W. Siebrand, Z. Smedarchina, E. Martínez-Núñez and A. Fernández-Ramos, Phys. Chem. Chem. Phys., 2016, 18, 22712.

PubMed

Shannon, R J; Gómez Martín, J C; Caravan, R L; Blitz, M A; Plane, J M C; Heard, D E; Antiñolo, M; Agúndez, M; Jiménez, E; Ballesteros, B; Canosa, A; El Dib, G; Albaladejo, J; Cernicharo, J

2018-03-28

The article "Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature" proposes a dimer mediated mechanism in order to explain the large low temperature rate coefficients for the OH + methanol reaction measured by several groups. It is demonstrated here theoretically that under the conditions of these low temperature experiments, there are insufficient dimers formed for the proposed new mechanism to apply. Experimental evidence is also presented to show that dimerization of the methanol reagent does not influence the rate coefficients reported under the conditions of methanol concentration used for the kinetics studies. It is also emphasised that the low temperature experiments have been performed using both the Laval nozzle expansion and flow-tube methods, with good agreement found for the rate coefficients measured using these two distinct techniques.

Creation of Novel Cores for β-Secretase (BACE-1) Inhibitors: A Multiparameter Lead Generation Strategy

PubMed Central

2014-01-01

In order to find optimal core structures as starting points for lead optimization, a multiparameter lead generation workflow was designed with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer’s disease. De novo design of core fragments was connected with three predictive in silico models addressing target affinity, permeability, and hERG activity, in order to guide synthesis. Taking advantage of an additive SAR, the prioritized cores were decorated with a few, well-characterized substituents from known BACE-1 inhibitors in order to allow for core-to-core comparisons. Prediction methods and analyses of how physicochemical properties of the core structures correlate to in vitro data are described. The syntheses and in vitro data of the test compounds are reported in a separate paper by Ginman et al. [J. Med. Chem.2013, 56, 4181–4205]. The affinity predictions are described in detail by Roos et al. [J. Chem. Inf.2014, DOI: 10.1021/ci400374z]. PMID:24900855