Physics Department

Johnny Powell | Thesis students

2019-06-11: In the process of reversing the order: latest theses appearing at the top, now.

Mitch Burdorf '21

Physics Thesis title: Analyzing Cosmological Evolution through n-body Simulation of Dark and Luminous Matter using ChaNGa

pages: 73 pages


In order to simulate the large scale cosmological structure of the universe as dis-covered by Geller and Huchra in their CfA Redshift Survey (M. J. Geller and J.P. Huchra, Science,246, 897, 1989), cosmological simulations were performed usingChaNGa (Charm N-body Gravity Solver) (T. R. Quinn et al., In Proceedings of the2010 ACM/IEEE International Conference for High Performance Computing, Net-working, Storage and Analysis, SC 2010 (IEEE Computer Society, 1996)), a highlyparallelized n-body solver. Simulations were initially performed with the Cube300 ini-tial conditions provided by ChaNGa, and later performed using MUSIC (MUlti-ScaleInitial Conditions) (O. Hahn and T. Abel, Monthly Notices of the Royal Astronom-ical Society,415, 2101, 2011) to generate unique initial conditions containing gasparticles in addition to dark matter for up to five million particles. The output ofboth simulations was visualized in two and three dimensions using yt (M. J. Turk etal., The ApJS,192, 9, 2011), an open source visualization package. Both simulationssuccessfully formed dark matter filaments – connective threads with high density ofdark matter that form a weblike structure – and the dark matter and gas simulationappears to have a higher density of gas within the filaments, which is in agreementwith current cosmology.



Beckett Cummings '20

Physics Thesis title: N-Body Simulation of Cosmological Structure

pages: 66 pages


In an effort to simulate the distribution of large-scale cosmological structure observed by Margaret Geller and John Huchra (M. J. Geller and J. P. Huchra, Science, vol. 246 no. 4932, pp. 897–903, 1989.), we have run numerous cosmological simulations using ChaNGa (Charm N-body Gravity Solver) (Jetley et al., in 2008 IEEE International Symposium on Parallel and Distributed Processing, (Miami, FL, USA), pp. 1–12, IEEE, Apr. 2008. ISSN: 1530-2075.). The first set of simulations used “Cube300” ChaNGa’s native, dark-matter-only cosmological test simulation, which produced fibrils (large, strand-like regions of matter overdensity). The second set of simulations used data from the AGORA (Assembling Galaxies of Resolved Anatomy) simulation suite (Kim et al., The Astrophysical Journal Supplement Series, vol. 210, p. 14, Dec. 2013.), which produced fibrils of dark matter and gas, as well as galactic disks with active star formation by redshift z = 8. Both types of simulations used realistic, observationally-motivated values for physical parameters. These results, in the form of images of the simulation space, coincide strongly with previously published simulations, and qualitatively agree with the results of Geller’s sky surveys.


Chris Hale '18

Physics Thesis title: Tracking Resonances of Dark Matter Particles in Frequency Maps of a Galaxy

pages: 47 pages


The orbital behavior of particles which constitute the dark matter halo of evolving galaxies is a topic of great astrophysical interest (Valluri, 2010). In this thesis, the fundamental concepts for understanding orbits of dark matter particles, including gravitational potential and phase-space are discussed; this foundation is used for the discussion of resonances, including their formation and significance in the evolution of the galaxy. From this point, the primary topic of discussion is addressed: the behavior of particles within resonances as the halo changes shape due to perturbation. In order to study this matter, a previously produced N-body simulation was used (V. Debattista, personal communication) was used, modeling the growth of a triaxial dark matter halo evolving in the presence of a growing baryonic disk; fundamental frequency data is calculated for 50,000 particles over a simulated period of 10 Gyr, with data taken at 500 Myr intervals. Once all data is obtained, a series of frequency maps is generated using specially designed Python code; these include black-and-white ``proof-of-concept'' frequency maps, as well as color-coded maps designed to allow for the tracking of particles based on their initial fundamental frequency values. From these frequency maps, it is clear -- and the major result of this thesis -- that particles do indeed move between resonances during the evolution of the halo; however, further analysis is needed in order to determine the mechanism for such motion.

Logan Emery '14

Physics Thesis title: Spectroscopic Characterization of Water Absorption on Calcium Carbonated and its Astrophysical Implications

pages: 71

Abstract (Apologies for the TeX code format): 

The far infrared (FIR) absorption lines of CaCO$_3$ have been measured at a range of relative humidities (RH) between 33 and 92\% RH using a Bruker 66v/S spectrometer.  Hydration measurements on CaCO$_3$ have been made in the mid-infrared (MIR) by [H. A. Al-Hosney and V. H. Grassian, Phys. Chem. Chem. Phys \textbf{7}, 1266 (2005)], and astrophysically-motivated temperature-dependent FIR measurements of CaCO$_3$ in vacuum have also been reported [T. Posch, A. Baier, H. Mutschke, and T. Henning, Astrophys J. (2007)].  The custom sample cell constructed for these hydrated-FIR spectra is required because the 66v/S bench is under vacuum (3 mbar) during typical measurements.  Briefly, the sample cell consists of two Thalium Bromoiodide (KRS-5) windows, four O-rings, and a plastic ring for separating the windows and providing a volume for the saturated atmosphere.  CaCO$_3$ was deposited on KRS-5 windows using doubly-distilled water as an intermediary.  The KRS-5 window with sample and assembled sample cell were placed in a desiccator with the appropriate saturated salt solution [E. W. Washburn, \emph{International Critical Tables of Numerical Data, Physics Chemistry and Technology} (McGraw-Hill, 1926)] and allowed to hydrate for 23 hours.  For spectroscopy the desiccator was quickly opened and the second KRS-5 window placed in the cell to seal the chamber.  A spectrum was then taken of the sample at the appropriate RH.  The spectra taken characterize the adsorption of water vapor and CaCO$_3$ that might occur in circumstellar environments [G. J. Melnick, \emph{et al.}, Nature \textbf{412}, 160 (2001)].


The MIR and FIR reflectance spectra of calcite (CaCO$_3$) have been thoroughly studied by [K. H. Hellwege, \emph{et al.}, Z. Phys. \textbf{232}, 61 (1970)].  Five Lorentzian curves were fit to our data in the range from 378-222 cm$^{-1}$ and each was able to be assigned to a known mode of CaCO$_3$.  The data does not support the conclusion of a hydration effect on these modes of CaCO$_3$, but it does suggest a possible broadening of three modes peaked at 281 cm$^{-1}$.  The goal of this work is to bridge the body of work on CaCO$_3$ in physical chemistry and previous laboratory astrophysical observations to aid interpretation of FIR spectra obtained by observatories such as the Spitzer Space Telescope.



