THE PHYSICS OF HIGH-INTENSITY LASER-MATTER INTERACTIONS AND APPLICATIONS

This dissertation consists of three separate research topics: First, the effect of laser noise on the propagation of high-power and high-intensity short pulse lasers in dispersive and nonlinear media is studied. We consider the coupling of laser intensity noise and phase noise to the spatial and temporal evolution of laser radiation. We show that laser noise can have important effects on the propagation of high-power as well as high-intensity lasers in a dispersive and nonlinear medium such as air. We present atmospheric propagation examples of the spatial and temporal evolution of intensity and frequency fluctuations due to noise for laser wavelengths of 0.85 μm, 1 μm, and 10.6 μm. Next, a concept for all-optical remote detection of radioactive materials is presented and analyzed. The presence of excess radioactivity increases the level of negative ions in the surrounding air region. This can act as a source of seed electrons for a laser-induced avalanche ionization breakdown process. We model irradiated air to estimate the density of negative ions and use a set of coupled rate equations to simulate a subsequent laser-induced avalanche ionization. We find that ion-seeded avalanche breakdown can be a viable signature for the detection of radioactivity, a conclusion which has been experimentally tested and verified. Finally, we propose and analyze a mechanism to accelerate protons from close to rest in a laser-excited plasma wave. The beating of two counter-propagating laser pulses in a plasma shock-excites a slow forward-propagating wakefield. The trapping and acceleration of protons is accomplished by tapering both the plasma density and the amplitude of the backward-propagating pulse. We present an example in which protons are accelerated from 10 keV to 10 MeV in a distance of approximately 1 cm

Bottom-up accountability initiatives to claim tenure rights in sub-saharan Africa : country report on South Africa

The research project uses the United Nations Food and Agriculture Organization (FAO) Voluntary Guidelines on the Responsible Governance of Tenure of land, fisheries and forests (VGGT or Tenure Guidelines) as a tool to assess the impact of various governance frameworks on small scale fishing communities. It uses the Tenure Guidelines to empower communities to protect their rights in the context of promoting food sovereignty. This case illustrates how Marine Protected Areas (MPAs) impact small scale fishers’ tenure rights, and how communities can resist and negotiate the challenges of exclusion. In terms of human rights, small-scale fishers continue to be marginalized

Tracking evaporative cooling of a mesoscopic atomic quantum gas in real time

The fluctuations in thermodynamic and transport properties in many-body systems gain importance as the number of constituent particles is reduced. Ultracold atomic gases provide a clean setting for the study of mesoscopic systems; however, the detection of temporal fluctuations is hindered by the typically destructive detection, precluding repeated precise measurements on the same sample. Here, we overcome this hindrance by utilizing the enhanced light--matter coupling in an optical cavity to perform a minimally invasive continuous measurement and track the time evolution of the atom number in a quasi two-dimensional atomic gas during evaporation from a tilted trapping potential. We demonstrate sufficient measurement precision to detect atom number fluctuations well below the level set by Poissonian statistics. Furthermore, we characterize the non-linearity of the evaporation process and the inherent fluctuations of the transport of atoms out of the trapping volume through two-time correlations of the atom number. Our results establish coupled atom--cavity systems as a novel testbed for observing thermodynamics and transport phenomena in mesosopic cold atomic gases and, generally, pave the way for measuring multi-time correlation functions of ultracold quantum gases.Comment: Significantly extended discussion of Fig. 4. Accepted for publication in Phys. Rev.

