Physical Sciences and Mathematics Commons^™

Single Molecule Emission Characteristics In Near-Field Microscopy, Randy X. Bian, Robert C. Dunn, X. Sunney Xie, P.T. Leung

Physics Faculty Publications and Presentations

In near-field scanning optical microscopy (NSOM), the measured fluorescence lifetime of a single dye molecule can be shortened or lengthened, sensitively dependent on the relative position between the molecule and aluminum coated fiber tip. The modified lifetimes and other emission characteristics are simulated by solving Maxwell equations with the finite-difference time-domain (FDTD) method. The 2D computation reveals insight into the lifetime behaviors and provides guidance for nonperturbative spectroscopic measurements with NSOM. This new methodology is capable of predicting molecular emission properties in front of a metal/dielectric interface of arbitrary geometry.

Adaptive Methods For Distributed Video Presentation, Crispin Cowan, Shanwei Cen, Jonathan Walpole, Carlton Pu

Computer Science Faculty Publications and Presentations

This paper describes problems and solutions for delivering real-time, multi-media presentations across the Internet. A key characteristic of presentations of continuous media datatypes, such as digital video and audio, is their need for predictable real-time data delivery. For example, an NTSC quality video presentation requires video frames to be displayed every 1/30th of a second. Variations in this display rate can be observable as stalls or glitches in the video stream and reduce the quality of the presentation [6]. Delivering such presentations across the Internet is difficult because highly variable band- width and latency make it difficult to predict the …

Complexity Properties Of The Cellular Automaton Game Of Life, Andreas Rechtsteiner

Dissertations and Theses

The Game of Life is probably the most famous cellular automaton. Life shows all the characteristics of Wolfram's complex Class IV cellular automata: long-lived transients, static and propagating local structures, and the ability to support universal computation.

We examine in this thesis questions about the geometry and criticality of Life. We find that Life has two different regimes with different dimensionalities. In the small scale regime Life shows a fractal dimensionality with D_s = 0.658 and in the large scale regime D₁ = 2.0, suggesting that the objects of Life are randomly distributed. We find that Life …

Quality Of Service Specification For Multimedia Presentations, Richard Staehli, Jonathan Walpole, David Maier

Computer Science Faculty Publications and Presentations

The bandwidth limitations of multimedia systems force tradeoffs between presentation data fidelity and real-time performance. For example, digital video is commonly encoded with lossy compression to reduce bandwidth and frames may be skipped during playback to maintain synchronization. These tradeoffs depend on device performance and physical data representations that are hidden by a database system. If a multimedia database is to support digital video and other continuous media data types, we argue that the database should provide a Quality of Service (QOS) interface to allow application control of presentation timing and information loss tradeoffs.

This paper proposes a data model …

Customizable Operating Systems, Jonathan Walpole, Crispin Cowan, Andrew P. Black, Jon Inouye, Calton Pu, Shanwei Cen

Computer Science Faculty Publications and Presentations

A customizable operating system is one that can adapt to improve its functionality or performance. The need for customizable and application-specific operating systems has been recognized for many years, but they have yet to appear in the commercial market. This paper explores the notion of operating system customizability and examines the limits of existing approaches. The paper begins by surveying system structuring approaches for the safe and efficient execution of customizable operating systems. Then it discusses the burden that existing approaches impose on application software, and explores techniques for reducing this burden. Finally, support for customizability in the Synthetix project …

Device And Physical Data Independence For Multimedia Presentations, Richard Staehli, Jonathan Walpole, David Maier

Computer Science Faculty Publications and Presentations

Multimedia computing promises access to any type of visual or aural medium on the desktop. But in this networked future, will every type of media be accessible from every terminal device? Current multimedia standards do not allow content that is authored for high-bandwidth workstations to scale down for low-bandwidth applications. The problem is that application requests are commonly interpreted as requests for the highest possible quality and resource overloads are handled by ad hoc methods. We can begin to solve this problem by specifying Quality of Service (QOS) requirements based on functionality rather than on content encoding and device capabilities.

