Efficient Global Sensitivity Analysis of Structural Vibration for a Nuclear Reactor System Subject to Nonstationary Loading

The structures associated with the nuclear steam supply system (NSSS) of a pressurized water reactor (PWR) include significant epistemic and aleatory uncertainties in the physical parameters, while also being subject to various non-stationary stochastic loading conditions over the life of a nuclear power plant. To understand the influence of these uncertainties on nuclear reactor systems, sensitivity analysis must be performed. This work evaluates computational design of experiment strategies, which execute a nuclear reactor equipment system finite element model to train and verify Gaussian Process (GP) surrogate models. The surrogate models are then used to perform both global and local sensitivity analyses. The significance of the sensitivity analysis for efficient modeling and simulation of nuclear reactor stochastic dynamics is discussed

Spatial and temporal distribution of sperm whales (Physeter macrocephalus) within the Kaikoura submarine canyon in relation to oceanographic variables

The Kaikoura area is a valuable feeding spot for sperm whales with the presence of a submarine canyon close to shore. Male sperm whales can be found there year around, close to the shore and exhibiting almost constant foraging activities. This thesis investigates the distribution and habitat use, both spatially and temporally, of sperm whales (Physeter macrocephalus) within the Kaikoura submarine canyon, New Zealand. The primary aim was to determine which oceanographic variables and bathymetric features influence the sperm whale distribution patterns off Kaikoura. A theodolite was used to track surfacing and movement of sperm whales from a shore-based station. The accuracy of positions recorded by the theodolite was investigated by comparing theodolite measurements of an object of known position. A calibration technique was then developed as the vertical angle was not accurately determined by the theodolite. In addition to investigating the distribution of sperm whales, the daily abundance of sperm whales within the Kaikoura submarine canyon was estimated. Distance sampling and mark-resight models showed an average of 4 (SEM = 0.13) individuals present in the study area at any given time. The mark-resight technique using photo-identification was not possible from a shore-based station so a spatio-temporal model was built in order to track the identity of individuals. The model was tested using photo-identification of sperm whales collected from a boat-based station. Results showed that 88% of the modeled identifications corresponded to the photo-identification database. Sperm whales off Kaikoura were strongly associated with depth, slope and distance from the nearest coast. They were found in waters between 500 m to 1250 m deep and preferred shallower waters in winter. In spring, sperm whales occurred further from the coast, mainly in the Hikurangi Trough, north-east of the shore-based station. Generalized Additive Models (GAM) were used to identify significant oceanographic variables predicting the presence of sperm whales off Kaikoura. Models indicated that sea surface temperature (SST), chlorophylla (Chla) and distance from sea surface temperature fronts were all important parameters in predicting sperm whales presence. Results showed that sperm whales aggregated in the section of the study area with the lowest SST and near SST fronts. This study provides a detailed insight into the use of the Kaikoura submarine canyon by male sperm whales

The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films

Infrared spectroscopy is used to probe the dynamics of invitro samples of DNA prepared as solutions and as solid unoriented films.The lowest frequency DNA mode identified in the far-infrared spectra ofthe DNA samples is found to shift in frequency when the solvent influencein the hydration shell is altered. The lowest frequency mode also hascharacteristics that are similar to beta - relaxations identified inother glass forming polymers

Chemical Imaging on Liver Steatosis Using Synchrotron Infrared and ToF-SIMS Microspectroscopies

Fatty liver or steatosis is a frequent histopathological change. It is a precursor for steatohepatitis that may progress to cirrhosis and in some cases to hepatocellular carcinoma. In this study we addressed the in situ composition and distribution of biochemical compounds on tissue sections of steatotic liver using both synchrotron FTIR (Fourier transform infrared) and ToF-SIMS (time of flight secondary ion mass spectrometry) microspectroscopies. FTIR is a vibrational spectroscopy that allows investigating the global biochemical composition and ToF-SIMS lead to identify molecular species in particular lipids. Synchrotron FTIR microspectroscopy demonstrated that bands linked to lipid contribution such as -CH3 and -CH2 as well as esters were highly intense in steatotic vesicles. Moreover, a careful analysis of the -CH2 symmetric and anti-symmetric stretching modes revealed a slight downward shift in spectra recorded inside steatotic vesicles when compared to spectra recorded outside, suggesting a different lipid environment inside the steatotic vesicles. ToF-SIMS analysis of such steatotic vesicles disclosed a selective enrichment in cholesterol as well as in diacylglycerol (DAG) species carrying long alkyl chains. Indeed, DAG C36 species were selectively localized inside the steatotic vesicles whereas DAG C30 species were detected mostly outside. Furthermore, FTIR detected a signal corresponding to olefin (C = C, 3000-3060 cm−1) and revealed a selective localization of unsaturated lipids inside the steatotic vesicles. ToF-SIMS analysis definitely demonstrated that DAG species C30, C32, C34 and C36 carrying at least one unsaturated alkyl chain were selectively concentrated into the steatotic vesicles. On the other hand, investigations performed on the non-steatotic part of the fatty livers have revealed important changes when compared to the normal liver. Although the non-steatotic regions of fatty livers exhibited normal histological aspect, IR spectra demonstrated an increase in the lipid content and ToF-SIMS detected small lipid droplets corresponding most likely to the first steps of lipid accretion

Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy

The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium

Noncovalent Interactions of Hydrated DNA and RNA Mapped by 2D-IR Spectroscopy

Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific electrostatic and many-body interactions. Structural fluctuations of the water shell result in fluctuating Coulomb forces on polar and/or ionic groups of the biomolecular structure and in a breaking and reformation of hydrogen bonds. Two-dimensional infrared (2D-IR) spectroscopy of vibrational modes of DNA and RNA gives insight into local hydration geometries, elementary molecular dynamics, and the mechanisms behind them. In this chapter, recent results from 2D-IR spectroscopy of native and artificial DNA and RNA are presented, together with theoretical calculations of molecular couplings and molecular dynamics simulations. Backbone vibrations of DNA and RNA are established as sensitive noninvasive probes of the complex behavior of hydrated helices. The results reveal the femtosecond fluctuation dynamics of the water shell, the short-range character of Coulomb interactions, and the strength and fluctuation amplitudes of interfacial electric fields.Comment: To appear as Chapter 8 of Springer Series in Optical Sciences: Coherent Multidimensional Spectroscopy -- Editors: Cho, Minhaeng (Ed.), 201

Microscopic structure of the polymer-induced liquid precursor for calcium carbonate

Many biomineral crystals form complex non-equilibrium shapes, often via transient amorphous precursors. Also in vitro crystals can be grown with non-equilibrium morphologies, such as thin films or nanorods. In many cases this involves charged polymeric additives that form a polymer-induced liquid precursor (PILP). Here, we investigate the CaCO3 based PILP process with a variety of techniques including cryoTEM and NMR. The initial products are 30–50 nm amorphous calcium carbonate (ACC) nanoparticles with ~2 nm nanoparticulate texture. We show the polymers strongly interact with ACC in the early stages, and become excluded during crystallization, with no liquid–liquid phase separation detected during the process. Our results suggest that “PILP” is actually a polymer-driven assembly of ACC clusters, and that its liquid-like behavior at the macroscopic level is due to the small size and surface properties of the assemblies. We propose that a similar biopolymer-stabilized nanogranular phase may be active in biomineralization