Biological and Chemical Physics Commons^™

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Flash-Rt: Using High-Dose Radiation For Clinical Radiation Therapy, Deja Stubbs

University Honors Theses

This paper is a literature review on the possible mechanisms behind the FLASH effect and why such research can advance the world of radiology treatment by modifying current clinical linear accelerators to produce ultra-high doses of radiation. Radiation Therapy, also known as external Beam Radiation Therapy, is a common type of cancer treatment. Globally, cancer is the second-leading cause of death, but has seen an increase in survival rates over the past couple of years. Cancer can develop in almost any part of the body since cancer is defined as uncontrolled cell growth. The FLASH Effect is seen when treating …

A Machine Learning Algorithm For Identifying And Tracking Bacteria In Three Dimensions Using Digital Holographic Microscopy, Manuel Bedrossian, Marwan El-Kholy, Daniel Neamati, Jay Nadeau

Physics Faculty Publications and Presentations

Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of microorganisms due to its high throughput and large depth of field relative to traditional microscopy techniques. While it has shown substantial success for use with eukaryotes, it has proven challenging for bacterial imaging because of low contrast and sources of noise intrinsic to the method (e.g. laser speckle). This paper describes a custom written MATLAB routine using machine-learning algorithms to obtain three-dimensional trajectories of live, lab-grown bacteria as they move within an essentially unrestrained environment with more than 90% precision. A fully annotated version of the software used …

Mixing Times Of Organic Molecules Within Secondary Organic Aerosol Particles: A Global Planetary Boundary Layer Perspective, Adrian M. Maclean, Christopher L. Butenhoff, James W. Grayson, Kelley Barsanti, Jose L. Jimenez, Allan K. Bertram

Physics Faculty Publications and Presentations

When simulating the formation and life cycle of secondary organic aerosol (SOA) with chemical transport models, it is often assumed that organic molecules are well mixed within SOA particles on the timescale of 1 h. While this assumption has been debated vigorously in the literature, the issue remains unresolved in part due to a lack of information on the mixing times within SOA particles as a function of both temperature and relative humidity. Using laboratory data, meteorological fields, and a chemical transport model, we estimated how often mixing times are < 1 h within SOA in the planetary boundary layer (PBL), the region of the atmosphere where SOA concentrations are on average the highest. First, a parameterization for viscosity as a function of temperature and RH was developed for α-pinene SOA using room-temperature and low-temperature viscosity data for α-pinene SOA generated in the laboratory using mass concentrations of ∼ 1000 µg m−3. Based on this parameterization, the mixing times within α-pinene SOA are < 1 h for 98.5 % and 99.9 % of the occurrences in the PBL during January and July, respectively, when concentrations are significant (total organic aerosol concentrations are > 0.5 µg m−3 at the surface). Next, as a starting …

Communication: Visualization And Spectroscopy Of Defects Induced By Dehydrogenation In Individual Silicon Nanocrystals, Dmitry A. Kislitsyn, Jon M. Mills, Vancho Kocevski, Sheng-Kuei Chiu, William J.I. Debenedetti, Christian F. Gervasi, Benjamen N. Taber, Ariel E. Rosenfield, Olle Eriksson, Ján Rusz, Andrea Mitchell Goforth, George V. Nazin

Chemistry Faculty Publications and Presentations

We present results of a scanning tunneling spectroscopy (STS) study of the impact of dehydrogenation on the electronic structures of hydrogen-passivated silicon nanocrystals (SiNCs) supported on the Au(111)surface. Gradual dehydrogenation is achieved by injecting high-energy electrons into individual SiNCs, which results, initially, in reduction of the electronic bandgap, and eventually produces midgap electronic states. We use theoretical calculations to show that the STS spectra of midgap states are consistent with the presence of silicon dangling bonds, which are found in different charge states. Our calculations also suggest that the observed initial reduction of the electronic bandgap is attributable to the …

Mapping Of Defects In Individual Silicon Nanocrystals Using Real- Space Spectroscopy, Dmitry A. Kislitsyn, Vancho Kocevski, Jon M. Mills, Sheng-Kuei Chiu, Christian F. Gervasi, Benjamen N. Taber, Ariel E. Rosenfield, Olle Eriksson, Ján Rusz, Andrea Mitchell Goforth, George V. Nazin

