Tropospheric distribution of sulphate aerosols mass and number concentration during INDOEX-IFP and its transport over the Indian Ocean: A GCM study

International audienceThe sulphate aerosols mass and number concentration during the Indian Ocean Experiment (INDOEX) Intensive Field Phase-1999 (INDOEX-IFP) has been simulated using an interactive chemistry GCM. The model considers an interactive scheme for feedback from chemistry to meteorology with internally resolving microphysical properties of aerosols. In particular, the interactive scheme has the ability to predict both particle mass and number concentration for the Aitken and accumulation modes as prognostic variables. On the basis of size distribution retrieved from the observations made along the cruise route during IFP-1999, the model successfully simulates the order of magnitude of aerosol number concentration. The results show the southward migration of minimum concentrations, which follows ITCZ (Inter Tropical Convergence Zone) migration. Sulphate surface concentration during INDOEX-IFP at Kaashidhoo (73.46° E, 4.96° N) gives an agreement within a factor of 2 to 3. The measured aerosol optical depth (AOD) from all aerosol species at KCO was 0.37 ± 0.11 while the model simulated sulphate AOD ranged from 0.05 to 0.11. As sulphate constitutes 29% of the observed AOD, the model predicted values of sulphate AOD are hence fairly close to the measured values. The model thus has capability to predict the vertically integrated column sulphate burden. Furthermore, the model results indicate that Indian contribution to the estimated sulphate burden over India is more than 60% with values upto 40% over the Arabian Sea. © 2012 Author(s)

Tropospheric distribution of sulphate aerosol mass and number concentration during INDOEX-IFP and its transport over the Indian Ocean: a GCM study

International audienceAn interactive sulphate aerosol chemistry module has been incorporated in the Laboratoire de Météorologie Dynamique General Circulation Model (LMD-GCM) to simulate the sulphur chemistry during the Indian Ocean Experiment (INDOEX) Intensive Field Phase-1999 (INDOEX-IFP). The originality of this module is its ability to predict particle mass and number concentration for the Aitken and accumulation modes. The model qualitatively reproduces the spatial patterns of observations on sulphate aerosol during INDOEX. On the basis of size distribution retrieved from the observations made along the cruise route during 1998 and 1999, the model successfully simulates the order of magnitude and the general north-south gradient in aerosol number concentration. The result shows the southward migration of minimum concentrations, which follows ITCZ (Inter Tropical Convergence Zone) migration. Sulphate surface concentration during INDOEX-IFP at Kaashidhoo (73.46° E, 4.96° N) gives an agreement within a factor of 2 to 3. Predicted sulphate aerosol optical depth (AOD) matches reasonably with measured values, indicating the capability of this model to predict the vertically integrated column sulphate burden. The Indian contribution to estimated sulphate burden over India is more than 60% with values upto 40% over the Arabian Sea

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

DESIGN FOR MANUFACTURE OF SUPERCONDUCTING HALF WAVE CAVITIES *

Abstract 322 MHz medium velocity half wave resonators (HWR) with β = 0.29 and 0.53 have been designed at the Facility for Rare Isotope Beams (FRIB) at Michigan State University (MSU) for use in a heavy ion linac. The β = 0.29 and β = 0.53 are to provide 1.9M V and 3.7M V of accelerating voltage with a peak magnetic field of 54mT and 77mT , respectively. The cavities are designed for a peak surface electric field of 30M V /m. The cavities were optimized for manufacturing recommendations based on previous design as well as for stiffness, tunability, assembly, and cleaning. Finite element analysis simulations were performed for mechanical modal frequency analysis, liquid helium bath pressure sensitivity, Lorentz force detuning factor and mechanical force to complete the tuning range. The helium vessel, fundamental power coupler (FPC), and frequency tuner systems which interface to the cavity have been designed and prototypes fabricated

A plume-in-grid approach to characterize air quality impacts of aircraft emissions at the Hartsfield-Jackson Atlanta International Airport

