This chapter will address some of the many issues associated with the identification of signatures based on genomic DNA/RNA, which can be used to identify and characterize pathogens for biodefense and microbial forensic goals. For the purposes of this chapter, we define a signature as one or more strings of contiguous genomic DNA or RNA bases that are sufficient to identify a pathogenic target of interest at the desired resolution and which could be instantiated with particular detection chemistry on a particular platform. The target may be a whole organism, an individual functional mechanism (e.g., a toxin gene), or simply a nucleic acid indicative of the organism. The desired resolution will vary with each program's goals but could easily range from family to genus to species to strain to isolate. The resolution may not be taxonomically based but rather pan-mechanistic in nature: detecting virulence or antibiotic-resistance genes shared by multiple microbes. Entire industries exist around different detection chemistries and instrument platforms for identification of pathogens, and we will only briefly mention a few of the techniques that we have used at Lawrence Livermore National Laboratory (LLNL) to support our biosecurity-related work since 2000. Most nucleic acid based detection chemistries involve …

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Ultra intense short pulse laser pulses incident on solid targets can generate energetic protons. In additions to their potentially important applications such as in cancer treatments and proton fast ignition, these protons are essential to understand the complex physics of intense laser plasma interaction. To better understand these laser-produced protons, we designed and constructed a novel, spatially imaging proton spectrometer that will not only provide at high-resolution the energy distribution, but also the protons angular characteristics. The information obtained from this spectrometer compliments those from other methods using radiochromic film packs, CR39 films and other protons spectrometers. The basic characterizations and example data from this diagnostics will be presented. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, as part of the Cimarron project funded by LDRD-09SI11.

We develop a model based on simulation and experiment that explains the behavior of solid-state laser-supported absorption fronts generated in fused silica during high intensity (up to 5GW/cm{sup 2}) laser exposure. We find that the absorption front velocity is constant in time and is nearly linear in laser intensity. Further, this model can explain the dependence of laser damage site size on these parameters. This behavior is driven principally by the temperature-activated deep sub band-gap optical absorptivity, free electron transport and thermal diffusion in defect-free silica for temperatures up to 15,000K and pressures < 15GPa. The regime of parameter space critical to this problem spans and extends that measured by other means. It serves as a platform for understanding general laser-matter interactions in dielectrics under a variety of conditions.

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