Oceanographic observations in the Gulf of Guayaquil, 1962-1964. Part I. Physical and Chemical

ENGLISH: During 1961 the government of Ecuador, with the financial assistance of the Special Fund of the United Nations and the technical assistance of FAO experts, initiated an extensive program of fisheries research centered in a fisheries institute established in Guayaquil. In cooperation with this program, and in connection with Ecuador's adherence in 196l to the Convention for the Establishment of an Inter-American Tropical Tuna Commission, a two-and-a-half year investigation of the ecology of the Gulf of Guayaquil and adjacent waters was started by the Inter-American Tropical Tuna Commission. SPANISH: En 1961 el gobierno del Ecuador con el apoyo financiro del Fondo Especial de las Naciones Unidas y la asistencia tenica de los expertos de la FAO, inicio un programa extensivo de investigacion pesquera centralizado en el instituto de pesquerias establecido en Guayaquil. En cooperacion con este programa y en conexion con la adhesion del Ecuador en 1961 a la Convencion para el establecimiento de una Comision Interamericana del Atun Tropical, se comenzo por esta misma Comision una investigacion de dos anos y medio sobre la ecologia del Golfo de Guayaquil y las aguas adyacentes. (PDF contains 1532 pages.)

Physical Modeling And Parametric Study On Two-Degree-Of-Freedom Viv Of A Cylinder Near Rigid Wall

Unlike most previous studies on the transverse vortex-induced vibration(VIV) of a cylinder mainly under the wallfree condition (Williamson & Govardhan,2004),this paper experimentally investigates the vortex-induced vibration of a cylinder with two degrees of freedom near a rigid wall exposed to steady flow.The amplitude and frequency responses of the cylinder are discussed.The lee wake flow patterns of the cylinder undergoing VIV were visualized by employing the hydrogen bubble technique.The effects of the gap-to-diameter ratio (e0/D) and the mass ratio on the vibration amplitude and frequency are analyzed.Comparisons of VIV response of the cylinder are made between one degree (only transverse) and two degrees of freedom (streamwise and transverse) and those between the present study and previous ones.The experimental observation indicates that there are two types of streamwise vibration,i.e.the first streamwise vibration (FSV) with small amplitude and the second streamwise vibration (SSV) which coexists with transverse vibration.The vortex shedding pattem for the FSV is approximately symmetric and that for the SSV is alternate.The first streamwise vibration tends to disappear with the decrease of e0/D.For the case of large gap-to-diameter ratios (e.g.e0/D = 0.54～1.58),the maximum amplitudes of the second streamwise vibration and transverse one increase with the increasing gapto-diameter ratio.But for the case of small gap-to-diameter ratios (e.g.e0/D = 0.16,0.23),the vibration amplitude of the cylinder increases slowly at the initial stage (i.e.at small reduced velocity V,),and across the maximum amplitude it decreases quickly at the last stage (i.e.at large Vr).Within the range ofthe examined small mass ratio (m＜4),both streamwise and transverse vibration amplitude of the cylinder decrease with the increase of mass ratio for the fixed value of V,.The vibration range (in terms of Vr ) tends to widen with the decrease of the mass ratio.In the second streamwise vibration region,the vibration frequency of the cylinder with a small mass ratio (e.g.mx = 1.44) undergoes a jump at a certain Vr,.The maximum amplitudes of the transverse vibration for two-degree-of-freedom case is larger than that for one-degree-of-freedom case,but the transverse vibration frequency of the cylinder with two degrees of freedom is lower than that with one degree of freedom (transverse).

Oceanographic observations in the Gulf of Guayaquil, 1962-1964. Part II. Biological, chemical and physical.

ENGLISH: During 1961 the government of Ecuador, with the financial assistance of the Special Fund of the United Nations and the technical assistance of FAO experts, initiated an extensive program of fisheries research centered in a fisheries institute established in Guayaquil. In cooperation with this program, and in connection with Ecuador's adherence in 1961 to the Convention for the Establishment of an Inter-American Tropical Tuna Commission, a two-and-a-half year investigation of the ecology of the Gulf of Guayaquil and adjacent waters was started by the Inter-American Tropical Tuna Commission. SPANISH: Durante 1961 el gobierno ecuatoriano con el apoyo financiero del Fondo Especial de las Naciones Unidas y la ayuda técnica de los expertos de la FAO, inició un programa extensivo de investigación pesquera, centralizado en el instituto pesquero establecido en Guayaquil. En cooperación con este programa y en conexión a la afiliaci6n del Ecuador a la Convención, en 1961, para el establecimiento de una Comisión Interamericana del Atún Tropical, Cue iniciada por la Comisión una investigación de dos aftos y medio sobre la ecología del Golfo de Guayaquil y de las aguas adyacentes. (PDF contains 501 pages.)

