The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both …

Short-pulse ultraviolet and x-ray free electron lasers of unprecedented peak brightness are in the process of revolutionizing physics, chemistry, and biology. Optical components for these new light sources have to be able to withstand exposure to the extremely high-fluence photon pulses. Whereas most optics have been designed to stay intact for many pulses, it has also been suggested that single-pulse optics that function during the pulse but disintegrate on a longer timescale, may be useful at higher fluences than multiple-pulse optics. In this paper we will review damage-resistant single-pulse optics that recently have been demonstrated at the FLASH soft-x-ray laser facility at DESY, including mirrors, apertures, and nanolenses. It was found that these objects stay intact for the duration of the 25-fs FLASH pulse, even when exposed to fluences that exceed the melt damage threshold by fifty times or more. We present a computational model for the FLASH laser-material interaction to analyze the extent to which the optics still function during the pulse. Comparison to experimental results obtained at FLASH shows good quantitative agreement.

This report describes the procedures and the results of a series of downhole measurements of shear- and compression-wave velocities performed as part of the Seismic Boreholes Project at the site of the Waste Treatment Plant (WTP). The measurements were made in several stages from October 2006 through early February 2007. Although some fieldwork was carried out in conjunction with the University of Texas at Austin (UT), all data acquired by UT personnel are reported separately by that organization.

Spatially resolved measurements of deuterium Balmer and Paschen line emission have been performed in the divertor region of the National Spherical Torus Experiment using a commercial 0.5 m Czerny-Turner spectrometer. While the Balmer emission lines, Balmer and Paschen continua in the ultraviolet and visible regions have been extensively used for tokamak divertor plasma temperature and density measurements, the diagnostic potential of infrared Paschen lines has been largely overlooked. We analyze Stark broadening of the lines corresponding to 2-n and 3-m transitions with principle quantum numbers n = 7-12 and m = 10-12 using recent Model Microfield Method calculations (C. Stehle and R. Hutcheon, Astron. Astrophys. Supl. Ser. 140, 93 (1999)). Densities in the range (5-50) x 10{sup 19} m{sup -3} are obtained in the recombining inner divertor plasma in 2-6 MW NBI H-mode discharges. The measured Paschen line profiles show good sensitivity to Stark effects, and low sensitivity to instrumental and Doppler broadening. The lines are situated in the near-infrared wavelength domain, where optical signal extraction schemes for harsh nuclear environments are practically realizable, and where a recombining divertor plasma is optically thin. These properties make them an attractive recombining divertor density diagnostic for a burning plasma experiment.

High spatial-resolution secondaryion microprobespectrometry, synchrotron radiation Fourier-transform infraredspectroscopy and polyacrylamide gel analysis demonstrate the intimateassociation of proteins with spheroidal aggregates of biogenic zincsulfide nanocrystals, an example of extracellular biomineralization.Experiments involving synthetic ZnS nanoparticles and representativeamino acids indicate a driving role for cysteine in rapid nanoparticleaggregation. These findings suggest that microbially-derivedextracellular proteins can limit dispersal of nanoparticulatemetal-bearing phases, such as the mineral products of bioremediation,that may otherwise be transported away from their source by subsurfacefluid flow.

A major goal for microbiologists in the twenty-first century is to develop an understanding of the microbial cell in all its complexity. In addition to understanding the function of individual gene products we need to focus on how the cell regulates gene expression at a global level to respond to different environmental parameters. Development of genomic technologies such as complete genome sequencing, proteomics, and global comparisons of mRNA expression patterns allows us to begin to address this issue. This proposal focuses on a number of phylogenetically related bacteria that are involved in environmentally important processes such as carbon sequestration and bioremediation. Genome sequencing projects of a number of these bacteria have revealed the presence of a small family of regulatory genes found thus far only in the alpha-proteobacteria. These genes encode proteins that are related to the global regulatory protein RosR in Rhizobium etli, which is involved in determining nodulation competitiveness in this bacterium. Our goal is to examine the function of the proteins encoded by this gene family in several of the bacteria containing homologs to RosR. We will construct gene disruption mutations in a number of these bacteria and characterize the resulting mutant strains using two-dimensional gel electrophoresis …