Noah Muldavin '13

Physics Thesis title: The N-body simulation of galaxy dynamics

pages: 116


The N-Body simulation is discussed and applied as a tool for studying the dynamics of disk galaxies, with particular attention paid to the formation of spiral arms and their relation to dark matter. As a comparison and in order to build intuition about the dynamical processes at work, analytical results on the statistical mechanics and stability of galactic disks are presented.  The rational for the N-Body simulation in presented in relation to these analytical results, and an algorithm is developed. Two simulations are performed: one of a typical Sc class disk galaxy \emph{without} and encompassing dark matter halo, and on of a typical Sc class disk galaxy \emph{with} an encompassing dark matter halo.  The results show that without a dark matter halo the disk is unstable.  Furthermore, in the case with a halo a spiral arm develops with is persistent for 20 - 30 crossing times.

Alec Jackkson '13

Physics Thesis title: Observation of optical variability in BL Lac object MRK 421


In this thesis, 15 observations of the visible emissions from BL Lac object MRK 421 were performed to study the exhibition of optical flux variability by this active source. The maximum variation was determined to be .52 mag between JD 2456297.9372569444 and JD 2456323.8861111109, and is reasonably consistent with previous published literature. While this result offers insight into the amplitude of the flux variability exhibited by MRK 421 in the visible regime, more observations are required to establish the existence of a period of oscillation. 

Will Eichelberger '13

Physics Thesis title: Numerical model for the partial coalescence of small fluid drops: Navier-Stokes and the damped harmonic oscillator

pages: website work in progress.


This thesis attempts to work through the theory supporting viscous fluid flow with the end goal of utilizing the Navier-Stokes equations to numerically model the partial coalescence event. To provide background, we will derive and solve the Young-Laplace equation. We also suggest an alternate model for the fluid interface that will allow us to test our theoretical predictions while avoiding the difficult task of solving the Navier-Stokes equations in closed form. Ultimately, the inherent complexity of these equations rules out a solution of any useful form.

The main result of this thesis, besides the presentation of the theory, is to model the surface as a mesh of masses and springs. We are able to show that this model supports complex fluid phenomena, which makes it an intriguing option as a vehicle to produce relevant results while avoiding the computational complexity required of a full solution.

Elisabeth Thomas '13

Physics Thesis title: The  problem of microwave absorption in DNA


We investigate a controversy regarding microwave absorption in DNA by analyzing theoretical models of molecules vibrating in a water-based solution [M. Kohli, W. N. Mei, E. W. Prohofsky and L. L. Van Zandt, Biopolymers, \textbf{20}, 853 (1981)] and summarizing several experiments that were designed to detect any effects of microwave absorption in DNA, one having observed microwave absorption [ G, ?S, ?Edwards, C. C. Davis, aJ. D. Saffer, and M. L. Swicord, Biophys. j. \textbf{47}, 799 (1985)] and two following that could not reproduce those results [K. R. Foster, B. R. Epstein, and M.A. Gealt, Biophys. J. \textbf{52}, 421, (1987) and C. Gabriel, E. H. Grant, R. Tata, P.R. Brown, B. Gestblom, and E. Noreland, Biophys. J. \textbf{55}, 29 (1989)].  /We use a theory [B.H. Dorfman and L.L. Van Zandt, Biopolymers \textbf{22}, 2639 (1983)] predicting overdamping for DNA molecules in solution to explain the observed lack of microwave absorption, but later find that all of these theories and experiments have their basis in a model of a DNA molecule in an infinite sea of water that does not correspond to the nucleus of the eukaryotic cell.  We discover from the literature that there is in fact very little water available inside a cell, as most water molecules are bonded to DNA and other cellular biomolecules.  We propose that in order to provide clarity to this controversy, future experiments must be performed that take into account a more realistic model of cellular DNA  \textit{in vivo}.

Matt Lambert '12

Physics Thesis title -- approximately : The shape of a the perfect skipping stone

pages: website work in progress.


This thesis explores the effect of shape on the dynamics of skipping stones by comparing flat disks, rings, and cones using video analysis techniques. 

The prior literature has focused on modeling the behavior of the skipping stone by treating it as an idealized flat disk. We begin by presenting the existing model of the skipping stone. The relevant parameters are the stone’s velocity V , the rotational speed φ, the incident angle β, and the attack angle θ. We then outline the new complexities introduced when a conical stone is used rather than a flat disk. Using aluminum we machined 5 flat disks, 3 rings of varying inner radii Ri, and 7 cones of varying cone angle γ (defined with respect to the horizontal). All of the shapes had the same (outer) diameter of 6.35 cm. We recorded high speed video of the human-thrown skipping stones using a Canon ZR40 Digital Video camcorder, a Casio High Speed Exilim EX-FH25 10.1 MP Digital Camera, and a Lowel DP 1000W Tungsten-Halogen f! or illumination. We analyzed the high speed video in Tracker, an open source video analysis program. Using data exported from Tracker, we extracted the energy before the skip E0 and the energy after the skip Ef . We then define the efficiency Ef /E0 . We sort the data into high and low velocity regimes corresponding to different throwing styles. In each regime we examine the efficiency Ef /E0 and collision time tcoll as a function of cone angle γ. We also present the minimum observed initial skipping velocity as a function of cone angle γ. Based on this analysis, we conclude that cones with angle (γ = 5 → 35◦ ) inhabit a much broader parameter space than flat disks, meaning they are much easier to skip. Cones of small angle (γ = 5, 10, & 15◦ ) perform exceptionally well. In the high velocity regime, their efficiency (allowing for error) is roughly equal to that of flat disks (Ef /E0 = 0.63 ± 0.19). In the low velocity regime (where flat disks were not observe! d skipping successfully), they skip remarkably efficiently (Ef /E0 = 0.99 ± 0.13, 0.77 ± 0.22, and 0.71 ± 0.28, respectively), making them ideal candidates for maximizing the number of skips. Thus given our current level of understanding, we conclude the ideal shape for a skipping stone is a cone of angle γ between 5 and 15 degrees. Finally, we discuss this result and present possible avenues of further experimentation and theoretical work. 

Status: Finished his Reed thesis.

Ben Larson '12

Physics Thesis title -- approximately : The power of iPALM to explain the structure of clathrin

pages: website work in progress.


Status: Finished his Reed thesis.

Alexa Ross (AKA 598) '12

Physics Thesis title -- approximately : The secular evolution of offset bars

pages: website work in progress.


This thesis is a search for secularly evolved disk galaxies that possess a certain type of asymmetric stellar structure known as offset bars. Beginning with galaxies included in the Spitzer Survey of Stellar Structure in Galaxies, an initial sample of offset bars is narrowed down until only truly isolated cases remain. Most galaxies are eliminated from the sample due to either inherent asymmetries in the case of Magellanic systems or gravitational interaction with neighboring galaxies. Using archival data from the Very Large Array, two definite cases of isolated host disks are found. The status of isolation of the remaining thirty-seven galaxies is ambiguous. In addition to searching for truly isolated cases, this thesis examines bars as general stellar structure and aims to explain the existence of bars in disk galaxies.

