The Development of Biosensor with Imaging Ellipsometry

The concept of biosensor with imaging ellipsometry was proposed about ten years ago. It has become an automatic analysis technique for protein detection with merits of label-free, multi-protein analysis, and real-time analysis for protein interaction process, etc. Its principle, andrelated technique units, such as micro-array, micro-fluidic and bio-molecule interaction cell, sampling unit and calibration for quantitative detection as well as its applications in biomedicine field are presented here.

A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations

There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video system to estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” were captured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using image analysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacoustic survey and from direct measures of fish size using visual census techniques. We discovered a possible bias in length measures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations.

Design, Construction and Testing of a Hydraulic Power Take-Off for Wave Energy Converters

This paper presents the construction, mathematical modeling and testing of a scaled universal hydraulic Power Take-Off (PTO) device for Wave Energy Converters (WECs). A specific prototype and test bench were designed and built to carry out the tests. The results obtained from these tests were used to adjust an in-house mathematical model. The PTO was initially designed to be coupled to a scaled wave energy capture device with a low speed and high torque oscillating motion and high power fluctuations. Any Energy Capture Device (ECD) that fulfils these requirements can be coupled to this PTO, provided that its scale is adequately defined depending on the rated power of the full scale prototype. The initial calibration included estimation of the pressure drops in the different components, the pressurization time of the oil inside the hydraulic cylinders and the volumetric efficiency of the complete circuit. Since the overall efficiency measured during the tests ranged from 0.69 to 0.8 and the dynamic performance of the PTO was satisfactory, the results are really promising and it is believed that this solution might prove effective in real devices.

Integrated Sensor Systems for Vessels of Opportunity, National Oceanographic Centre, Southampton, UK, October 10-12,2006 : workshop proceedings

The use of self-contained, low-maintenance sensor systems installed on commercial vessels is becoming an important monitoring and scientific tool in many regions around the world. These systems integrate data from meteorological and water quality sensors with GPS data into a data stream that is automatically transferred from ship to shore. To begin linking some of this developing expertise, the Alliance for Coastal Technologies (ACT) and the European Coastal and Ocean Observing Technology (ECOOT) organized a workshop on this topic in Southampton, United Kingdom, October 10-12, 2006. The participants included technology users, technology developers, and shipping representatives. They collaborated to identify sensors currently employed on integrated systems, users of this data, limitations associated with these systems, and ways to overcome these limitations. The group also identified additional technologies that could be employed on future systems and examined whether standard architectures and data protocols for integrated systems should be established. Participants at the workshop defined 17 different parameters currently being measured by integrated systems. They identified that diverse user groups utilize information from these systems from resource management agencies, such as the Environmental Protection Agency (EPA), to local tourism groups and educational organizations. Among the limitations identified were instrument compatibility and interoperability, data quality control and quality assurance, and sensor calibration andlor maintenance frequency. Standardization of these integrated systems was viewed to be both advantageous and disadvantageous; while participants believed that standardization could be beneficial on many levels, they also felt that users may be hesitant to purchase a suite of instruments from a single manufacturer; and that a "plug and play" system including sensors from multiple manufactures may be difficult to achieve. A priority recommendation and conclusion for the general integrated sensor system community was to provide vessel operators with real-time access to relevant data (e.g., ambient temperature and salinity to increase efficiency of water treatment systems and meteorological data for increased vessel safety and operating efficiency) for broader system value. Simplified data displays are also required for education and public outreach/awareness. Other key recommendations were to encourage the use of integrated sensor packages within observing systems such as 100s and EuroGOOS, identify additional customers of sensor system data, and publish results of previous work in peer-reviewed journals to increase agency and scientific awareness and confidence in the technology. Priority recommendations and conclusions for ACT entailed highlighting the value of integrated sensor systems for vessels of opportunity through articles in the popular press, and marine science. [PDF contains 28 pages]

Measures of turbidity in coastal waters, Coconut Island, Oahu, Hawaii, August 31 - September 2, 2005: workshop proceedings