This paper describes the design and simulation of the electron beam collimation system in the Linac Coherent Light Source (LCLS). Dark current is expected from the gun and some of the accelerating cavities. Particle tracking of the expected dark current through the entire LCLS linac, from gun through FEL undulator, is used to estimate final particle extent in the undulator as well as expected beam loss at each collimator or aperture restriction. A table of collimators and aperture restrictions is listed along with halo particle loss results, which includes an estimate of average continuous beam power lost. In addition, the transverse wakefield alignment tolerances are calculated for each collimator.

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The purpose of Task 3.b under PL02-OP211I-PD07 (CBW simulant detection) was to demonstrate the applicability of the sensor work developed under this project for chemical and biological weapons detection. To this end, the specific goal was to demonstrate the feasibility of detection of chemical agents via that of simulants (Freons) with similar spectroscopic features. This has been achieved using Freon-125 as a simulant, a tunable external cavity quantum cascade laser (ECQCL), and a Herriott cell-based sensor developed at Pacific Northwest National Laboratory (PNNL) specifically for this task. The experimentally obtained spectrum of this simulant matches that found in the Northwest Infrared (NWIR) spectral library extremely well, demonstrating the ability of this technique to detect the exact shape of this feature, which in turn indicates the ability to recognize the simulant even in the presence of significant interference. It has also been demonstrated that the detected features of a typical interferent, namely water, are so different in shape and width to the simulant, that they are easily recognized and separated from such a measurement. Judging from the signal-to-noise ratio (SNR) of the experimental data obtained, the noise equivalent absorption sensitivity is estimated to be 0.5 x 10-7 to 1 x 10-6 …

An extensive set of covariances for neutron cross sections in the energy range 5 keV-20 MeV has been developed to provide initial, low-fidelity but consistent uncertainty data for nuclear criticality safety applications. The methodology for the determination of such covariances combines the nuclear reaction model code EMPIRE, which calculates sensitivity to nuclear reaction model parameters, and the Bayesian code KALMAN to propagate uncertainty of the model parameters to cross sections. Taking into account the large scale of the project (219 fission products), only partial reference to experimental data has been made. Therefore, the covariances are, to a large extent, derived from the perturbation of several critical model parameters selected through the sensitivity analysis. These parameters define optical potential, level densities and pre-equilibrium emission. This work represents the first attempt ever to generate nuclear data covariances on such a scale.

Traditionally, the susceptibility of Alloy 22 (N06022) to suffer crevice corrosion has been measured using the Cyclic Potentiodynamic Polarization (CPP) technique (ASTM G 61). When the alloy is not very susceptible to crevice corrosion, the values of repassivation potential obtained using the CPP technique are not highly reproducible. To circumvent the large uncertainty in the values of the repassivation potential by the CPP method, the repassivation potential of Alloy 22 may be measured using a slower method that combines sequentially potentiodynamic, galvanostatic and potentiostatic treatments (this method is called the Tsujikawa-Hisamatsu Electrochemical or THE method). In the THE method the anodic charge is applied to the specimen in a more controlled manner, which avoids driving the alloy to transpassivity and therefore results in more reproducible repassivation potential values. Results using THE method under various testing conditions are presented. A new standard has been prepared for ASTM balloting for the THE method. The round robin matrix results are also discussed.

This report summarizes the activities conducted by the UA group under the auspices of the DoE/EPSCoR grant number DE--FG02--04ER46112 since the date of the previous progress report, i.e., since November 2005. It also provides a final report of the accomplishments achieved during the entire period of this grant (February 2004 to January 2007). The grant has fully supported the work of Dr. Yong Liu (postdoctoral research assistant -- in residence at Fermilab) on the MiniBooNE reconstruction and particle identification (PID) algorithms.

