Harvesting only 4 % of light striking the Earth could possibly fulfill present energy demands of a mankind. Chlorosome of green sulfur bacteria is re- garded as suitable light-harvesting system for photosynthesis imitation. This work presents comparison of absorption and hole burning spectra of artificially prepared aggregates similar to chlorosomes with different compositions in order to verify the proposed role of quinones in excitation quenching and its redox de- pendence. Absorption spectra at room and helium temperature showed a resem- blance between artificial aggregates and chlorosomes. Hole burning experiments verified the role of quinones in excitation quenching under aerobic conditions. Even more pronounced excitation quenching was observed under anaerobic con- ditions. Significant improvements of the original experimental set-up provided better experimental data which raised many further question that are worth trying to answer in the future.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering and the Woods Hole Oceanographic Institution), September 2001. / Includes bibliographical references (leaves 65-67). / As part of Phase III of the U.S. GLOBEC Georges Bank program, drogued drifters and dye tracer were released into the pycnocline on the southern flank of Georges Bank to measure advective and diffusive transport relative to the tidal mixing front in May 1999. Potential density measurements placed the tidal mixing front around the 50-55 m isobath on the southern flank. Drogued drifter movement relative to the front was on the order of the drifter's slip velocity and therefore did not support the existence of a mean, advective flow. No movement relative to the front of the dye patch center of mass also indicated a lack of advective flow. Diffusive transport did occur as the dye patch spread laterally both toward and away from the front much as would be predicted by the diffusion relationship of Okubo (1971), who summarized diffusion experiments in the surface ocean. The dye did not spread symmetrically, but was rather elongated along the isobaths. This can be attributed to vertical shear in the along-isobath current that was measured by the shipboard ADCP. / by Jody M. Katerin. / S.M.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering and the Woods Hole Oceanographic Institution), 2002. / Includes bibliographical references (p. 105). / This thesis examines data collected in the South China Sea (SCS) component of the 2001 Asian Seas International Acoustic Experiment (ASIAEX), where a fixed Horizontal Linear Array (HLA) was deployed to study transverse array coherence in a coastal environment. Arrays obtain their gain and directivity by coherently adding the energy that impinges on them. Therefore, to maximize the efficiency of an array, the size of the aperture over which the signal remains coherent needs to be determined. Scattering of sound by the ocean environment, especially in coastal areas, reduces the coherence of acoustic signals, and thereby limits the useful aperture of an acoustic array. During ASIAEX, a horizontal linear array was deployed on the continental shelf of the South China Sea in order to directly measure the acoustic coherence in a coastal environment. 224 Hz and 400 Hz sources were placed on the continental slope to provide an up slope propagation path and a 400 Hz source was placed on the shelf to provide an along shelf propagation path. This thesis analyzes one day of transmissions from these three sources and gives the first look at coherence lengths of the HLA determined by sensor-to-sensor correlations. To achieve this, the thesis analyzes continuous time series data from the Long Base Line (LBL) navigation system and two days of light bulb drops to provide array sensor localization. Accurate sensor positions are needed to determine the correlation versus sensor separation distance and ultimately the array coherence length. / by Theodore Herbert Schroeder. / S.M.

Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering and the Woods Hole Oceanographic Institution), February 2001. / Includes bibliographical references (p. 211-219). / This thesis develops methods useful for estimating zooplankton distributions in the field by combining acoustic scattering models and an integrated set of field data. The accuracy of existing scattering models for fluid-like and elastic-shelled animals is determined by analysis of scattering data from individual animals in a laboratory tank. Results indicate that simple two-ray scattering models are accurate and allow predictions of size or orientation of an animal to be made for certain animal orientations. A scattering model for gas-bearing zooplankton is compared with in situ multiple frequency acoustic measurements from siphonophores. Estimates of the numerical density of these animals are made using echo integration data from a scientific echo-sounder. Multiple frequency acoustic scattering data from a survey of an internal wave are analyzed to determine the contributions from biological and physical sources. Net tow data provide information about biological scatterers while temperature and salinity profiles are used with a theoretical scattering model to predict contributions from physical sources. Results indicate that scattering from physical sources is comparable to that from biological sources in certain regions and that scattering spectra may be used to distinguish these sources. Improved estimates of biomass from acoustic scattering data were made by accounting for the scattering contributions from physical sources. This is the first work to quantify the scattering contributions from biological and physical sources of scattering in a field study. / by Joseph David Warren. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 85-89). / Autonomous Underwater Vehicles (AUVs) have been established as a viable tool for Oceanographic Sciences. Being untethered and independent, AUVs fill the gap in Ocean Exploration left by the existing manned submersible and remotely operated vehicles (ROV) technology. AUVs are attractive as cheaper and efficient alternatives to the older technologies and are breaking new ground in many applications. Designing an autonomous vehicle to work in the harsh environment of the deep ocean comes with its set of challenges. This paper discusses how the current engineering technologies can be adapted to the design of AUVs. Recently, as the AUV technology has matured, we see AUVs being used in a variety of applications ranging from sub-surface sensing to sea-floor mapping. The design of the AUV, with its tight constraints, is very sensitive to the target application. Keeping this in mind, the goal of this thesis is to understand how some of the major issues affect the design of the AUV. This paper also addresses the mechanical and materials issues, power system design, computer architecture, navigation and communication systems, sensor considerations and long term docking aspects that affect AUV design. With time, as the engineering sciences progress, the AUV design will have to change in order to optimize its performance. Thus, the fundamental issues discussed in this paper can assist in meeting the challenge of maintaining AUV design on par with modern technology. / by Vikrant P. Shah. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and, the Woods Hole Oceanographic Institution), 2004. / Includes bibliographical references. / The purpose of this thesis is to study campanulariid life cycle evolution and systematics. The Campanulariidae is a hydrozoan family with many life cycle variations, and provide an excellent model system to study life cycle evolution. Additionally, the unique campanulariid Obelia medusae may have been "re-invented" from ancestors without medusae. Chapter 1 reviews campanulariid life cycles and taxonomy. Chapter 2 presents a phylogeny based on 18S rDNA, calmodulin, 16S rDNA and cytochrome c oxidase I (COI). Ancestral life cycles are reconstructed using parsimony. Medusa loss is common, and Obelia may derive from ancestors with typical medusae. Taxonomic results are discussed in Chapter 3. Billardia, a nominal campanulariid, appears phylogenetically distant, while Bonneviella spp. (Bonneviellidae), are nested within the Campanulariidae. Campanulariid genera are not monophyletic. Orthopyxis integra and Clytia gracilis may represent cryptic species, while Obelia longissima may be cosmopolitan. Chapter 4 investigates Obelia geniculata phylogeography. Japanese and North Atlantic 16S rDNA and COI sequences are calibrated against the opening of the Bering Strait. Substitution rates are faster than in anthozoans and comparable to non-cnidarian invertebrates. Comparison of Pacific and Atlantic sequences suggests cryptic species exist. Finally, hydroids in New Brunswick, Canada and Iceland may have survived the last glaciation. / by Annette Frese Govindarajan. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2002. / Includes bibliographical references (p. 130-138). / Mark-recapture analysis of populations is becoming an important tool in population biology. Mark-recapture methods can be used to estimate transition probabilities among life-stages from capture histories of marked individuals for which stages can be determined at each sampling occasion. This method is called a multi-stage mark-recapture (MSMR) method. In this thesis, I describe advances I made in the MSMR method and present analyses that apply this method to actual data. The advances I made in the MSMR method are motivated by a need to provide a link between mark-recapture data and demographic models such as matrix population models and integrodifference models. I resolve some issues that are commonly encountered during sampling, such as the fact that the sex or life-stage of some individuals is unknown during some sampling occasions and that individuals become unobservable during some life-stages. I introduce a stage-structure that permits simple conversion of estimated transition probabilities into a matrix population model. I describe an algorithm to simplify programming for parameter estimation. I also introduce a method to estimate the distribution of dispersal displacements (a dispersal kernel) from mark-recapture data. I apply some of the methods described above to data of the North Atlantic right whale (Eubalaena glacialis). The right whales are considered one of the most endangered mammals. The current population size is about 300 in the northwestern Atlantic, and the number is declining. I applied the multi-stage mark-recapture statistics to the 17-year in- dividual sighting history data. / (cont.) Using the estimated transition probabilities, I constructed a population projection matrix, which was used for further demographic analyses. I found that the population was slowly increasing in 1980, but it started to decline slowly around 1992. I show that (1) this change was caused by increased mortality of females that have just given birth, (2) protecting two females a year from the deaths is enough to prevent the declining trend, and (3) demographic stochasticity is a more important factor influencing their long-term viability than environmental stochasticity. / by Masami Fujiwara. / Ph.D.