A three day workshop on turbidity measurements was held at the Hawaii Institute of Marine Biology from August 3 1 to September 2, 2005. The workshop was attended by 30 participants from industry, coastal management agencies, and academic institutions. All groups recognized common issues regarding the definition of turbidity, limitations of consistent calibration, and the large variety of instrumentation that nominally measure "turbidity." The major recommendations, in order of importance for the coastal monitoring community are listed below: 1. The community of users in coastal ecosystems should tighten instrument design configurations to minimize inter-instrument variability, choosing a set of specifications that are best suited for coastal waters. The IS0 7027 design standard is not tight enough. Advice on these design criteria should be solicited through the ASTM as well as Federal and State regulatory agencies representing the majority of turbidity sensor end users. Parties interested in making turbidity measurements in coastal waters should develop design specifications for these water types rather than relying on design standards made for the analysis of drinking water. 2. The coastal observing groups should assemble a community database relating output of specific sensors to different environmental parameters, so that the entire community of users can benefit from shared information. This would include an unbiased, parallel study of different turbidity sensors, employing a variety of designs and configuration in the broadest range of coastal environments. 3. Turbidity should be used as a measure of relative change in water quality rather than an absolute measure of water quality. Thus, this is a recommendation for managers to develop their own local calibrations. See next recommendation. 4. If the end user specifically wants to use a turbidity sensor to measure a specific water quality parameter such as suspended particle concentration, then direct measurement of that water quality parameter is necessary to correlate with 'turbidity1 for a particular environment. These correlations, however, will be specific to the environment in which they are measured. This works because there are many environments in which water composition is relatively stable but varies in magnitude or concentration. (pdf contains 22 pages)

In situ measurement of dissolved inorganic carbon speciation in natural waters, pH, pC02, TA, & TC02, Honolulu, Hawaii, February 16-18, 2005: workshop proceedings

The Alliance for Coastal Technology (ACT) convened a workshop on the in situ measurement of dissolved inorganic carbon species in natural waters in Honolulu, Hawaii, on February 16, 17, and 18, 2005. The workshop was designed to summarize existing technologies for measuring the abundance and speciation of dissolved inorganic carbon and to make strategic recommendations for future development and application of these technologies to coastal research and management. The workshop was not focused on any specific technology, however, most of the attention of the workshop was on in situ pC02 sensors given their recent development and use on moorings for the measurement of global carbon fluxes. In addition, the problems and limitations arising from the long-term deployment of systems designed for the measurement of pH, total dissolved inorganic carbon (DIC), and total alkalinity (TA) were discussed. Participants included researchers involved in carbon biogeochemistry, industry representatives, and coastal resource managers. The primary questions asked during the workshop were: I. What are the major impediments to transform presently used shipboard pC02 measurement systems for use on cost-eficient moorings? 2. What are the major technical hurdles for the in situ measurement of TA and DIC? 3. What specific information do we need to coordinate efforts for proof of concept' testing of existing and new technologies, inter-calibration of those technologies, better software development, and more precise knowledge quantzjjing the geochemistry of dissolved inoeanic carbon species in order to develop an observing system for dissolved inorganic carbon? Based on the discussion resulting from these three questions, the following statements were made: Statement No. 1 Cost-effective, self-contained technologies for making long-term, accurate measurements of the partial pressure of C02 gas in water already exist and at present are ready for deployment on moorings in coastal observing systems. Statement No. 2 Cost-effective, self-contained systems for the measurement of pH, TA, and DIC are still needed to both fully define the carbonate chemistry of coastal waters and the fluxes of carbon between major biogeochemical compartments (e.g., air-sea, shelf-slope, water column-sediment, etc.). (pdf contains 23 pages)

Applications of in situ Fluorometers in Nearshore waters, Cape Elizabeth, Maine, February 2-4,2005: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop "Applications of in situ Fluorometers in Nearshore Waters" was held in Cape Elizabeth, Maine, February 2-4,2005, with sponsorship by the Gulf of Maine Ocean Observing System (GoMOOS), one of the ACT partner organization. The purpose of the workshop was to explore recent trends in fluorometry as it relates to resource management applications in nearshore environments. Participants included representatives from state and federal environmental management agencies as well as research institutions, many of whom are currently using this technology in their research and management applications. Manufacturers and developers of fluorometric measuring systems also attended the meeting. The Workshop attendees discussed the historical and present uses of fluorometry technology and identified the great potential for its use by coastal managers to fulfill their regulatory and management objectives. Participants also identified some of the challenges associated with the correct use of Fluorometers to estimate biomass and the rate of primary productivity. The Workshop concluded that in order to expand the existing use of fluorometers in both academic and resource management disciplines, several issues concerning data collection, instrument calibration, and data interpretation needed to be addressed. Participants identified twelve recommendations, the top five of which are listed below: Recommendations 1) Develop a "Guide" that describes the most important aspects of fluorescence measurements. This guide should be written by an expert party, with both research and industry input, and should be distributed by all manufacturers with their instrumentation. The guide should also be made available on the ACT website as well as those of other relevant organizations. The guide should include discussions on the following topics: The benefits of using fluorometers in research and resource management applications; What fluorometers can and cannot provide in terms of measurements; The necessary assumptions required before applying fluorometry; Characterization and calibration of fluorometers; (pdf contains 32 pages)