Device And Physical Data Independence For Multimedia Presentations, Richard Staehli, Jonathan Walpole, David Maier

Computer Science Faculty Publications and Presentations

Multimedia computing promises access to any type of visual or aural medium on the desktop. But in this networked future, will every type of media be accessible from every terminal device? Current multimedia standards do not allow content that is authored for high-bandwidth workstations to scale down for low-bandwidth applications. The problem is that application requests are commonly interpreted as requests for the highest possible quality and resource overloads are handled by ad hoc methods. We can begin to solve this problem by specifying Quality of Service (QOS) requirements based on functionality rather than on content encoding and device capabilities.

Evaluable Functions In The GöDel Programming Language: Parsing And Representing Rewrite Rules, Janet Vorvick

Dissertations and Theses

The integration of a functional component into a logic language extends the expressive power of the language. One logic language which would benefit from such an extension is Gödel, a prototypical language at the leading edge of the research in logic programming. We present a modification of the Gödel parser which enables the parsing of evaluable functions in Gödel. As the first part of an extended Gödel, the parser produces output similar to the output from the original Gödel parser, ensuring that Gödel modules are properly handled by the extended-Gödel parser. Parser output is structured to simplify, as much as …

Geochemistry Of The Boring Lava Along The West Side Of The Tualatin Mountains And Of Sediments From Drill Holes In The Portland And Tualatin Basins, Portland, Oregon, Michelle Lynn Barnes

Dissertations and Theses

Instrumental Neutron Activation Analysis (INAA) was used to identify geochemical groups in Boring Lava along the west side of the Tualatin Mountains, and in sediments of the Portland and Tualatin basins. Samples of Boring Lava were obtained from TriMet drill core collected during planning of the tunnel alignment for the Westside Light Rail line. Additional samples of Boring Lava were collected from outcrops along the west side of the Tualatin Mountains. Samples of sediment from the Tualatin and Portland basins were obtained from drill core collected during an Oregon Department of Geology and Mineral Industries (DOGAMI) Earthquake Hazards Mapping project. …

Electrostatic Interactions At Membrane-Water Interfaces And Distribution Of 2, 4, 6-Trichlorophenol In A Membrane Model System, Isolde Sieder

Dissertations and Theses

It is generally accepted that biological membranes consist of a lipid bilayer matrix with proteins incorporated into the lipid bilayer. Typically, these membranes are negatively charged due to the presence of negatively charged lipids in the bilayer as well as negatively charged molecular groups on proteins. Biologically active molecules, such as environmental pollutants, enter the membrane from the aqueous phase by adsorption or partitioning into the lipid bilayer. The thesis consists of two parts. Part I is a computational study of spatial distribution of electric potential in the aqueous portion of the membrane-water interface using two models of charge distribution: …

An Unbalanced Debate. Review Of: Scarcity Or Abundance: A Debate On The Environment By Norman Myers And Julian Simon, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

Book Review of Scarcity or Abundance? A Debate on the Environment by Norman Myers and Julian Simon

Intercomparison Of Local Hydroxyl Measurements By Radiocarbon And Fage Techniques, Malcolm J. Campbell, Brad D. Hall, John C. Sheppard, Philip L. Utley, Robert J. O'Brien, Thomas M. Hard, Linda Acha George

Environmental Science and Management Faculty Publications and Presentations

A direct intercomparison of near-surface tropospheric HO concentration measurements by two different techniques was made in October–November 1992 at a rural site near Pullman, Washington. The atmosphere at the site is believed to contain low levels of anthropogenic pollution. The instruments' inlets were located at the same height (3.5 m) above the ground and were separated by 10 m along a line normal to the prevailing wind. Readings of the FAGE3 and radiocarbon instruments showed a high correlation (r² = 0.74) despite HO concentrations that were frequently near the detection limit of the instruments. An unweighted least squares regression shows …

Doubled Co2 Experiments With The Global Change Research Center Two-Dimensional Statistical Dynamical Climate Model, R. M. Mackay, M. A. K. Khalil