Physical circulation measurements in Pamlico Sound, used to locate new oyster sanctuaries

The population of eastern oyster, C. virginica, has declined over the last century on most areas of the east and gulf coasts. North Carolina’s restoration efforts depend on the construction of subtidal oyster reefs to be used as broodstock sanctuaries in Pamlico Sound, NC. Successful restoration of the oyster population requires several thriving reefs connected as a meta-population. C. virginica has a 2-3 week larval stage, during which it gradually settles through the water column. Larvae that can travel from one reef to another during that stage form the basis of a meta-population. (PDF contains 3 pages)

Physical investigations of small particles : (I) aerosol particle charging and flux enhancement and (II) whispering gallery mode sensing

Part I

Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement.

Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes.

The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an “enhancement factor” to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth.

Part II

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, \lambda_{R}, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Earthquakes of the Nepal Himalaya : towards a physical model of the seismic cycle

Home to hundreds of millions of souls and land of excessiveness, the Himalaya is also the locus of a unique seismicity whose scope and peculiarities still remain to this day somewhat mysterious. Having claimed the lives of kings, or turned ancient timeworn cities into heaps of rubbles and ruins, earthquakes eerily inhabit Nepalese folk tales with the fatalistic message that nothing lasts forever. From a scientific point of view as much as from a human perspective, solving the mysteries of Himalayan seismicity thus represents a challenge of prime importance. Documenting geodetic strain across the Nepal Himalaya with various GPS and leveling data, we show that unlike other subduction zones that exhibit a heterogeneous and patchy coupling pattern along strike, the last hundred kilometers of the Main Himalayan Thrust fault, or MHT, appear to be uniformly locked, devoid of any of the “creeping barriers” that traditionally ward off the propagation of large events. The approximately 20 mm/yr of reckoned convergence across the Himalaya matching previously established estimates of the secular deformation at the front of the arc, the slip accumulated at depth has to somehow elastically propagate all the way to the surface at some point. And yet, neither large events from the past nor currently recorded microseismicity nearly compensate for the massive moment deficit that quietly builds up under the giant mountains. Along with this large unbalanced moment deficit, the uncommonly homogeneous coupling pattern on the MHT raises the question of whether or not the locked portion of the MHT can rupture all at once in a giant earthquake. Univocally answering this question appears contingent on the still elusive estimate of the magnitude of the largest possible earthquake in the Himalaya, and requires tight constraints on local fault properties. What makes the Himalaya enigmatic also makes it the potential source of an incredible wealth of information, and we exploit some of the oddities of Himalayan seismicity in an effort to improve the understanding of earthquake physics and cipher out the properties of the MHT. Thanks to the Himalaya, the Indo-Gangetic plain is deluged each year under a tremendous amount of water during the annual summer monsoon that collects and bears down on the Indian plate enough to pull it away from the Eurasian plate slightly, temporarily relieving a small portion of the stress mounting on the MHT. As the rainwater evaporates in the dry winter season, the plate rebounds and tension is increased back on the fault. Interestingly, the mild waggle of stress induced by the monsoon rains is about the same size as that from solid-Earth tides which gently tug at the planets solid layers, but whereas changes in earthquake frequency correspond with the annually occurring monsoon, there is no such correlation with Earth tides, which oscillate back-and-forth twice a day. We therefore investigate the general response of the creeping and seismogenic parts of MHT to periodic stresses in order to link these observations to physical parameters. First, the response of the creeping part of the MHT is analyzed with a simple spring-and-slider system bearing rate-strengthening rheology, and we show that at the transition with the locked zone, where the friction becomes near velocity neutral, the response of the slip rate may be amplified at some periods, which values are analytically related to the physical parameters of the problem. Such predictions therefore hold the potential of constraining fault properties on the MHT, but still await observational counterparts to be applied, as nothing indicates that the variations of seismicity rate on the locked part of the MHT are the direct expressions of variations of the slip rate on its creeping part, and no variations of the slip rate have been singled out from the GPS measurements to this day. When shifting to the locked seismogenic part of the MHT, spring-and-slider models with rate-weakening rheology are insufficient to explain the contrasted responses of the seismicity to the periodic loads that tides and monsoon both place on the MHT. Instead, we resort to numerical simulations using the Boundary Integral CYCLes of Earthquakes algorithm and examine the response of a 2D finite fault embedded with a rate-weakening patch to harmonic stress perturbations of various periods. We show that such simulations are able to reproduce results consistent with a gradual amplification of sensitivity as the perturbing period get larger, up to a critical period corresponding to the characteristic time of evolution of the seismicity in response to a step-like perturbation of stress. This increase of sensitivity was not reproduced by simple 1D-spring-slider systems, probably because of the complexity of the nucleation process, reproduced only by 2D-fault models. When the nucleation zone is close to its critical unstable size, its growth becomes highly sensitive to any external perturbations and the timings of produced events may therefore find themselves highly affected. A fully analytical framework has yet to be developed and further work is needed to fully describe the behavior of the fault in terms of physical parameters, which will likely provide the keys to deduce constitutive properties of the MHT from seismological observations.