Genauigkeit von Alterslesungen, ihre Standardisierung und Kalibrierung

Age reading by use of otoliths is one of the basic but also most essential elements in practical fish population dynamics. Unfortunately, many factors can influence the readings of a single reader. Erronous readings, however, have a consequential effect on the evaluation and prediction of the development of the fish stock under consideration. In order to master this problem and to reduce out the effect of those factors, it seems neccessary to standardize the whole process of age reading between collaborating readers. From a statistical point of view calibration techniques can be used to identify those factors and to correct the readings with respect to them. The current article presents an overview over the basic idea behind this, over how to balance out the existing deviations and how to correct the age readings.

Historie und aktueller Stand des Internationalen Heringslarvensurveys in der Nordsee

Since years the International Herring Larvae Survey Program (IHLS) is an important and internationally established survey program in the North Sea. The IHLS serves the calibration of stock abundance estimates based on information from the commercial fishery and the method of Integrated Catch Analysis (ICA) which is a specific derivate of the Virtual Population Analysis (VPA). Meanwhile the IHLS database has been transferred from Aberdeen to Kiel and it has been agreed that the Institut für Meereskunde Kiel should continue to maintain this database and provide the abundance indices to be utilized by the ICES Herring Assessment Working Group as one of the means for assessing the state of the herring stock in the North Sea. For establishing the calculation procedure at Kiel, it was necessary to optimize both, the survey design and the index calculation. This article gives an overview over the survey’s history, it’s geography, the sampling design, the information content of the IHLS data base and the various methods of calculating the different indices necessary for the calibration.

Leistungsmessung an Bord von Fischereifahrzeugen zur Kontrolle der 300-PS-Begrenzung in der Schollenbox

For monitoring of the engine power of fishing vessels permitted for fishery in the plaice box with engine power of 300 HP or less at sea three different portable power measurement systems are developed and tested. A system measuring the twist of the propeller shaft by two divisible gearwheels mounted on the shaft worked well at shafts with roller bearing at both sides of the measured interval of 100–300 mm length. Only at a very few fishing vessels this system is applicable and therefore for monitoring purposes not suitable. The application of a commercial available system measuring the stress at the surface of the shaft was simplified for application by non experts. The torque is measured by strain gauges. The calibration of the system, measuring and recording of the power is done by a PC automatically. A small polished facet on the shaft protected against oxidation is needed for easy and quick application. In this case the system can be used by technical personnel of supervision boats for monitoring of the engine power at sea in a short time. A third power measurement system determinates the torque by measuring the displacement of two supports clamped on the shaft at a distance of 100 mm. The displacement is measured by a micrometer gauge mounted on one of the supports. Readout of the rotating gauge display is possible taking advantage of stroboscopic effect. The system needs no conditioning of the shaft and can be used by non technicians. The development is not finished until now and some additional investigations and tests are required. Additional measures for monitoring of the power on fishing vessels by self recording power measurement systems and sealed fuel racks with limited injection are reported and discussed.

MODELING EVOLUTION OF INTERNAL WAVES IN SOUTH CHINA SEA

Internal waves are an important factor in the design of drill operations and production in deep water, because the waves have very large amplitude and may induce large horizontal velocity. How the internal waves occur and propagate over benthal terrain is of great concern for ocean engineers. In the present paper, we have formulated a mathematical model of internal wave propagation in a two-layer deep water, which involves the effects of friction, dissipation and shoaling, and is capable of manifesting the variation of the amplitude and the velocity pattern. After calibration by field data measured at the Continental Slope in the Northern South China Sea, we have applied the model to the South China Sea, investigating the westward propagation of internal waves from the Luzon Strait, where internal waves originate due to the interaction of benthal ridge and tides. We find that the internal wave induced velocity profile is obviously characterized by the opposite flow below and above the pycnocline, which results in a strong shear, threatening safety of ocean structures, such as mooring system of oil platform, risers, etc. When internal waves propagate westwards, the amplitude attenuates due to the effects of friction and dissipation. The preliminary results show that the amplitude is likely to become half of its initial value at Luzon Strait when the internal waves propagate about 400 kilometers westwards.

