Single molecule detection and underwater fluorescence imaging with cantilevered near-field fiber optic probes

This is the published version, also available here: http://dx.doi.org/10.1063/1.121505.Tapping-mode near-field scanning optical microscopy (NSOM) employing a cantilevered fiber optic probe is utilized to image the fluorescence from single molecules and samples in aqueous environments. The single molecule fluorescenceimages demonstrate both the subdiffraction limit spatial resolution and low detection limit capabilities of the cantilevered probe design. Images taken as a function of tip oscillation drive amplitude reveal a degradation in the resolution as the amplitude is increased. With all cantilevered probes studied, however, a minimum plateau region in the resolution is reached as the drive amplitude is decreased, indicating that the tapping mode of operation does not reduce the optical resolution. Images of fluorescently dopedlipid films illustrate the ability of the probe to track small height changes (<1.5 nm) in ambient and aqueous environments, while maintaining high resolution in the fluorescenceimage. When the tip is immersed in water (1.3 mm), the cantilevered NSOM tip resonance, 25–50 kHz, shifts approximately 100–150 Hz, the amplitude dampens less than 40% and the Q factor is reduced from 300–500 to 100–200

Response of selected microorganisms to experimental planetary environments

The anaerobic utilization of phosphite or phosphine and the significance of this conversion to potential contamination of Jupiter were investigated. A sporeforming organism was isolated from Cape Canaveral soil which anaerobically converts hypophosphite to phosphate. This conversion coincides with an increase in turbidity of the culture and with phosphate accumulation in the medium. Investigations of omnitherms (organisms which grow over a broad temperature range, i.e. 3 -55 C were also conducted. The cellular morphology of 28 of these isolates was investigated, and all were demonstrated to be sporeformers. Biochemical characterizations are also presented. Procedures for replicate plating were evaluated, and those results are also presented. The procedures for different replicate-plating techniques are presented, and these are evaluated on the basis of reproducibility, percentage of viable transfer, and ease of use. Standardized procedures for the enumeration of microbial populations from ocean-dredge samples from Cape Canaveral are also presented

The Global Ocean Biogeochemistry (GO-BGC) array of profiling floats to observe changing ocean chemistry and biology

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Matsumoto, G., Johnson, K., Riser, S., Talley, L., Wijffels, S., & Hotinski, R. The Global Ocean Biogeochemistry (GO-BGC) array of profiling floats to observe changing ocean chemistry and biology. Marine Technology Society Journal, 56(3), (2022): 122–123, https://doi.org/10.4031/mtsj.56.3.25.The Global Ocean Biogeochemistry (GO-BGC) Array is a project funded by the US National Science Foundation to build a global network of chemical and biological sensors on Argo profiling floats. The network will monitor biogeochemical cycles and ocean health. The floats will collect from a depth of 2,000 meters to the surface, augmenting the existing Argo array that monitors ocean temperature and salinity. Data will be made freely available within a day of being collected via the Argo data system. These data will allow scientists to pursue fundamental questions concerning ocean ecosystems, monitor ocean health and productivity, and observe the elemental cycles of carbon, oxygen, and nitrogen through all seasons of the year. Such essential data are needed to improve computer models of ocean fisheries and climate, to monitor and forecast the effects of ocean warming and ocean acidification on sea life, and to address key questions identified in “Sea Change: 2015–2025 Decadal Survey of Ocean Sciences” such as: What is the ocean’s role in regulating the carbon cycle? What are the natural and anthropogenic drivers of open ocean deoxygenation? What are the consequences of ocean acidification? How do physical changes in mixing and circulation affect nutrient availability and ocean productivity?Funding for the GO-BGC Array is provided through the NSF’s Mid-Scale Research Infrastructure-2 Program (MSRI-2; NSF Award 1946578)