Physics Faculty Publications and Presentations

The zonally averaged response of the Global Change Research Center two-dimensional statistical dynamical climate model (GCRC 2-D SDCM) to a doubling of atmospheric carbon dioxide (350 parts per million by volume (ppmv) to 700 ppmv) is reported. The model solves the two-dimensional primitive equations in finite difference form (mass continuity, Newton's second law, and the first law of thermodynamics) for the prognostic variables: zonal mean density, zonal mean zonal velocity, zonal mean meridional velocity, and zonal mean temperature on a grid that has 18 nodes in latitude and 9 vertical nodes (plus the surface). The equation of state, p=rhoRT, and …

Ionization-Excitation Of Helium By Fast Charged Particles, L. Nagy, J. Wang, Jack C. Straton, James H. Mcguire

Physics Faculty Publications and Presentations

Probabilities and cross sections for ionization plus excitation in helium produced by fast heavy-particle impact have been evaluated. In these calculations, contributions from shake-off, time ordering, and independent interactions of the frozen-target electrons with the projectile are included. A comparison is made to recent experimental observations for the ratio of excitation-ionization to single-ionization total cross sections. A comparison is also made to calculations of excitation-ionization by fast electron impact.

Origins And Effects Of Thermal Processes On Near-Field Optical Probes, Andres H. La Rosa, B. I. Yakobson, H. D. Hallen

Physics Faculty Publications and Presentations

An aluminum-coated tapered fiber probe, as used in near-field scanning optical microscopy (NSOM), is heated by the light coupled into it. This can destroy the probe or may modify the sample, which can be problematic or used as a tool. To study these thermal effects, we couple modulated visible light of various power through probes. Simultaneously coupled infrared light senses the thermal effects. We report their magnitude, their spatial and temporal scales, and real-time probe damage observations.Amodel describes the experimental data, the mechanisms for induced IR variation, and their relative importance.

Origins Of Effective Charge Of Multivalent Ions At A Membrane/Water Interface And Distribution Of 2,3,4,5-Tetrachlorophenol In A Membrane Model System, Piet O. Schmidt

Dissertations and Theses

Biological cells and subcellular organelles are surrounded by membranes to form compartments performing specialized functions. Adsorption or partitioning of biologically active compounds into the membrane is the first step in the process of modification of cell function. This work is concerned with the problem of distribution of charged molecules between water and electrically charged membrane surface and between water and octanol. Part I of this thesis is focused on the electrostatic interactions taking place between charges on the membrane and ions present in the aqueous region of the membrane/water interface. The objective was to explore theoretically the origin of anomalous …

The Interaction Between A Thiol Specific Probe (Opa) And The Single Channel Characteristics Of The Reconstituted Ca++ Release Protein From Skeletal Muscle Sarcoplasmic Reticulum, Alexander Braun

Dissertations and Theses

One advantage of higher life-forms over less developed organisms is their ability to respond to signals from their environment with motion. This requires highly specialized contractile cells and a whole locomotion apparatus. In vertebrates, the cells responsible for movement are the skeletal muscle cells. They receive signals from the autonomic nervous system in the form of an action potential, and they contract in an appropriate manner. Calcium is a vital intracellular passenger whose role in muscular function is to initiate contraction. It is released via specific channel proteins from an internal Ca++ store, the sarcoplasmic reticulum, and triggers muscular contraction, …

Synthesis And Characterization Of Novel Fluorine Containing Alkylsulfonyls And Sulfonates : Fluorinated Sulfonyl Methanes And Derivatives, Nelson R. Holcomb