Status: In grad. school for atmospheric sciences.

Maggie Post '11

Physics Thesis title: Avian Acoustic Communication: The Ground Effect.

pages: website work in progress.

Abstract: Bird calls are affected by many acoustic parameters of the environment in which they are transmitted. If birds are to successfully communicate over large distances, their calls must have either been evolved for or be adaptable to that environment.  Details regarding the ground effect, frequency-dependent attenuation of sound levels due to both absorption of waves and reflection off of the ground are examined both theoretically and experimentally.  American Crow (Corvus brachychychos) calls are transmitted across a grassy field close to the ground, and attenuation is measured at 1 m, 20 m, 40 m, and 60 m.  The primary frequency of the American Crow Short-medium Caw is found to be 1550 Hz, while the largest attenuation occurred from 50 - 1100 Ha and again around 1900 - 2200 Ha, while the 1550 Hz region remained the strongest signal. While this does not necessarily indicate that crow calls evolved to be transmitted from low altitudes over grassy fields. it does indicate that they are well suited to communicate in this environment.

Status: Last known to be working at the wildlife care center of the Audubon Society of Portland.

Manu Gomez '11 

Physics Thesis title: Observations on a new cataclysmic variable candidate

pages: website work in progress.

Abstract: Stellar properties and evolution pertaining to the cataclysmic variables and the catacylsmic variable model was discussed in detail.  The object 1RXS Jo72103.3-055854 (DN07) suggested to be a dwarf nova, was observed to confirm its cataclysmic variable status remotely with the Pomona Internet New Mexico Skies (PINTO) telescope.

Aaron Deich '11 

Physics Thesis title: Implication of the lack of pulsar-orbiting planets on pre-supernova planetary orbital distributions

pages: website work in progress.

Abstract: In this thesis, a Monte Carlo simulation is performed to model the effect of a star's supernova explosion on its planetary system, with the goal of testing which planets are most likely to remain orbitally bound to the remaining neutron star core. The relevance of planets likely to survive is that, because there are no detected planets around pulsars which have survived supernova, such likely-survival planets are therefore less likely to exist around pulsar progenitors at the moment of the explosion.  The simulation finds that the planets most likely to survive bear a .002 survival probability and are those with the semi-major axes of 2 AU (the smallest possible before engulfment by the giant pre-supernova star), while there is not clear dependence on orbital eccentricity. While this result allows a insight about the lower likelihood of the existence of planets in that orbital regime, the current number of detect pulsars (1,973) is too low to allow for strong non-existence predictions.

Ryan Lau '10

Physics Thesis title: Exploration of extra-solar planet properties

pages: 102 including a couple of awesome light curves and extensive instructions on remote observation at New Mexico Skies Observatory.


In this thesis six observations of extra-solar planets transit, two of HAT-P-12b and four of XO-2b, were performed to analyze their orbital and planetary properties and to search for timing variations that would indicate the existence of an additional perturbing body in the system.  The radius and orbital period of HAT-P-12b are determined to be 1.10+/- 0.3 R$_{\mbox{Jupiter}}$ and 3.2135 +/- 0.0008 days, respectively, and are reasonably consistent with previously published literature.  However, mid-transit times of  HAT-P-12b are found to occur 8 - 11 minutes before the predicted mid-transit times, with necessitates further observations to confirm the timing shift.  The radius and orbital period off XO-2b is determined to be 1.13 +/- 0.1 R$_{\mbox{Jupiter}}$ and 2.6160 +/- 0.0001 days respectively.   Although the XO-2b results are reasonably consistent with the previous literature our orbital period result deviates on the same order of magnitude as the discrepancy between two previously published values: 3.5 seconds.  Therefore, more precise measurements are required to determine if the timing variations are genuine or are due to underestimated timing errors.

Status: Presently --- 2012 --- in the Astronomy Ph.D. program at Cornell University working on SOPHIA.

Yasinul Karim '10

Physics Thesis title: Infrared spectroscopy of oligonucleotides.

pages: website work in progress.

Abstract: website work in progress.

Status: Presently in the Physics Ph.D. program at the University of Oregon.

Carl Pelz '87

Thesis title: A Wet Spinning Apparatus of Preparation of Highly Oriented Films of DNA Suited for Spectroscopic Studies

61 pages: In this thesis was constructed the only operational wet-spinning apparatus outside of Stockholm, Sweden. As such this apparatus serve as a template for other wet spinning rigs and a source of several thesis topics.

Abstract: We have constructed a wet spinning apparatus and used it to produce a film of oriented salmon testes DNA.

Status: As of 2012, I have not heard from Carl in about 25 years.

Brain Combs '87

Thesis direction by Professor Al Eisner, OHSU.

Thesis title: Foveal Chromatic Flicker Sensitivity During Dark Adaptation

73 pages: My first collaborative thesis.

Abstract: Foveal detection of chromatic flicker was found to be uninfluenced by variations in bleach wavelength when the bleaches' intensities were equated for red cone quantum absorption.

Status: I have not heard from Brian in a long time -- 2002.

Vale Krenik '88

Thesis title: Inelastic Light Scattering Studies and Fiber Characterization of pBR322 Plasmid DNA Oriented Fibers

163 pages: This thesis has a excellent review of the biological physics of DNA and experimental methods such as fiber pulling.

Abstract: pBR322 plasmid DNA was isolated and made into oriented fiber for light scattering experiments.

Status: Vale reportedly dropped by Reed in the Fall of 2002.

Mark Mason '88

Thesis title: Exploring Microwave Vibrations in Eucaryotic DNA

65 pages: This thesis has some excellent analysis of a wonderful problem that still has currency in 2002.

Abstract: An overview of the structure of DNA is given, with an emphasis on the physical characteristics that make DNA susceptible to developing longitudinal acoustic modes of vibrations with exposed to microwave radiation.

Status: I have not heard from Mark in a long time -- 2002.

Mike Rutenberg '89

Thesis title: Structural Image Filtering in the Frequency Domain: the Enhancement of Visual Data

58 pages: Excellent pedagogy on image processing.

Abstract: This thesis proposes the basis of a technique for filtering known regular structural features from a digital image.

Status: As of Mar. 2012, Mike is working in Canada.

Melanie Bennett '89

Thesis title: Counterion effects on the Far infrared spectra of calf thymus DNA

Thesis Publications:

Bennett, M. J., Powell, J. W., Weidlich, T., Genzel, L., Peticolas, and W., Rupprecht, A., "Counterion Effects on the Far-Infrared Spectra of Oriented DNA Films," Bull. Am. Phys. Soc. 34, 782 (1988).