Scattering and leapfrogging of vortex rings in a superfluid

The dynamics of vortex ring pairs in the homogeneous nonlinear Schr\"odinger equation is studied. The generation of numerically-exact solutions of traveling vortex rings is described and their translational velocity compared to revised analytic approximations. The scattering behavior of co-axial vortex rings with opposite charge undergoing collision is numerically investigated for different scattering angles yielding a surprisingly simple result for its dependence as a function of the initial vortex ring parameters. We also study the leapfrogging behavior of co-axial rings with equal charge and compare it with the dynamics stemming from a modified version of the reduced equations of motion from a classical fluid model derived using the Biot-Savart law.Comment: 12 pages, 11 figure

Feasibility of Single Molecule DNA Sequencing using Surface-Enhanced Raman Scattering

We have used a combined theoretical and experimental approach in order to assess the feasibility of using surface-enhanced Raman scattering (SERS) for DNA sequencing at the single molecule level. We have developed a numerical tool capable of calculating the E-field and resulting SERS enhancement factors for metallic structures of arbitrary size and shape. Measurements of the additional SERS enhancement by combining SERS with coherent antistokes Raman scattering (CARS) show that only modest increases in the signal are achievable due to thermal damage at higher laser powers. Finally, measurements of the SERS enhancement from nanoparticles coated with an insulating layer show that the SERS enhancement is decreased by as much as two orders of magnitude when the molecule is not in contact with the metal surface

The present and future system for measuring the Atlantic meridional overturning circulation and heat transport

of the global combined atmosphere-ocean heat flux and so is important for the mean climate of the Atlantic sector of the Northern Hemisphere. This meridional heat flux is accomplished by both the Atlantic Meridional Overturning Circulation (AMOC) and by basin-wide horizontal gyre circulations. In the North Atlantic subtropical latitudes the AMOC dominates the meridional heat flux, while in subpolar latitudes and in the subtropical South Atlantic the gyre circulations are also important. Climate models suggest the AMOC will slow over the coming decades as the earth warms, causing widespread cooling in the Northern hemisphere and additional sea-level rise. Monitoring systems for selected components of the AMOC have been in place in some areas for decades, nevertheless the present observational network provides only a partial view of the AMOC, and does not unambiguously resolve the full variability of the circulation. Additional observations, building on existing measurements, are required to more completely quantify the Atlantic meridional heat transport. A basin-wide monitoring array along 26.5°N has been continuously measuring the strength and vertical structure of the AMOC and meridional heat transport since March 31, 2004. The array has demonstrated its ability to observe the AMOC variability at that latitude and also a variety of surprising variability that will require substantially longer time series to understand fully. Here we propose monitoring the Atlantic meridional heat transport throughout the Atlantic at selected critical latitudes that have already been identified as regions of interest for the study of deep water formation and the strength of the subpolar gyre, transport variability of the Deep Western Boundary Current (DWBC) as well as the upper limb of the AMOC, and inter-ocean and intrabasin exchanges with the ultimate goal of determining regional and global controls for the AMOC in the North and South Atlantic Oceans. These new arrays will continuously measure the full depth, basin-wide or choke-point circulation and heat transport at a number of latitudes, to establish the dynamics and variability at each latitude and then their meridional connectivity. Modeling studies indicate that adaptations of the 26.5°N type of array may provide successful AMOC monitoring at other latitudes. However, further analysis and the development of new technologies will be needed to optimize cost effective systems for providing long term monitoring and data recovery at climate time scales. These arrays will provide benchmark observations of the AMOC that are fundamental for assimilation, initialization, and the verification of coupled hindcast/forecast climate models

Unabated bottom water warming and freshening in the south Pacific Ocean.