Experimental and finite element studies of a large arch dam

Forced vibration field tests and finite element studies have been conducted on Morrow Point (arch) Dam in order to investigate dynamic dam-water interaction and water compressibility. Design of the data acquisition system incorporates several special features to retrieve both amplitude and phase of the response in a low signal to noise environment. These features contributed to the success of the experimental program which, for the first time, produced field evidence of water compressibility; this effect seems to play a significant role only in the symmetric response of Morrow Point Dam in the frequency range examined. In the accompanying analysis, frequency response curves for measured accelerations and water pressures as well as their resonating shapes are compared to predictions from the current state-of-the-art finite element model for which water compressibility is both included and neglected. Calibration of the numerical model employs the antisymmetric response data since they are only slightly affected by water compressibility, and, after calibration, good agreement to the data is obtained whether or not water compressibility is included. In the effort to reproduce the symmetric response data, on which water compressibility has a significant influence, the calibrated model shows better correlation when water compressibility is included, but the agreement is still inadequate. Similar results occur using data obtained previously by others at a low water level. A successful isolation of the fundamental water resonance from the experimental data shows significantly different features from those of the numerical water model, indicating possible inaccuracy in the assumed geometry and/or boundary conditions for the reservoir. However, the investigation does suggest possible directions in which the numerical model can be improved.

Nonlinear optics in planar silica-on-silicon disk resonators

Optical frequency combs (OFCs) provide direct phase-coherent link between optical and RF frequencies, and enable precision measurement of optical frequencies. In recent years, a new class of frequency combs (microcombs) have emerged based on parametric frequency conversions in dielectric microresonators. Micocombs have large line spacing from 10's to 100's GHz, allowing easy access to individual comb lines for arbitrary waveform synthesis. They also provide broadband parametric gain bandwidth, not limited by specific atomic or molecular transitions in conventional OFCs. The emerging applications of microcombs include low noise microwave generation, astronomical spectrograph calibration, direct comb spectroscopy, and high capacity telecommunications.

In this thesis, research is presented starting with the introduction of a new type of chemically etched, planar silica-on-silicon disk resonator. A record Q factor of 875 million is achieved for on-chip devices. A simple and accurate approach to characterize the FSR and dispersion of microcavities is demonstrated. Microresonator-based frequency combs (microcombs) are demonstrated with microwave repetition rate less than 80 GHz on a chip for the first time. Overall low threshold power (as low as 1 mW) of microcombs across a wide range of resonator FSRs from 2.6 to 220 GHz in surface-loss-limited disk resonators is demonstrated. The rich and complex dynamics of microcomb RF noise are studied. High-coherence, RF phase-locking of microcombs is demonstrated where injection locking of the subcomb offset frequencies are observed by pump-detuning-alignment. Moreover, temporal mode locking, featuring subpicosecond pulses from a parametric 22 GHz microcomb, is observed. We further demonstrated a shot-noise-limited white phase noise of microcomb for the first time. Finally, stabilization of the microcomb repetition rate is realized by phase lock loop control.

For another major nonlinear optical application of disk resonators, highly coherent, simulated Brillouin lasers (SBL) on silicon are also demonstrated, with record low Schawlow-Townes noise less than 0.1 Hz^2/Hz for any chip-based lasers and low technical noise comparable to commercial narrow-linewidth fiber lasers. The SBL devices are efficient, featuring more than 90% quantum efficiency and threshold as low as 60 microwatts. Moreover, novel properties of the SBL are studied, including cascaded operation, threshold tuning, and mode-pulling phenomena. Furthermore, high performance microwave generation using on-chip cascaded Brillouin oscillation is demonstrated. It is also robust enough to enable incorporation as the optical voltage-controlled-oscillator in the first demonstration of a photonic-based, microwave frequency synthesizer. Finally, applications of microresonators as frequency reference cavities and low-phase-noise optomechanical oscillators are presented.