This study examined the impacts of aircraft emissions during the landing and takeoff cycle on PM2.5 concentrations during the months of June 2002 and July 2002 at the Hartsfield-Jackson Atlanta International Airport. Primary and secondary pollutants were modeled using the Advanced Modeling System for Transport, Emissions, Reactions, and Deposition of Atmospheric Matter (AMSTERDAM). AMSTERDAM is a modified version of the Community Multiscale Air Quality (CMAQ) model that incorporates a plume-in-grid process to simulate emissions sources of interest at a finer scale than can be achieved using CMAQ's model grid. Three fundamental issues were investigated: the effects of aircraft on PM2.5 concentrations throughout northern Georgia, the differences resulting from use of AMSTERDAM's plume-in-grid process rather than a traditional CMAQ simulation, and the concentrations observed in aircraft plumes at sub-grid scales. Comparison of model results with an air quality monitor located in the vicinity of the airport found that normalized mean bias ranges from -77.5% to 6.2% and normalized mean error ranges from 40.4% to 77.5%, varying by species. Aircraft influence average PM2.5 concentrations by up to 0.232 μg m-3 near the airport and by 0.001-0.007 μg m-3 throughout the Atlanta metro area. The plume-in-grid process increases concentrations of secondary PM pollutants by 0.005-0.020 μg m-3 (compared to the traditional grid-based treatment) but reduces the concentration of non-reactive primary PM pollutants by up to 0.010 μg m-3, with changes concentrated near the airport. Examination of sub-grid scale results indicates that puffs within 20 km of the airport often have average PM2.5 concentrations one order of magnitude higher than aircraft contribution to the grid cells containing those puffs, and within 1-4 km of emitters, puffs may have PM2.5 concentrations 3 orders of magnitude greater than the aircraft contribution to their grid cells. 21% of all aircraft-related puffs from the Atlanta airport have at least 0.1 μg m-3 PM2.5 concentrations. Median daily puff concentrations vary between 0.017 and 0.134 μg m-3, while maximum daily puff concentrations vary between 6.1 and 42.1 μg m-3 during the 2-month period. In contrast, median daily grid concentrations vary between 0.015 and 0.091 μg m-3, while maximum daily grid concentrations vary between 0.751 and 2.55 μg m-3. Future researchers may consider using AMSTERDAM to understand the impacts of aircraft emissions at other airports, for proposed future airports, for airport expansion projects under various future scenarios, and for other national-scale studies specifically when the maximum impacts at fine scales are of interest

Modeling the impact of sea-spray on particle concentrations in a coastal city

Abstract 18 An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry 19 on the particle composition in and downwind of a coastal city -Vancouver, British Columbia. 20 Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution 21 of particle nitrate. 2

Modeling the impact of sea-spray on particle concentrations in a coastal city

An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry on the particle composition in and downwind of a coastal city--Vancouver, British Columbia. Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution of particle nitrate. Urban air quality, and particularly airborne particles, is a major concern in terms of human health impacts. Sea-spray is known to be a major component of the particle ensemble at coastal sites yet relatively few air quality models include the interaction of gases with sea-spray and the fate of the particles produced. Sea-spray is not an inert addition to the particle ensemble because heterogeneous chemistry in/on sea-spray droplets changes the droplets composition and the particle size distribution, which impacts deposition and the ion balance in different particle size fractions. It is shown that the ISOPART model is capable of simulating gas and particle concentrations in the coastal metropolis of Vancouver and the surrounding valley. It is also demonstrated that to accurately simulate ambient concentrations of particles and reactive/soluble gases in a coastal valley it is absolutely critical to include heterogeneous chemistry in/on sea-spray. Partitioning of total particle-NO{sub 3}{sup -} between sea-spray and NH{sub 4}NO{sub 3} is highly sensitive to the amount of sea-spray present, and hence the initial vertical profile, sea-spray source functions [48] and the wind speed. When a fixed wind speed is used to initialize the sea-spray vertical profiles, as expected, the sea-spray concentration decays with distance inland, but the particle-NO{sub 3}{sup -} concentration decays more slowly because it is also a function of the uptake rate for HNO{sub 3}. The simulation results imply model analyses of air quality in coastal cities conducted without inclusion of sea-spray interactions may yield highly misleading results in terms of emission sensitivities of the PM size distribution. The sensitivity of the model results to the initial sea spray profile further suggests there would be great benefit in better definition of the vertical profile of size resolved sea-spray for use in such model studies

CloneQC: lightweight sequence verification for synthetic biology

Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source