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans 124(3), (2019): 1778-1794, doi:10.1029/2018JC014775.Abyssal ocean warming contributed substantially to anthropogenic ocean heat uptake and global sea level rise between 1990 and 2010. In the 2010s, several hydrographic sections crossing the South Pacific Ocean were occupied for a third or fourth time since the 1990s, allowing for an assessment of the decadal variability in the local abyssal ocean properties among the 1990s, 2000s, and 2010s. These observations from three decades reveal steady to accelerated bottom water warming since the 1990s. Strong abyssal (z > 4,000 m) warming of 3.5 (±1.4) m°C/year (m°C = 10−3 °C) is observed in the Ross Sea, directly downstream from bottom water formation sites, with warming rates of 2.5 (±0.4) m°C/year to the east in the Amundsen‐Bellingshausen Basin and 1.3 (±0.2) m°C/year to the north in the Southwest Pacific Basin, all associated with a bottom‐intensified descent of the deepest isotherms. Warming is consistently found across all sections and their occupations within each basin, demonstrating that the abyssal warming is monotonic, basin‐wide, and multidecadal. In addition, bottom water freshening was strongest in the Ross Sea, with smaller amplitude in the Amundsen‐Bellingshausen Basin in the 2000s, but is discernible in portions of the Southwest Pacific Basin by the 2010s. These results indicate that bottom water freshening, stemming from strong freshening of Ross Shelf Waters, is being advected along deep isopycnals and mixed into deep basins, albeit on longer timescales than the dynamically driven, wave‐propagated warming signal. We quantify the contribution of the warming to local sea level and heat budgets.S. G. P. was supported by a U.S. GO‐SHIP postdoctoral fellowship through NSF grant OCE‐1437015, which also supported L. D. T. and S. M. and collection of U.S. GO‐SHIP data since 2014 on P06, S4P, P16, and P18. G. C. J. is supported by the Global Ocean Monitoring and Observation Program, National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce and NOAA Research. B. M. S and S. E. W. were supported by the Australian Government Department of the Environment and CSIRO through the Australian Climate Change Science Programme and by the National Environmental Science Program. We are grateful for the hard work of the science parties, officers, and crew of all the research cruises on which these CTD data were collected. We also thank the two anonymous reviewers for their helpful comments that improve the manuscript. This is PMEL contribution 4870. All CTD data sets used in this analysis are publicly available at the website (https://cchdo.ucsd.edu).2019-08-2

Sensitivity of the Atlantic meridional overturning circulation to South Atlantic freshwater anomalies

The sensitivity of the Atlantic Meridional Overturning Circulation (AMOC) to changes in basin integrated net evaporation is highly dependent on the zonal salinity contrast at the southern border of the Atlantic. Biases in the freshwater budget strongly affect the stability of the AMOC in numerical models. The impact of these biases is investigated, by adding local anomaly patterns in the South Atlantic to the freshwater fluxes at the surface. These anomalies impact the freshwater and salt transport by the different components of the ocean circulation, in particular the basin-scale salt-advection feedback, completely changing the response of the AMOC to arbitrary perturbations. It is found that an appropriate dipole anomaly pattern at the southern border of the Atlantic Ocean can collapse the AMOC entirely even without a further hosing. The results suggest a new view on the stability of the AMOC, controlled by processes in the South Atlantic. <br/

Nanoparticle based surface-enhanced raman spectroscopy

Abstract. Surface-enhanced Raman scattering is a powerful tool for the investigation of biological samples. Following a brief introduction to Raman and surface-enhanced Raman scattering, several examples of biophotonic applications of SERS are discussed. The concept of nanoparticle based sensors using SERS is introduced and the development of these sensors is discussed

Radiation Damage Mechanisms for Luminescence in Eu-doped GaN

Thin films of Eu-doped GaN are irradiated with 500 keV He{sup +} ions to understand radiation damage mechanisms and to quantify luminescence efficiency. Ion beam induced luminescence was monitored spectroscopically as function of fluence. Behavior observed is consistent with simultaneous creation of non-radiative defects and destruction of luminescent centers associated with the 4f-4f core-level transition in Eu{sup 3+}. This model contrasts with a previous description which takes into account only non-radiative defect generation in GaN:Eu. Based on light from a BaF{sub 2} scintillator standard, the luminescent energy generation efficiency of GaN:Eu films doped to {approx}3 x 10{sup 18} cm{sup -3} Eu is estimated to be {approx}0.1%