Diffraction-limited imaging on the 200-inch telescope

We have used the technique of non-redundant masking at the Palomar 200-inch telescope and radio VLBI imaging software to make optical aperture synthesis maps of two binary stars, β Corona Borealis and σ Herculis. The dynamic range of the map of β CrB, a binary star with a separation of 230 milliarcseconds is 50:1. For σ Her, we find a separation of 70 milliarcseconds and the dynamic range of our image is 30:1. These demonstrate the potential of the non-redundant masking technique for diffraction-limited imaging of astronomical objects with high dynamic range.

We find that the optimal integration time for measuring the closure phase is longer than that for measuring the fringe amplitude. There is not a close relationship between amplitude errors and phase errors, as is found in radio interferometry. Amplitude self calibration is less effective at optical wavelengths than at radio wavelengths. Primary beam sensitivity correction made in radio aperture synthesis is not necessary in optical aperture synthesis.

The effects of atmospheric disturbances on optical aperture synthesis have been studied by Monte Carlo simulations based on the Kolmogorov theory of refractive-index fluctuations. For the non-redundant masking with τ_c-sized apertures, the simulated fringe amplitude gives an upper bound of the observed fringe amplitude. A smooth transition is seen from the non-redundant masking regime to the speckle regime with increasing aperture size. The fractional reduction of the fringe amplitude according to the bandwidth is nearly independent of the aperture size. The limiting magnitude of optical aperture synthesis with τ_c-sized apertures and that with apertures larger than τ_c are derived.

Monte Carlo simulations are also made to study the sensitivity and resolution of the bispectral analysis of speckle interferometry. We present the bispectral modulation transfer function and its signal-to-noise ratio at high light levels. The results confirm the validity of the heuristic interferometric view of image-forming process in the mid-spatial-frequency range. The signal-to- noise ratio of the bispectrum at arbitrary light levels is derived in the mid-spatial-frequency range.

The non-redundant masking technique is suitable for imaging bright objects with high resolution and high dynamic range, while the faintest limit will be better pursued by speckle imaging.

Sunyaev-Zel'dovich observations using large-format millimeter arrays

Galaxy clusters are the largest gravitationally bound objects in the observable universe, and they are formed from the largest perturbations of the primordial matter power spectrum. During initial cluster collapse, matter is accelerated to supersonic velocities, and the baryonic component is heated as it passes through accretion shocks. This process stabilizes when the pressure of the bound matter prevents further gravitational collapse. Galaxy clusters are useful cosmological probes, because their formation progressively freezes out at the epoch when dark energy begins to dominate the expansion and energy density of the universe. A diverse set of observables, from radio through X-ray wavelengths, are sourced from galaxy clusters, and this is useful for self-calibration. The distributions of these observables trace a cluster's dark matter halo, which represents more than 80% of the cluster's gravitational potential. One such observable is the Sunyaev-Zel'dovich effect (SZE), which results when the ionized intercluster medium blueshifts the cosmic microwave background via Compton scattering. Great technical advances in the last several decades have made regular observation of the SZE possible. Resolved SZE science, such as is explored in this analysis, has benefitted from the construction of large-format camera arrays consisting of highly sensitive millimeter-wave detectors, such as Bolocam. Bolocam is a submillimeter camera, sensitive to 140 GHz and 268 GHz radiation, located at one of the best observing sites in the world: the Caltech Submillimeter Observatory on Mauna Kea in Hawaii. Bolocam fielded 144 of the original spider web NTD bolometers used in an entire generation of ground-based, balloon-borne, and satellite-borne millimeter wave instrumention. Over approximately six years, our group at Caltech has developed a mature galaxy cluster observational program with Bolocam. This thesis describes the construction of the instrument's full cluster catalog: BOXSZ. Using this catalog, I have scaled the Bolocam SZE measurements with X-ray mass approximations in an effort to characterize the SZE signal as a viable mass probe for cosmology. This work has confirmed the SZE to be a low-scatter tracer of cluster mass. The analysis has also revealed how sensitive the SZE-mass scaling is to small biases in the adopted mass approximation. Future Bolocam analysis efforts are set on resolving these discrepancies by approximating cluster mass jointly with different observational probes.