We describe new method for energy-energy covariance calculation from the thermal energy up to 20 MeV. It is based on three powerful basic components: (i) Atlas of Neutron Resonances in the resonance region; (ii) the nuclear reaction model code EMPIRE in the unresolved resonance and fast neutron regions, and (iii) the Bayesian code KALMAN for correlations and error propagation. Examples for cross section uncertainties and correlations on {sup 90}Zr and {sup 193}Ir illustrate this approach in the resonance and fast neutron regions.

We report on recent progress for the development of a new cold X-ray optical test capability using the Omega Facility located at the Laboratory for Laser Energetics (LLE) at the University of Rochester. These tests were done on the 30 kJ OMEGA laser at the Laboratory for Laser Energetics (LLE) at the University of Rochester, Rochester, NY. We conducted a six-shot series called OMEGA II on 14 July 2006 in one eight-hour day (supported by the Defense Threat Reduction Agency). The initial testing was performed using simple protected gold optical coatings on fused silica substrates. PUFFTFT analyses were completed and the specimen's thermal lateral stress and transverse stress conditions were calculated and interpreted. No major anomalies were detected. Comparison of the pre- and posttest reflective measurements coupled with the TFCALC analyses proved invaluable in guiding the analyses and interpreting the observed damage. The Omega facility is a high quality facility for performing evaluation of optical coatings and coupons and provides experience for the development of future National Ignition Facility (NIF) testing.

The benthic sediments in Lake Coeur d Alene, northern Idaho,have been contaminated by metals (primarily Zn, Pb, and Cu) from decadesof upstream mining activities. As part of ongoing research on thebiogeo-chemical cycling of metals in this area, a diffusivereactive-transport model has been developed to simulate metal transportin the lake sediments. The model includes 1-D inorganic diffusivetransport coupled to a biotic reaction network with multiple terminalelectron acceptors under redox disequilibrium conditions. Here, the modelis applied to evaluate the competing effects of heavy-metal mobilizationthrough biotic reductive dissolution of Fe(III) (hydr)oxides, andimmobilization as biogenic sulfide minerals. Results indicate that therelative rates of Fe and sulfate reduction could play an important rolein metal transport through the envi-ronment, and that the formation of(bi)sulfide complexes could significantly enhance metal solubility, aswell as desorption from Fe hydroxides.

To maintain stable performance of the Linac Coherent Light Source (LCLS) x-ray free-electron laser, one must control the electron trajectory stability through the undulator to a small fraction of the beam size. BPM-based feedback loops running at 120 Hz will be effective in controlling jitter at low frequencies less than a few Hz. On the other hand, linac and injector stability tolerances must be chosen to limit jitter at higher frequencies. In this paper we study possible sources of high frequency jitter, including: (1) steering coil current regulation; (2) quadrupole magnet transverse vibrations; (3) quadrupole current regulation with transverse misalignments; (4) charge variations coupled to jitter through transverse wakefields of misaligned RF structures; and (5) bunch length variations coupled through coherent synchrotron radiation in the bunch compressor chicanes. Based on this study, we set component tolerances and estimate expected trajectory stability in the LCLS.

We have built a velocity imaging (VMI) spectrometer optimized for angle-resolved photoionization experiments with synchrotron radiation (SR) in the VUV and soft X-tay range. The spectrometer is equiped with four electrostatic lenses that focus the charged photoionization products onto a position-sensitive multi-hit delay-line anode. The use of two additional electrostatic lens elements as compared to the standard design of Eppink and Parker [T.J.B. Eppink and D.H. Parker, Rev. Sci. Instrum. 68 (1997) 3477]provides better focusing of an extended interaction region, which is crucial for most SR applications. Furthermore, the apparatus is equipped with a second micro-channel plate detector opposite to the VMI spectrometer, enabling electron-ion coincidence experiments and thereby mass-resolved ion spectroscopy independent of the time structure of the synchrotron radiation. First results for the photofragmentation of CO2 molecules are presented.