Status: As of Mar. 2012, Melanie is the webmaster for a protein structure database (?) having earned a Ph.D. at UCLA.

Larry Myers '90

Thesis title: Far infrared spectra of single helical DNA - poly(rC)

Thesis Publications:

1. Lee, S. A., Myers, L. C., Powell, J. W., Smith, T., Suleski, T. J., and Rupprecht, A. R., "Raman and infrared studies of wet-spun films of Nahyaluronate" J. Biomole. Struct. Dynams., 11, 191 - 202 (1993).

2. Lee, S. A., Myers, L. C., Powell, J. W., Smith, T., Suleski, T. J., and Rupprecht, A. R., "Raman and infrared studies of wet-spun films of Na-hyaluronate" Bull. Am. Phys. 36, 403 (1991).

3. Stuart, A., Myers, L. C., Powell, J. W., and Peticolas, W. L. "Far-Infrared Vibrational Spectra of Intrinsic Bending Sequences and Dickerson Dodecamer Variants," Bull. Am. Phys. 36, 403 (1991).

4. Myers, L. C., Weidlich, T., Powell, J. W., and Genzel, L., and Rupprecht, A., "Counterion Effects on the Low Frequency Dynamics of Double and Single Helical Polynucleotides," Bull. Am. Phys. Soc. 35, 650 (1990).

Status: As of Mar. 2012, Larry is a professor at Dartmouth having earned a Ph.D at Harvard in biophysics.

Mike Reerink '90

Thesis title: Counterion Concentration Effects on the Far-Infrared Spectra of Oriented DNA Films

188 pages: an excellent reference on the physics of DNA.

Abstract: The effects of the concentration of RbCl on the far-infrared spectra of films of oriented calf thymus DNA were measured.

Jennifer Katz '90

Thesis title: Far Infrared Reflection Spectroscopy of Semiconductor Superlattices

145 pages: My only thesis student to use the Bruker 113v for semiconductor physics.

Abstract: The effects of the concentration of RbCl on the far-infrared spectra of films of oriented calf thymus DNA were measured.

Paul Terdal '90

Thesis title: Shooting in the Dark: A Resonance Raman Excitation Profile o Cr(CO)6

Thesis was directed by Professor Dan Gerrity, Department of Chemistry, Reed College.

Abstract: Part of an ongoing resonance Raman study of group 6 transition metal hexacarbonyl complexes, this thesis extends an existing excitation profile for Cr(CO)6 over its second charge transfer band.

Andrew Stuart '91

Thesis title: Low Frequency Phonons in DNA: The Search for the Mechanism of DNA Denaturation

116 pages: One of the last of my thesis students to wrestle with the far infrared vibrations in DNA.

Abstract: Particular low frequency vibrational modes in DNA associated with denaturation have been predicted, and are reviewed. General lattice dynamics are discussed for linear and cubic crystal, to develop a basis for understanding the approximations and techniques applices in dynamical models of DNA, which treat the double helix as a crystal lattice.

Status: As of Mar. 2012, Andrew had moved to Santa Barbara for work reasons.

Jeff Bradford '91

Thesis title: Determination of the Optical Constants by the Kramers-Kronig Relationship

88 pages: The best thesis from my lab on the Kramers-Kronig dispersion relation.

Abstract: A Kramers-Kronig analysis was done on previously acquired reflectance data of GaAs-Ga(.73)Al(.27)As superlattice at room temperature.

Tempel Smith '91

Thesis title: The Polyelectrolyte Nature of Hyaluronic Acid Explored with Middle and Far Infrared Spectroscopy

91 pages: An excellent thesis for understanding how to really orient a biopolymer and polyelectrolyte theory.

Abstract: The effects of monovalent counterions (Li+, Na+, K+, Rb+, and Cs+ on the far (50 - 500 wavenumbers) and middles (500 - 1800 wavenumbers) infrared spectra of oriented films of human umbilical cord Hyaluronic Acid (HA) using Fourier transform spectroscopy.

Adam Messinger '91

Thesis title: Counterion effects of the vibrational properties of Guanosine Monophosphate

174 pages: An tour de force in oscillator fitting. My first attempt at publishing a thesis after completion.

Abstract: For the first time far infrared (0 - 600 wavenumbers) transmission spectra and middle infrared (600 - 2000 wavenumbers) absorbance spectra of the gel and crystal confromation of 5'-Guanosine Monophosphate are presented for both the sodium and potassium counterion.

Thesis Publications:

1. Messinger, A., Weidlich, T., Powell, J. W., and Genzel, L., "Far-Infrared study of the vibrational modes of 5'-GMP gels and crystals of Na+ and K+," J. Biomole. Struct. Dynams. 10, 1841 - 852 (1993).

2. Messinger, A., Powell, J. W., Weidlich, T., and Genzel, L. "Far-Infrared vibrational Spectra of 5-Guansoine Monophate,Bull. Am. Phys. 36, 403 (1991).

Status: Adam was last heard of as a great reference (to his Ph.D. work at UCSD) in a talk presented at the meeting Oregon Chapter of the Society for Neuroscience 2002. He is working at the NIH.

Nicole Corre '92

Thesis title: A Study of the Aniostroic Swelling of Wet-Spun Films of DNA

114 pages: A wonderful review of polyelectrolyte theory

Abstract: The details of the two existing theories which attempt to account for the very large anisotropic swelling of wet-spun films of DNA have bee reviewed.

Status: Nicole where are you?

Bianca Sclavi '92

Thesis title: Conformational Study of d(GGTATACC) and d(GGUAUACC) by Middle Infrared Spectroscopy

Thesis signed by Professor Arthur Glasfeld, Department of Chemistry, Reed College.

109 pages: This laboratory's seminal contribution in middle infrared spectroscopy of biomolecules.

Abstract: Middle Infrared Spectroscoy was used to determine the conformation of two oligonucleotide sequences, d(GGTATAC) and d(GGUAUACC), under a wide range of relative humidities and excess sodium concentrations.

Thesis Publications:

1. B. Sclavi, W. L. Peticolas, and J. W. Powell, Biopolymers, 34, 1105 (1994).

2. S. A. Lee, B. Sclavi, J. W. Powell, W. Williamson, and A. Rupprecht, Phys. Rev E. 48, 2240 (1993).

3. B.SCLAVI, J.W. POWELL, J.KIM, and S.A. LEE, "Low frequency vibrational dynamics of polynucleotide DNA films." Bull. Am. Phys. 39, 885 (1994).

4. J.W. Powell and B. Sclavi, "Conformational Study of d(GGTATACC) and d(GGUAUACC) and Associated Polynucleotides by Infrared Spectroscopy" Bull. Am. Phys. 38, 119 (1993).

5. S. A. Lee, B. Sclavi, J. W. Powell, W. Williamson III, and A. Rupprecht, "Raman and infrared study of the vibrational dynamics of the netropsin-DNA complex" Bull. Am. Phys. Soc. 38, 119 (1993).