Dissertations and Theses

A series of salts of the strong fluorocarbon acid bis(trifluoromethylsulfonyl)methane were made: (CF3S02 ) 2CHK, (CF3S02 ) 2CHLi, [ (CF3S02 ) 2CH] 2Ca, [ (CF3S02 ) 2CH] 2Hg, (CF3S02 ) 2CHAg, [ (CF3S02 ) 2CH] 3La. Their reactivity and use as organic intermediates were investigated. The salts were made from their corresponding carbonates, oxides, or hydrides. The reaction times for the salts is generally short, however the purification process was laborious, involving recrystallization from organic solvents and drying under vacuum. The lithium salt is being evaluated as a solid state battery electrolyte. Derivatives of bis(trifluoromethylsulfonyl)methane were made by using the …

O-Phthalaldehyde Modification Of Sarcoplasmic Reticulum Calcium Release, Steffen Koehler

Dissertations and Theses

Muscle contraction is a phenomena which fascinated already the ancient Greeks. People have long sought to understand the mechanism of muscle contraction. Today we know that in order for muscle to contract, an action potential propagates from the nerve cell to the muscle cell. Upon arriving at the muscle cell, via a mechanism called Excitation- Contraction (E-C) coupling, Ca2 + is released from an intracellular membrane system, the sarcoplasmic reticulum (SR), into the intracellular fluid. The increase of intracellular Ca2 + initiates the interaction between the contractile units which results in force development and tension. The least well understood step …

Weakest Pre-Condition And Data Flow Testing, Griffin David Mcclellan

Dissertations and Theses

Current data flow testing criteria cannot be applied to test array elements for two reasons: 1. The criteria are defined in terms of graph theory which is insufficiently expressive to investigate array elements. 2. Identifying input data which test a specified array element is an unsolvable problem. We solve the first problem by redefining the criteria without graph theory. We address the second problem with the invention of the wp_du method, which is based on Dijkstra's weakest pre-condition formalism. This method accomplishes the following: Given a program, a def-use pair and a variable (which can be an array element), the …

Electrolysis Of Palladium In Heavy Water, Christoph Zaczek

Dissertations and Theses

Following several reports in the past few years about compositional changes on palladium used as a cathode in heavy water electrolysis, the purpose of this research project was to reproduce this results.

Two experiments were performed using two cells connected in series, an experimental cell and a control cell.

Both experiments used platinum anodes, the experimental cell had a palladium cathode and the control cell had a platinum cathode. The electrolyte was D₂O with H₂SO₄. Radiation was monitored during both experiments. Also temperature and voltage were recorded for both experiments, to allow statements about …

Electrolysis Of Titanium In Heavy Water, Radovan Kopecek

Dissertations and Theses

The purpose of these studies was to determine if results similar to those of Fleischmann and Pons could be obtained using a titanium cathode instead of palladium in an electrolysis in a heavy water cell. The electrolyte consists of D₂O and H₂SO₄. Two experiments have been performed to examine the features of this electrolysis. As titanium shows the same properties to attract hydrogen, it seemed possible that excess heat could be produced. Radiation was monitored, and the surface of the titanium cathode was examined before and after electrolysis for any changes in the morphology …

The Distribution Of Naturally Occurring Soil Radionuclides And Radon Potential Of Northwest Oregon, Stuart Graham Ashbaugh

Dissertations and Theses

Radon, a naturally occurring radioactive gas produced as one of the decay products of soil/rock uranium and thorium, is considered to be a leading cause of pulmonary disease. Gamma spectrometry of 146 samples of soil were used to quantify radon source potential relative to lithology by measuring Bi²¹⁴ activity of the U²³⁸ decay series. Additional soil radio nuclide data (Th²³², Ac²²⁸, K40 and C¹³⁷ ) were used to help identify regional source provenance geochemistry and soil development. Ac²²⁸, Bi²¹⁴ and Th²³² activities in northwest Oregon soils range from five …

Synthesis And Characterization Of A Porphyrin Dyad, Dale A. Braden

Dissertations and Theses

The sun is a bountiful source of energy for our planet. .With the advent of photovoltaic cells, man has begun harnessing the sun's radiant energy, turning it into a form more directly useful: electricity. Commercially available solar cells currently operate at about 13% efficiency, sufficiently high to make them a viable source of electrical energy. It is of great interest, however, to improve their conversion efficiency, and to lower the cost of production so as to make them more economical, and thereby reduce our dependence upon traditional "dirty" sources of energy such as coal and oil. It has been found …