Chemistry Faculty Publications and Presentations

The photophysical properties of silicon semiconductor nanocrystals (SiNCs) are extremely sensitive to the presence of surface chemical defects, many of which are easily produced by oxidation under ambient conditions. The diversity of chemical structures of such defects and the lack of tools capable of probing individual defects continue to impede understanding of the roles of these defects in SiNC photophysics. We use scanning tunneling spectroscopy to study the impact of surface defects on the electronic structures of hydrogen-passivated SiNCs supported on the Au(111) surface. Spatial maps of the local electronic density of states (LDOS) produced by our measurements allowed us …

Shaping The Future Past: Finding History, Creating Identity In The Kwan Hsu Papers, Lisa Chere' Donnelly

Dissertations and Theses

Dr. Kwan Hsu was neither a superstar nor a celebrity. Her name does not come up in conversations about important contributors to her field of biophysics nor is she instantly recognizable for her contributions to Portland State University's international program or the state of Oregon's business ties with China. Yet she was a contributor, a cog-in-the-wheel, at the very least, in all of these areas and more. She was a peripheral member of a well-known Chinese family, but few in the United States know of or perhaps have interest in, but otherwise, she had no great connections or family ties …

The Temperature Dependent Modification Of The Ca2+ Release Mechanism Of Skeletal Muscle Sarcoplasmic Reticulum, Shawn Patrick Mullen

Dissertations and Theses

The Ca²⁺ release protein/ryanodine receptor from skeletal muscle sarcoplasmic reticulum is shown to be modulated in a unique manner by small changes in temperature. Thiol oxidants and reducing agents modify channel function in a biphasic manner at 40° C, while at 34° C the channel exhibits only a monophasic behavior. Elevated temperature appears to expose a second set of reactive groups that, when either oxidized or reduced, alter function. Previous studies have focused on the properties of the release mechanism at or below 37° C. This study shows that at 40° C, which more reflects the body temperature of …

Copper Electrodeposition In A Magnetic Field, Hiroshi Takeo

Dissertations and Theses

The effect of a magnetic field on copper electrodeposition was investigated. Copper was electrodeposited onto square copper cathodes 1 sq cm in area from an aqueous solution (0.5 M CuSO₄, 0.5 M H₂SO₄. A glass cell was placed between the pole pieces of an electromagnet, and the magnetic fields applied were in the range from 0 to 12.5 kG. The current density was in the range from 80 mA/sq cm to 880 mA/sq cm. In each of the experiments, cell current, cell voltage, and cell temperature were monitored with a microcomputer. The weight …

Alternating Current Studies And Kinetic Analysis Of Valinomycin Mediated Charge-Transport Through Lipid Bilayer Membranes, Kenneth Lee Cox

Dissertations and Theses

In this study we have investigated the frequency dependence of bilayer lipid membranes for a series of glycerylmonoolein/n-decane bilayers in various aqueous ionic solutions containing the ionophore valinomycin. Reliable values of membrane capacitance and conductance were obtained over the frequency range 0.2 - 200 KHz using an automatic balancing bridge under the control of a microprocessor unit. The admittance data was then normalized and curve-fitted to produce relaxation times and amplitudes from which the kinetic rate parameters, as deduced from a single slab dielectric membrane model, were calculated. These ac experimental rate constants were then compared with those obtained from …

Investigation Of The Alpha-Sub-Gamma Phase In Alnico 6, Cortez Samuel

Dissertations and Theses

The purpose of this research project was to study the αᵧ phase in Alnico 6. Other phases were studies for comparison. Also the effect of an applied magnetic field on the formation of the αᵧ phase was investigated.

Three single crystals of Alnico 6 were heat treated for one hour--one at 1250°C, one at 1000°C, and one at 800°C--and water-quenched. The microstructure of each sample was observed with the optical microscope, and X-ray diffraction patterns were taken to determine the crystal structure of the phases present.

Several single crystal samples of Alnico 6 were heat treated at 1000°C and furnace-cooled. …