Status: Bianca received her Ph.D. from the Albert Einstein College of Medicine and accepted a postdoctoral position at the Louis Pasteur Institute in Paris. As of 2012, Bianca has a position as a biophysicist  in Paris.

Yuka Nagashima '92

Thesis title: The Physics of Sonolumiscence: Making Light of Sound

132 pages: This laboratory's first contribution in sonoluminescence.

Abstract: Empirical studies were performed on the light emission, called sonoluminescence, from various concentrations of sodium chloride through acoust cavitation.

Status: Yuka was heading to Hawaii for a teaching post ,last I knew.

Sabbatical in Warner Peticolas's Laboratory, Department of Chemistry, University of Oregon.

Andrew White '94

Thesis title: The Structure of Triple-Stranded Nucleic Acids

121 pages: This laboratory's only contribution to make it to the review literature. My first thesis student to TeX the document.

Abstract: Polynucleotide and olionucleotide triple-stranded nucleic acids were investigated using Fourier Transform Infrared Spectroscopy. Some molecular structural features of the poly(u).poly(A).poly(U) triplex and of the (dG)20.(dG)20.(dC)20 triplex were determined through the identification and characterization of molecular normal modes of vibration. The effect of hydration and counterionic state on molecular conformation was observed.

Thesis Publications and HHMI grant :

1. White, A. P., Smith, T., Powell, J. W., Sulesi, and Lee, S. A., "Counterion interactions with Haluronic acid" beginning stages of preparation.

2. White, A. P., Powell, J. W., Lee, S. A., and Rupprecht, A. R., "Vibrational spectroscopy of the bipy.DNA complex," beginning stages of preparation

3. Chen, Y. Z., White, A. Powell, J. W., and Prohofsky, E. W., Calculation of normal modes and dynamical stability of DNA triplex Poly(dA)$\cdot$2Poly(dT): S-type structure is more stable and in better agreement with observations in solution submitted to Biochemistry Oct. 1995.

4. White, A. P., Reeves, K. K., Snyder, E., Powell, J. W., Mohan, V., and Griffey, R. H., Hydration of DNA: FTIR studies of single-stranded phosphodiester and phosporothioate oligonucleotides, Accepted by Nuc. Acid Res. Feb. 1996.

5. White, A. and Powell, J. W.,, "Infrared Observation of the anti-syn Conformation shift in Triple Helical DNA" Biochemistry, 34 1137 - 1142 (1995).

6. A. P. White, and J. W. Powell,, "Infrared Observation of the Hydration Dependent Conformation of (dG)20(dG)20(dC)20," Bull. Am. Phys. Soc. 00, 1995.

7. White,and S. A. Lee, "Mid- and far-infrared study of the hydration of the DNA(bipy)Pt(en)2 complex.", Bull. Am. Phys. Soc. 00, 1995.

8. White, A. P. and Powell, J. W., ``Infrared observation of the hydration dependent conformation of (dG)20(dG)20(dC)20," Bull. Am. Phys. Soc. 40, 1995.

9. White A.P. and Powell, J.W.,at the Ninth Conversation in Biomolecular Stereodynamics, ``Observation of Daunomycin d(CGTA).d(TACG) Interactions using Infrared Spectroscopy'', J. Biomol. Struct. Dynamics 12, a259 1995.

10. White, A. P., Reeves, K. K., Snyder, E., Farrell, J. Powell, J.W., Mohan, V., and Griffey, R., ``Antisense physics," Bull. Am. Phys. Soc. 41, 1996.

Status: As of Mar. 2012, Andrew has a practice as an MD on the east coast.

Jason Gayton '95

Thesis title: Thermal Conductivity of Binary Gas Mixtures

60 pages: This laboratory's only contribution to the infrared spectroscopy of gases.

Abstract: The thermal conductivity of mixtures of He and CO2 is investigated.

Status: As of 2004 Jason is operations manager at GE Contractual Services and owner of a U.S. patent. The patent allows the determination of the overall influences of individual physical changes to a power plant electrical-thermo-mechanical system. So, Jason's career is proof that one can earn a handsome living by understanding the nature of enthalpy! As of 2012, Jason moved to Portland OR and is living in the Pearl.

Kathy Reeves

Thesis title: Structural Investigation of Phosphorothioate Oligodeoxyribonucleotides

91 pages: This work is the archetypal "two theses" in one thesis. Kathy solved one difficult problem after six months then solved another one in the remaining couple of months. She met the challenge of being my first thesis student to hand in a draft of a professional paper before turning in her thesis.

Abstract: A heterogeneous duplex consisting of one strand of normal DNA and one strand of phosphootioate DNA was examined using FTIR spectroscopy.

Thesis publications and grant activity:

1.C. A. Steinke, K. K. Reeves, J. W. Powell, S. A. Lee, Y. Z. Chen, Wyrzykiewicz, R. H. Griffey,
and V. Mohan, J. Biomol. Struct. Dynam. 14, 509 (1997).

2. A. P. White, K. K. Reeves, E. Snyder, J. W. Powell, V. Mohan, and R. H. Griffey, Nuc. Acid Res. 24, 3261 (1996).

3. A. P. White, K. K. Reeves, E. Snyder, J. Farrell, J.W. Powell, V. Mohan, and R. H.Griffey, Bull. Am. Phys. Soc. 41, (1996).

4. K. K. Reeves, J. W. Powell, V. Mohan, and R. H. Griffey, ,"Hydration induced structural changes in phosphorothioate-phosphorodiester hetero-duplex, " In preparation. A Structural Investigation of Phosphorothioate DNA Through Infrared Spectroscopy of Model Compounds

1. GRANT Hughes Faculty Development Fund Award Proposal: A Structural Investigation of Phosphorothioate DNA Through Infrared Spectroscopy of Model Compounds J. W. Powell and K. K. Reeves, $12,000 Fall 1996 - Fall 1997.

Status: As of Mar. 2012, Kathy is working in solar physics after receiving her Ph.D in astronomy from U. New Hampshire (?).

Kevin Day '95

Thesis title: Raman and UV-visible Spectroscopic Studies of Polyaniline Films

50 pages: This work was a Chemistry/Physics interdisciplinary thesis supervised largely by Professor Dan Gerrity, Department of Chemistry, Reed College.

Abstract: Raman and UV-visiible spectroscopic studies of polyaniline films were undertaken.

Status: As of Mar. 2012, Kevin is working at OHSU and living in Portland OR.

James Farrell '97

Thesis title: Dynamics of DNA Melting

81 pages: A tour de force of Prohofsky's self-consistent phonon approximation. The data in this thesis is certainly publishable.



1. A. P. White, K. K. Reeves, E. Snyder, J. Farrell, J.W. Powell, V. Mohan, and R. H.Griffey, Bull. Am. Phys. Soc. 41, (1996).