Report on the physical, bacteriological and biochemical analyses of seawater samples collected off existing sewage outfalls in the Sierra Leone River Estuary

The studies reported were undertaken as part of a wide environmental feasibility study for the establishment of a modern sewage system in Freetown. The aim of this part of the study was to determine whether the hydrological regime of the Sierra Leone River Estuary would permit the large-scale introduction of sewage into the estuary without damaging the environment. The important factors were whether: 1) there would be sufficient dilution of the sewage; 2) fleatable particles or other substances would create significant adverse effects in the estuarine ecosystem. The outfall sites are described together with the sampling stations, methods and analyses. Results include: 1) T/S profiles; 2) chemical analysis of the water. A review of literature on the Sierra Leone River Estuary is included which provides information on the plankton, benthos and fisheries. Results suggest that at certain points where local circulations occur it would be inadvisable to locate untreated sewage outfalls. Such points are frequently observed in small embayments. These studies have been of short duration but the data can serve as baseline for more extended investigations which would give a more complete picture of the seasonal patterns in the estuary.

Seismic reflection experiments imaging the physical nature of crustal structures in southern California

Seismic reflection methods have been extensively used to probe the Earth's crust and suggest the nature of its formative processes. The analysis of multi-offset seismic reflection data extends the technique from a reconnaissance method to a powerful scientific tool that can be applied to test specific hypotheses. The treatment of reflections at multiple offsets becomes tractable if the assumptions of high-frequency rays are valid for the problem being considered. Their validity can be tested by applying the methods of analysis to full wave synthetics.

Three studies illustrate the application of these principles to investigations of the nature of the crust in southern California. A survey shot by the COCORP consortium in 1977 across the San Andreas fault near Parkfield revealed events in the record sections whose arrival time decreased with offset. The reflectors generating these events are imaged using a multi-offset three-dimensional Kirchhoff migration. Migrations of full wave acoustic synthetics having the same limitations in geometric coverage as the field survey demonstrate the utility of this back projection process for imaging. The migrated depth sections show the locations of the major physical boundaries of the San Andreas fault zone. The zone is bounded on the southwest by a near-vertical fault juxtaposing a Tertiary sedimentary section against uplifted crystalline rocks of the fault zone block. On the northeast, the fault zone is bounded by a fault dipping into the San Andreas, which includes slices of serpentinized ultramafics, intersecting it at 3 km depth. These interpretations can be made despite complications introduced by lateral heterogeneities.

In 1985 the Calcrust consortium designed a survey in the eastern Mojave desert to image structures in both the shallow and the deep crust. Preliminary field experiments showed that the major geophysical acquisition problem to be solved was the poor penetration of seismic energy through a low-velocity surface layer. Its effects could be mitigated through special acquisition and processing techniques. Data obtained from industry showed that quality data could be obtained from areas having a deeper, older sedimentary cover, causing a re-definition of the geologic objectives. Long offset stationary arrays were designed to provide reversed, wider angle coverage of the deep crust over parts of the survey. The preliminary field tests and constant monitoring of data quality and parameter adjustment allowed 108 km of excellent crustal data to be obtained.

This dataset, along with two others from the central and western Mojave, was used to constrain rock properties and the physical condition of the crust. The multi-offset analysis proceeded in two steps. First, an increase in reflection peak frequency with offset is indicative of a thinly layered reflector. The thickness and velocity contrast of the layering can be calculated from the spectral dispersion, to discriminate between structures resulting from broad scale or local effects. Second, the amplitude effects at different offsets of P-P scattering from weak elastic heterogeneities indicate whether the signs of the changes in density, rigidity, and Lame's parameter at the reflector agree or are opposed. The effects of reflection generation and propagation in a heterogeneous, anisotropic crust were contained by the design of the experiment and the simplicity of the observed amplitude and frequency trends. Multi-offset spectra and amplitude trend stacks of the three Mojave Desert datasets suggest that the most reflective structures in the middle crust are strong Poisson's ratio (σ) contrasts. Porous zones or the juxtaposition of units of mutually distant origin are indicated. Heterogeneities in σ increase towards the top of a basal crustal zone at ~22 km depth. The transition to the basal zone and to the mantle include increases in σ. The Moho itself includes ~400 m layering having a velocity higher than that of the uppermost mantle. The Moho maintains the same configuration across the Mojave despite 5 km of crustal thinning near the Colorado River. This indicates that Miocene extension there either thinned just the basal zone, or that the basal zone developed regionally after the extensional event.

Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins

A summary of previous research is presented that indicates that the purpose of a blue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pK_a shifts.

The pK_a's of mutant amicyanins have been measured by pH-dependent electrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the reduced copper to adopt a relaxed conformation: the ability to relax drives the reduction potentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F) mV vs. NHE. The measured pK_a's are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The additional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the blue copper absorption and an increase in the parallel hyperfine splitting in the EPR spectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal imidazole.

Melting curves give a measure of the thermal stability of the protein. A thermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons with the electrochemistry and apoamicyanin suggest that the intermediate involves the region of the protein near the metal site. This region is destabilized in the P94F mutant; coupled with the evidence that the imidazole is stabilized under the same conditions confirms an original concept of the rack effect: a high energy configuration is stabilized at a cost to the rest of the protein.

Breaking the 400 ppm barrier: Physical and Social implications of the recent CO2 rise

6 p.

Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.