Modeling Of Decay Rate For Molecules At An Island Surface, Ting Xiong

Dissertations and Theses

The decay rates for molecules at rough surfaces are studied via an island surface model, with particular emphasis on the effect due to the distribution of surface roughness. Two extreme cases are studied when the surface islands distribute themselves evenly and when they coalesce to form local clusters at the molecule-substrate interface. The optical properties of the interfacial layer in these two cases are described by the Maxwell-Garnett and the fractal-cluster models, respectively. Among other results, it is found that both enhancement and suppression of the surface-induced decay rates are possible due to the presence of roughness, with more dramatic …

Fast Byte Copying: A Re-Evaluation Of The Opportunities For Optimization, Jon Inouye, Jonathan Walpole, Ke Zhang

Computer Science Faculty Publications and Presentations

High-performance byte copying is important for many operating systems because it is the principle method used for transferring data between kernel and user protection domains. For example, byte copying is commonly used for transferring data from kernel buffers to user buffers during file system read and IPC recv calls and to kernel buffers from user buffers during 'Write and-send calls. Because of its impact on overall system performance, commercial operating systems tend to employ many specialized byte copy routines, each one optimized for a different circumstance.

This paper revisits the opportunities for optimizing byte copy performance by discussing a series …

A Hydrologic Analysis Of Government Island, Oregon, Scott Gregory Bittinger

Dissertations and Theses

Government Island, located in the Columbia River approximately 16 km (10 mi) upstream of the confluence with the Willamette River, is a wetland mitigation site prompted by expansion of the southwest quadrant of Portland International Airport. The purpose of the study is to predict water levels in two enclosed lowland areas, Jewit Lake and Southeast Pond, based on levels of the Columbia River, precipitation, and evapotranspiration. Mitigation is intended to convert 1.13 km2 (237 acres) of seasonally flooded wetland to 1.27 km2 (267 acres) of semi-permanently flooded wetland and seasonally flooded wetland. Flooding of the wetland is most likely to …

The Parser Converter Loader: An Implementation Of The Computational Chemistry Output Language (Ccol), Donald Randall Abel

Dissertations and Theses

A necessity of managing scientific data is the ability to maintain experimental legacy information without continually modifying the applications that create and use that information. By facilitating the management of scientific data we hope to give scientists the ability to effectively use additional modeling applications and experimental data. We have demonstrated that an extensible interpreter, using a series of stored directives, allows the loading of data from computational chemistry applications into a generic database. Extending the interpreter to support a new application involves supplying a list of directives for each piece of information to be loaded. This research confirms that …

Differentiable Circle Maps With A Flat Interval, J. Graczyk, L. B. Jonker, G. Swiatek, F. M. Tangerman, J. J. P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

We study weakly order preserving circle maps with a flat interval, which are differentiable even on the boundary of the flat interval. We obtain estimates on the Lebesgue measure and the Hausdorff dimension of the non-wandering set. Also, a sharp transition is found from degenerate geometry to bounded geometry, depending on the degree of the singularities at the boundary of the flat interval.

Mist: Pvm With Transparent Migration And Checkpointing, Jeremy Casas, Dan Clark, Phil Galbiati, Ravi Konuru, Steve Otto, Robert Prouty, Jonathan Walpole

Computer Science Faculty Publications and Presentations

We are currently involved in research to enable PVM to take advantage of shared networks of workstations (NOWs) more effectively. In such a computing environment, it is important to utilize workstations unobtrusively and recover from machine failures. Towards this goal, we have enhanced PVM with transparent task migration, checkpointing, and global scheduling. These enhancements are part of the MIST project which takes an open systems approach in developing a cohesive, distributed parallel computing environment. This open systems approach promotes plug-and-play integration of independently developed modules, such as Condor, DQS, A VS, Prospero, XPVM, PIOUS, Ptools, etc. Transparent task migration, in …