This work presents the experimental study of the flow generated in the wakes of three three-dimensional bumps in the Virginia Polytechnic Institute and State University Boundary Layer Wind Tunnel. The three bumps examined are named bump 1, small bump 3, and large bump 3, and are the same test cases studied by Byun et al. (2004) and Ma and Simpson (2004) with a LDV system and a quad-wire hot-wire probe, respectively. Various experimental methods are used in this work: For measuring the mean velocity component in the planes examined, a seven-hole pressure probe is used with the data reduction algorithm developed by Johansen et al. (2001). A sixteen-hole pressure rake is used for boundary layer data on the sidewalls and ceiling of the test section and a Pitot-static probe is used to obtain mean velocity magnitude in the centerline of the test section. Specific techniques are developed to minimize the uncertainties due to the apparatus used, and an uncertainty analysis is used to confirm the efficiency of these techniques. Measurements in the wake of bump 1 reveal a strong streamwise vorticity creating large amounts of high moment fluid entrained close to the wall. In the wake of small bump 3, the amount of high momentum fluid entrained close to the wall is small as well as the streamwise vorticity. The flow in the wake of large bump 3 incorporate the characteristics of the two previous bumps by having a relatively large entrainment of high momentum fluid close to the wall and a low generation of streamwise vorticity. In the wakes of the three bumps, a pair of counter rotating vortices is created. The influence of large bump 3 on the incoming flow-field is found to be significant and induces an increase of the boundary layer thickness. By comparing LDV data and quad-wire hot-wire data with seven-hole probe data in the wakes of the bumps at the same locations, it is shown that uncertainties defined for a quasi-steady, non-turbulent flow-field without velocity gradient are bad indicators of the magnitude of the uncertainties in a more complex flow-field. A theoretical framework is discussed to understand the effects of the velocity gradient and of turbulence on the pressures measured by the seven-hole probe. In this fashion, a model is proposed and validated to explain these effects. It is observed that the main contribution to the uncertainties in seven-hole probe measurements due to the velocity gradient and to the turbulence comes from the velocity gradient. To correct for the effects of the velocity gradient on seven-hole probe measurements in an unknown flow-field, a technique is proposed. Using an estimation of the velocity gradient calculated from the seven-hole probe, the proposed model could be used to re-evaluate non-dimensional pressure coefficients used in the data reduction algorithm therefore correcting for the effects of the velocity gradient on seven-hole probe measurements. / Master of Science

A drag study was conducted on an oblate ellipsoid body in the Virginia Tech Stability Wind Tunnel. Two-dimensional wake surveys were taken with a seven-hole probe and an integral momentum method was applied to the results to calculate the drag on the body. Several different model configurations were tested; these included the model oriented at a 0° and 10° angle of attack with respect to the oncoming flow. For both angles, the model was tested with and without flow trip strips. At the 0° angle of attack orientation, data were taken at a speed of 44 m/s. Data with the model at a 10° angle of attack were taken at 44 m/s and 16 m/s. The high speed flow corresponded to a length-based Reynolds number of about 4.3 million; the low speed flow gave a Reynolds number of about 1.6 million. The results indicated that the length-squared drag coefficients ranged from around 0.0026 for the 0° angle of attack test cases and 0.0035 for the 10° angle of attack test cases. The 10° angle of attack cases had higher drag due to the increase in the frontal profile area of the model and the addition of induced drag. The flow trip strips appeared to have a tiny effect on the drag; a slight increase in drag coefficient was seen by their application but it was not outside of the uncertainty in the calculation. At the lower speed, uncertainties in the calculation were so high that the drag results could not be considered with much confidence, but the drag coefficient did decrease from the higher Reynolds number cases. Uncertainty in the drag calculations derived primarily from spatial fluctuations of the mean velocity and total pressure in the wake profile; uncertainty was estimated to be about 16% or less for the 44 m/s test cases. / Master of Science

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences and the Woods Hole Oceanographic Institution), 2003. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 299-310). / Inertial terms dominate the single-gyre ocean model and prevent western-intensification when the viscosity is small. This occurs long before the oceanically-appropriate parameter range. It is demonstrated here that the circulation is controlled if a mechanism for ultimate removal of vorticity exists, even if it is active only in a narrow region near the boundary. Vorticity removal is modeled here as a viscosity enhanced very near the solid boundaries to roughly parameterize missing boundary physics like topographic interaction and three dimensional turbulence over the shelf. This boundary-enhanced viscosity allows western-intensified mean flows even when the inertial boundary width is much wider than the frictional region because eddies flux vorticity from within the interior streamlines to the frictional region for removal. Using boundary-enhanced viscosity, western-intensified calculations are possible with lower interior viscosity than in previous studies. Interesting behaviors result: a boundary-layer balance novel to the model, calculations with promise for eddy param- eterization, eddy-driven gyres rotating opposite the wind, and temporal complexity including basin resonances. / (cont.) I also demonstrate that multiple-gyre calculations have weaker mean circulation than single-gyres with the same viscosity and subtropical forcing. Despite traditional understanding, almost no inter-gyre flux occurs if no-slip boundary conditions are used. The inter-gyre eddy flux is in control only with exactly symmetric gyres and free slip boundaries. Even without the inter-gyre flux, the multiple-gyre circulation is weak because of sinuous instabilities on the jet which are not present in the single-gyre model. These modes efficiently flux vorticity to the boundary and reduce the circulation without an inter-gyre flux, postponing inertial domination to much smaller viscosities. / by Baylor Fix-Kemper. / Ph.D.