2. A. P. White, K. K. Reeves, E. Snyder, J. Farrell, J. W. Powell, V. Mohan, H. Sasmor,
and R. H. Griffey, Nuc. Acid Res. 24, 3261 (1995).

Status: As Mar. 2012, James is working for Google.

Byron Smiley '97

Thesis title: Spectroscopic Investigation of Single Bubble Sonolumnescence

64 pages: A tour de force of focused independent work.

Abstract: During a process called single-bubble sonoluminescence, a single bubble of air collapses in response to a standing wave of sound.

Status: Byron received his Ph.D. in physics from the University of Colorado at Boulder in approximately 2002.


Rick Rezinas '98

Thesis title: Raman Spectroscopy of Deoxyribonucleic Acids

This thesis was codirected with John Essick. John was the official advisor.

34 pages: One of two theses at Reed on the Raman spectroscopy of nucleic acids.

Abstract: The Raman scattering signatures of two DNA samples were looked for in this thesis.

Status: In around 1998 Rick was headed toward earning a teaching secondary degree/credential at George Fox University, Oregon.

Alona Davis '98

Thesis title: Raman Spectroscopic Studies of Normal Mode Vibrations in Stretched Fiber and

Rupprecht Film Samples of DNA

87 pages: A marvellous example of a successful thesis against nearly impossible odds.

Abstract: Raman spectra were taken of benzene, a stretched fiber of sodium salmon testes deoxyribonucleic acid , and a Rupprecht flim of deoxyribonucleic acid.

Status: As recently as Oct. 2012, Alona is working in the field of environmental science in the Bay area.

Robert Holliday '98

Thesis title: Multiphoton Dissociation of Chromium Carbonyl Complexes Using s 266 nm

Dissociation Wavelength

This thesis was a Chemistry-Physics Interdisciplinary work focused on physical chemistry.

69 pages: A tour de force of focused independent work.

Abstract: The multiphoton dissociation of chrominum hexacarbonyl and toluene chromium tricarbonyl were studied using a 266 nmm dissociation wavelength.

Status: I have not heard from Robert in ages.

Brian Halbert '98

Thesis title: Gamma Induced Radiation Damage in DNA Using FTIR Spectroscopy

48 pages: The signal-to-noise-ratio of radiation damage to DNA is too small for FTIR detection.

Abstract: The effects of gamma irradiation on salmon testes DNA were investigated using FTIR spectroscopy.

Status: Brian was in the Peace Corps in Africa for two years, and now (2012) he is working on a Ph.D at the University of Washington.

Zoe vanHoover '99

Thesis title: Observation of Hydration Effects in Membrane Constituents via FTIR Spectroscopy

Zoe was, at one time, owner of the Doyle Owl.

90 pages: A wonderful and publishable thesis on the infrared spectroscopy of membrane components. This work should definitely be extended to help explain membrane-membrane interactions necessary to explain exocytosis.

Abstract: The effects of hydration on egg phophatidylcholine were examined using Fourier transform infrared spectroscopy (FTIR).

Status: As of 2012, Zoe was working at SLAC.

Kate Martin '00

Thesis title: Optical Tweezers: Theory, Application, and Construction

84 pages: The first successful construction of optical tweezers at Reed College.

Abstract: An optical tweezers apparatus was constructed using a simple, monocular microscope and an argon-ion laser.

Status: Kate did graduate work at MIT.

Sean Kellogg '00

Thesis title: Theory and Design of the Reed Magneto-Optical Trap

45 pages: An extraordinarily inspiring pedagogical treatment of the principles of magneto-optical traps and a noble display of independence in scientific instrument design and construction.

Abstract: It was proposed to trap and cool a sample of neutral rubidium vapor in a spontaneous force magneto-optical trap (MOT).

Status: Sean is working at FEI, Beaverton, Oregon. He can be found by standing around trendy corners in SW Portland. :-) .

Sasha Avanesov '00

Thesis title: Temperature-dependent Phase Transitions of Egg Phosphatidylcholice, Observed via Fourier Transform Infrared Spectroscopy

99 pages:

Abstract: This study explored the thermotropic properties of a ubiquitous phospholipid, egg phosphatidylcholine (egg PC), using Fourier transform infrared spectroscoply (FTIR).

Status: In 2004 Sasha indicated that he was going to Palo Alto to study for Ph.D.

Walter Reisner '00

Thesis title: Laser Light Scattering from Thermally Excited Capillary Waves: Experimental Investigation and Review of Fundamental Theory

120 pages: Walter's Reed thesis was a heroic, but unsuccessful, effort to observe capillary waves. His work was marked by truly outstanding drive and independence. The document it self is a brilliant expose on hydrodynamics and fluctuation theory.

Abstract: Laser light scattering from thermally excited capillary waves is a established technique for measuring the surface tension and viscosity of interfacial systems (such as simple liquids, biomembranes and monolayers).

Status: As of Mar. 2012, Walter is presently a professor of physics at McGill University. Walter was in the graduate physics program at Princeton working with Professor Bob Austin. In 2004 Walter was an author on a PNAS paper from Austin's lab.  

Emmy Olson '00

Thesis title: Time Resolved Imaging of Caveolae at the Cell Surface Using Evanescent Wave Microscopy and a FRET-based Technique

Scientific direction by Wolfhard Almers, Senior Scientist, Vollum Institute, Portland, Oregon.

92 pages: This thesis--in large part--has changed the entire course of my career in biological physics toward neuroscience. Emi's thesis was an absolutely outstanding attempt to observe time-resolved motions involved in the endocytosis of caveolae.

Abstract: Evanescent wave microscopy and voltage dependent fluorescence resonance energy transfer (FRET) were used in a attempt to develop a technique to study time-resolved movements and endocytosis of caveolae at the cell surface.

Status: As of Mar. 2012, Emi is working on an MD-Ph.D. at UCSD (?).

2001 SABBATICAL YEAR in Oscar Nassif Mesquita's laboratory in Belo Horizonte, Brasil.

Andy DeMond '02

Thesis title: The Physics of Bacterial Motility: Computer Modelling of Signal Transduction Networks.

96 pages: Andy thesis is a fantastic document for those interested in learning the physics of FRET and how it can be applied to understanding fundamental problems in cellular biology. He also has some very cool MATLAB code in his thesis.

Abstract: The chemotatic signal transduction system of Escherichia coli was simulated computationally and compared with recently published experimental results obtained using fluorescence resonance energy transfer (V. Sourjik and H. C. Berg, PNAS 99 123 (2002)). The simulations were found to be in qualitative agreement with the published results. Overviews of fluorescence resonance energy transfer, signal transduction, computational simulation, and bacterial motility are given.