Semi-automated segmentation of the lateral periventricular regions using diffusion magnetic resonance imaging

The lateral ventricular perimeter (LVP) of the brain is a critical region because in addition to housing neural stem cells required for brain development, it facilitates cerebrospinal fluid (CSF) bulk flow and functions as a blood-CSF barrier to protect periventricular white matter (PVWM) and other adjacent regions from injurious toxins. LVP injury is common, particularly among preterm infants who sustain intraventricular hemorrhage or post hemorrhagic hydrocephalus and has been associated with poor neurological outcomes. Assessment of the LVP with diffusion MRI has been challenging, primarily due to issues with partial volume artifacts since the LVP region is in close proximity to CSF and other structures of varying signal intensities that may be inadvertently included in LVP segmentation. This research method presents:•A novel MATLAB-based method to segment a homogenous LVP layer using high spatial resolution parameters (voxel size 1.2 × 1.2 × 1.2 m

MR diffusion changes in the perimeter of the lateral ventricles demonstrate periventricular injury in post-hemorrhagic hydrocephalus of prematurity

OBJECTIVES: Injury to the preterm lateral ventricular perimeter (LVP), which contains the neural stem cells responsible for brain development, may contribute to the neurological sequelae of intraventricular hemorrhage (IVH) and post-hemorrhagic hydrocephalus of prematurity (PHH). This study utilizes diffusion MRI (dMRI) to characterize the microstructural effects of IVH/PHH on the LVP and segmented frontal-occipital horn perimeters (FOHP). STUDY DESIGN: Prospective study of 56 full-term infants, 72 very preterm infants without brain injury (VPT), 17 VPT infants with high-grade IVH without hydrocephalus (HG-IVH), and 13 VPT infants with PHH who underwent dMRI at term equivalent. LVP and FOHP dMRI measures and ventricular size-dMRI correlations were assessed. RESULTS: In the LVP, PHH had consistently lower FA and higher MD and RD than FT and VPT (p\u3c.050). However, while PHH FA was lower, and PHH RD was higher than their respective HG-IVH measures (p\u3c.050), the MD and AD values did not differ. In the FOHP, PHH infants had lower FA and higher RD than FT and VPT (p\u3c.010), and a lower FA than the HG-IVH group (p\u3c.001). While the magnitude of AD in both the LVP and FOHP were consistently less in the PHH group on pairwise comparisons to the other groups, the differences were not significant (p\u3e.050). Ventricular size correlated negatively with FA, and positively with MD and RD (p\u3c.001) in both the LVP and FOHP. In the PHH group, FA was lower in the FOHP than in the LVP, which was contrary to the observed findings in the healthy infants (p\u3c.001). Nevertheless, there were no regional differences in AD, MD, and RD in the PHH group. CONCLUSION: HG-IVH and PHH results in aberrant LVP/FOHP microstructure, with prominent abnormalities among the PHH group, most notably in the FOHP. Larger ventricular size was associated with greater magnitude of abnormality. LVP/FOHP dMRI measures may provide valuable biomarkers for future studies directed at improving the management and neurological outcomes of IVH/PHH

Rational optimization of tolC as a powerful dual selectable marker for genome engineering

Selection has been invaluable for genetic manipulation, although counter-selection has historically exhibited limited robustness and convenience. TolC, an outer membrane pore involved in transmembrane transport in E. coli, has been implemented as a selectable/counter-selectable marker, but counter-selection escape frequency using colicin E1 precludes using tolC for inefficient genetic manipulations and/or with large libraries. Here, we leveraged unbiased deep sequencing of 96 independent lineages exhibiting counter-selection escape to identify loss-of-function mutations, which offered mechanistic insight and guided strain engineering to reduce counter-selection escape frequency by ∼40-fold. We fundamentally improved the tolC counter-selection by supplementing a second agent, vancomycin, which reduces counter-selection escape by 425-fold, compared colicin E1 alone. Combining these improvements in a mismatch repair proficient strain reduced counter-selection escape frequency by 1.3E6-fold in total, making tolC counter-selection as effective as most selectable markers, and adding a valuable tool to the genome editing toolbox. These improvements permitted us to perform stable and continuous rounds of selection/counter-selection using tolC, enabling replacement of 10 alleles without requiring genotypic screening for the first time. Finally, we combined these advances to create an optimized E. coli strain for genome engineering that is ∼10-fold more efficient at achieving allelic diversity than previous best practices

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.United States. Department of Energy (DE-FG02-02ER63445