Status: As of 2012 Andy had received a Ph. D. in Biophysics at Berkeley a few years ago. He has experience in optical tweezers, patch clamping, and rumor has it that he built his own TIRFM system.

Hayden McGuinness '02

Thesis title: Aspects of Microtubule Lattice Dynamics.

59 pages: Hayden had the seminal idea to exam the physics of microtubules (MT). His thesis is an excellent manuscript for understanding the nonlinear theories of excitations in MTs as well as many other aspects of MTs.

Abstract: web work in progress..

Status: As of Mar. 2012, Hayden had completed a Ph.D in physics at UO and is doing a postdoctoral fellowship (?).

Nicholas Nussbaum '02

Thesis title: Searching for the Polymorphism in Phosphorothioate DNA.

46 pages: work in progress

Abstract: web work in progress..

Status: As of Sept. 2004, Nicholas was working as a laboratory technician in UNLV.

Neelaksh Sadhoo '03

Thesis title: Pursuing a Vibrational Mechanism for microtubule lattice melting, using FTIR spectroscopy.

97 pages: Neelaksh is the first person outside of the former soviet block to have obtain FIR and MIR spectra of microtubules.

Abstract: web work in progress..

Status: As of Sept. 2004, Neelaksh is residing in Great Britain.

Kate Campbell '04

Thesis title: Applications of Scanning Tunneling Microscopy of Gap Junctions

88 pages: Kate did a heroic job of putting together this formidable project.

Abstract: web work in progress..

Status: As of Sept. 2004, Kate is working in a laboratory at OHSU.

Tim Coffey'04

Thesis title: Evanescent Waves and the Goos-Haenchen Shift of Water Waves.

46 pages: Tim's thesis is an outstanding work for a person desiring an introduction to evanescent waves in any context. Tim's appendices are particularly useful for those trying to understand total internal reflection fluorescence microscopy (TIRFM). But most importantly Tim's thesis explains the fundamental physics of the nature of evanescent waves. His thesis also have some monstrously cool references, such as the original publication of the observation of evanescent waves by none other than Sir Isaac Newton in Optiks.

Abstract: web work in progress..

Status: As of Sept. 2012, Tim had received Ph.D. in physics at the University of Texas, Austin. He is teaching modern physics at UT and eating lots of cinnamon mentos.

Owen Gross'04

Approximate Thesis title: Biophysical Mechanisms of Spike Generation Direction Selective Ganglion Cells

Scientific direction by Patrick Roberts, Senior Scientist, Neurological Science Institute, Portland, Oregon.

117 pages: Part of the reason this thesis was spectacular because Owen used both microscopic (Hodgkin-Huxley eqs.) and macrscopic approaches (Wiener Kernels) to understand the spike trains of stimulated directionally selective ganglion cells.


First-order Wiener kernels are calculated from extracellular and intercellular recordings of Direction Selective (DS) ganglion cells and used to predict spike bursts, which are compared to spike-train predictions from a Hodgkin-Huxley (HH)-like model [T. F. Weiss, Cellular Biophysics Vol. 2 (MIT press, Cambridge, MA, 1996)] of the cells created in Mathematica. A reverse correlation method is used to calculate the kernels [P. Dayan and L. Abbot, Theoretical Neuroscience (MIT press, Cambridge, MA, 2001)], which are convolved with the stimulus to estimate the response. Approximately 75% to 85% of the bursts can be predicted using this method, as demonstrated in Chapter 5.

The HH spike-train predictions are generated by transforming the stimulus into a membrane current. This method is motivated by the hypothesis that the DS cells respond linearly to stimulus velocities. The HH predictions are generally less successful that the kernel generated burst predictions. The model remains to be improved through the optimization of the method of stimulus transformation and the electrical parameters used in solving the HH equations.

The stimulus consists of an edge between a dark side and a bright side of a computer monitor that moves with random velocities along the axis parallel to the DS cell's preferred direction to stimulate the neurons. This stimulus was devised as a likely candidate to generate a high signal-to-noise ratio. Unforeseen problems arise, however, due to the temporal autocorrelations of the edge.

Status: As of Mar. 2012, Owen had just earned a Ph.D. in neuroscience    at UCD and looking for any really sour beer ;-).

Ritesh Nath '04

Approximate Thesis title: Fourier Transform Infrared Spectroscopy of Microtubules.

95 pages: Ritesh's thesis contains a spectacular review of microtubles as well as a review of the condensed matter physics and small oscillation theory required to understand his putative eigenvector assignments of the FIR and MIR bands of microtubules.

Abstract: Microtubules are tubular, polymeric aggregates of the protein tubulin. They exhibit a sophisticated dynamics, assembling and dissassembling under otherwise constant chemical conditions. Much is know about the details of this assembly behavior, but an understanding of the underlying mechanism remains elusive.

Status: Possibly in the Peace Corps under the auspices of a graduate program.

Adam Percival '05

Thesis title: The Physics of Skipping Stones.

78 pages: Adam's thesis was great fun and fantastic physics rolled up into one unforgettable experience--unfortunately I haven't skipped a stone since '05.

Abstract: A stone skipping on water is a familiar physical phenomenon to many people. The underlying physics of stone skipping, however, is surprisingly complicated and not well understood. Bocquet (2003) has provided a theoretical basis for the physics of stone skipping, and Clanet et al. (2004) have investigated stone skipping experimentally. I review the existing theory and attempt to apply it to high-speed video of skipping aluminum disks. Video analysis did not conclusively support the hypothesis of an optimal attack angle, previously reported by Clanet et al. to be 20 degrees. In addition, I confirm minimum velocity and minimum angular velocity criteria for skipping to occur, and make a number of qualitative observation based on the video.

Status: As of about 2010 Adam was working at an educational firm in Texas (?). He participated in Teach America. Teaching physics (?) in a high school in Brooklyn.

Prashant Luitel '05

Thesis title: Electrostatic Interaction During Exocytosis

pages: 62. A fantastic thesis project that we published with Darrell Schroeter in the Journal of Bimolecular Structure and Dynamics.

Abstract: The creation of a small opening called the fusion pore is a necessary prerequisite for neurotransmitter release from synaptic vesicles. It is known that high intensity electric fields can create pores in vesicles by a process called electroporation. Due to the presence of charged phosphatidylserine (PS) molecules on the inner leaflet of the cell membrane, an electric field that is strong enough to cause electroporation of a synaptic vesicle might be present. It was shown by K. Rosenheck (K. Rosenheck, Biophys. J., \bf 75\rm, 1237 (1998)) that in a planar geometry, fields sufficient to cause electroporation can occur at intermembrane separations of less than about 3 nm. It is frequently found, however, that the cell membrane is not planar but caves inward at the locations where a vesicle is close to it. Indentation of the cell membrane in the fusion region was modelled as a hemisphere and a theoretical study of the electric field in the vicinity of the cell membrane taking into account the screening effect of dissolved ions in the cytoplasm was performed. It was discovered that fields crossing the electroporation threshold occurred at a distance of 2 nm or less, supporting the claim that electroporation could be a possible mechanism for fusion pore formation.

Status: Very happy working on his Ph.D. in physics at MIT --> a project in systems biology.

Nicole Adelstein '06

Thesis title: Calculating the Depolarization Ratios for Resonance Raman Scattering by Octahedral Molecules

pages: 78. A tour de force of undergraduate theoretical physical chemistry that reminded me of learning group theory from John Page in 1980--and unfortunately forgetting it subsequently. But Nicole brought me up to speed.

Abstract: The symmetry of electronic states can be investigated using depolarization ratios from resonance Raman spectra. In particular, the depolarization ratios for vibrational peaks in a spectrum of chromium hexacarbonyl that are enhanced by resonance with a "forbidden" resonant electronic state transforming as T$_{1g}$ are calculated. These calculations do not follow obviously from similar calculations in the literature due to the triply degenerate octahedral point group of chromium hexacarbonyl.

V coefficients (also know a Clebsh-Gordon coefficients or Wigner 3j symbols) and group theory are used to calculate the depolarization ratios. The evaluation of the V coefficients is taken from J. S. Griffith [The Irreducible Tensor Method for Molecular Symmetry Groups, Prentice Hall. New Jersey, 1962. ]. This method and the theory for calculating depolarization ratios is extensively discussed. The calculated depolarization ratios for final vibronic states transforming as T$_{2u} \bigotimes T_{2u},$ T$_{1u} \bigotimes T_{2u},$ and T$_{2u} \bigotimes T_{1u}$ did not agree within the experimental uncertainty with the measured depolariation ratios for chromium hexacarbonyl [K. Wilson, (personal communication), 2002].

Status: Graduate student in Material Science, UCB, 2008.

Matt Davidson '06

Thesis title: Spatial Frequencies of Natural Scene Stimuli Determine the Response Functions in LIF Model Neurons

pages: 65. Reed's first ad hoc interdisciplinary major in Biology-Physics.

Abstract: The Fourier transform was used to create novel stimuli and
test an hypothesis that the spatial frequencies inherent
in natural scenes are responsible for the difference in
predicted and measured responses of retinal ganglion cells
to natural scenes and traditional white noise stimuli
reported by David {\em et al}. [David, S., Vinje, W. E., and Gallant,
J. L. {\em J. Neurosci.} {\bf 24}(31), 6991 (2004)].
Comparison of the power spectra of natural scenes
and traditional white noise stimuli typically used
in vision research exposed significant differences.
Autocorrelation of the newly developed, one-dimensional
natural scene stimulus revealed periodicity that was
absent in the white noise stimulus.
A linear leaky integrate-and-fire model
neuron was used to predict the
response of retinal ganglion cells to the stimuli.
The evidence collected in this investigation supports the
hypothesis that spatial frequencies within the stimuli play
a significant role in shaping the response functions.
The response to natural scene stimuli contains unique features while
the response to white noise resembles the response to constant
stimulus. This research demonstrates the importance of
spatial frequencies in visual stimuli and
emphasizes the need for further investigation
into the significance
of natural scenes in vision research through more
complex neural models and physiological experiments.

Status: As of Mar. 2012, Matt is in  Ph.D. program.

Dave Williams '06

Thesis title: Optical Tweezers: Accuracy and Automation

pages: 55. The following is a very inside joke, but here it is anyway:

Abstract: An optical tweezer system is improved through the simplification of its optics, the addition of a piezoelectric stage, the automation with LabVIEW of said stage, the use of a water immersion objective as the trap focusing lens, and the design and construction of an integrated flow cell/lighting block. The optical tweezer is used to demonstrate precise optical trapping on 1 $\mu$m dielectric particles and exert torque on 5 $\mu$m birefringent particles. The theoretical basis of these actions is presented and discussed.

This work was partially funded by a Reed Initiative Grant for Undergraduate Research.

Status: Dave's optical tweezer apparatus has been used in PHY 332 for several years.

Dewey Kim '07

Thesis title: Single Molecule Detection Using Total Internal Reflection Fluorescence Microscopy

pages: 43. Dewey's thesis has some world class MATLAB TIRF image analysis code.

Abstract: Total internal reflection fluorescence microscopy uses evanescent waves to selectively stimulate fluorophores for imaging purposes. This technique can break the diffraction limit, reaching levels of detection in optical microscopy that were previously only available to electron microscopy. Movies of Green Fluorescent Protein on a glass slide were acquired and tested for the existence of single molecule detection using image analysis algorithms programmed in MATLAB. All-or-none photobleaching effects were observed, confirming that evanescent wave microscopy is a viable method for single molecule detection.

This work is being extended in Summer 2007 thanks to a grant from the Levine Foundation.

Status: Graduate student in Biomedical Engineering at Johns Hopkins

Derek Oldridge '07

Chemistry-Physics Thesis title: Probing Conformational Changes of Streptococcal Cell Adhesion Regulator (ScaR) Protein: A $^{19}$F NMR Study

pages: work in progress--that is, the web presentation of Derek's thesis.

Abstract: work in progress--that is, the web presentation of Derek's thesis.

Status: Presently in an M.D.-Ph.D. program (?)

2008 SABBATICAL YEAR in Christien Merrifield's laboratory in Cambridge, England.

Ryan Loney '09

Physics Thesis title: Getting awesome about clathrin spectroscopy

pages: website work in progress.

Abstract: website work in progress.

Status: Presently publishing a paper in the Biophysical Journal based on work in a lab at OHSU.

Tristan Hormel '09

Physics Thesis title: Polarized Total Internal Reflection Fluorescence Microscopy

pages: 60 -- including some excellent MATLAB code on the theory of pTIRF.


Several biological macromolecules are known to be involved in the endocytosis of materials across a cell membrane.  The functional role of one such macromolecule, clathrin, is not well understood.  For various and different reasons, many experimental techniques employed in the study of other biological phenomena are incapable of determining the purpose of clathrin structures that form around the vesicles that bud from the membrane during endocytosis.

Polarized internal reflection fluorescence microscopy (PTIRFM) is a technique that may, among other uses, be able to assign clathrin a role in endocytosis.  PTIRFM uses (essentially) three physical principles/phenomena to form a representative image of the cell membrane that contains unambiguous information concerning its orientation.  The topology of the cell membrane of the cell membrane is of particular concern in events such as endocytosis, and so in addition to the possibility of expanding our understanding of clathrin PTIRFM is a promising avenue of inquiry into endocytosis in general.

Two topics are considered, one biological and one physical.  The first is the role of endocytosis within the (much larger) context of neurophysiology.  The second is the theory behind the construction and operation of the PTIRF microscope.

Status: Presently in the Physics Ph.D. program at the University of Oregon.