Physics Commons^™

Kinetic Monte Carlo Simulations Of Quantum Dot Self-Assembly, Matthew Abramson, Hunter J. Coleman, Paul J. Simmonds, Tim P. Schulze, Christian Ratsch

Physics Faculty Publications and Presentations

In the Stranski–Krastanov growth mode for heteroepitaxial systems, layer-by-layer growth is followed by the formation and growth of three-dimensional (3D) islands. In this paper, we use a kinetic Monte Carlo method to simulate this growth mode behavior. We present a detailed and systematic investigation into the effects of key model parameters including strain, growth temperature, and deposition rate on this phenomenon. We show that increasing the strain lowers the apparent critical thickness that is defined by the onset of 3D island formation. Similarly, increasing the growth temperature lowers the apparent critical thickness, until intermixing, and the resulting relevance of entropic …

Binding Of Alpha-Crystallin To Cortical And Nuclear Lens Lipid Membranes Derived From A Single Lens, Raju Timsina, Samantha Wellisch, Dieter Haemmerle, Laxman Mainali

Physics Faculty Publications and Presentations

Several studies reported that α-crystallin concentrations in the eye lens cytoplasm decrease with a corresponding increase in membrane-bound α-crystallin with age and cataracts. The influence of the lipid and cholesterol composition difference between cortical membrane (CM) and nuclear membrane (NM) on α-crystallin binding to membranes is still unclear. This study uses the electron paramagnetic resonance (EPR) spin-labeling method to investigate the α-crystallin binding to bovine CM and NM derived from the total lipids extracted from a single lens. Compared to CMs, NMs have a higher percentage of membrane surface occupied by α-crystallin and binding affinity, correlating with less mobility and …

Liposome Formulation For Tumor-Targeted Drug Delivery Using Radiation Therapy, Daniel Fologea

Physics Faculty Publications and Presentations

Targeted delivery of drugs or other therapeutic agents through internal or external triggers has been used to control and accelerate the release from liposomal carriers in a number of studies, but relatively few utilize energy of therapeutic X-rays as a trigger. We have synthesized liposomes that are triggered by ionizing radiation (RTLs) to release their therapeutic payload. These liposomes are composed of natural egg phosphatidylethanolamine (PE), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), cholesterol, and 1,2-disteroyl-sn-glycero-3-phosphoethanolamine-N-[methoxy (polyethylene glycol)-2000] (DSPE-PEG-2000), and the mean size of the RTL was in the range of 114 to 133 nm, as measured by nanoparticle tracking analysis (NTA). The trigger mechanism …

Transient Vision Loss Associated With Prefilled Aflibercept Syringes: A Case Series And Analysis Of Injection Force, Daniel J. Lee, Brittni A. Scruggs, Erik J. Sánchez, Merina Thomas, Ambar Faridi

Physics Faculty Publications and Presentations

Purpose

To describe cases of significant vision loss after intravitreal aflibercept administration using prefilled syringes (PFS) and to study the relationships among syringe design, injection speed, and injection force.

Design

Retrospective case series and experimental study.

Participants

Twelve patients who received intravitreal aflibercept via PFS.

Methods

All retina specialists (n = 13) at Oregon Health & Science University and the Veterans Affairs Portland Medical Center were queried in December 2020 to report episodes of significant vision loss after aflibercept PFS use. Chart review was completed for all affected patients. Using a commercially available force measuring system, injection force was measured …

Biogeochemical Responses To Mixing Of Glacial Meltwater And Hot Spring Discharge In The Mount St. Helens Crater, Ashley Dubnick, Q. Faber, J. R. Hawkings, N. Bramall, B. C. Christner, Peter T. Doran, Jay Nadeau, C. Snyder, Multiple Additional Authors

Physics Faculty Publications and Presentations

Environments where geothermal waters and glacier meltwater mix are common on Earth yet little is known about the biogeochemical processes that occur when hot, reduced geothermal water mixes with cold, oxidized glacial meltwater in natural systems. Mount St. Helens provides an ideal location to study the interaction between geothermal and glacier waters since the water sources, and their mixing environment in Step Creek, are exposed in the volcanic crater. We find that the two water sources contain distinct major ion, trace element, dissolved organic matter (DOM), and biological signatures. The hot spring contains high concentrations of biogeochemically reactive components (e.g., …

Optical Selection Bias And Projection Effects In Stacked Galaxy Cluster Weak Lensing, Hao-Yi Wu

Physics Faculty Publications and Presentations

Cosmological constraints from current and upcoming galaxy cluster surveys are limited by the accuracy of cluster mass calibration. In particular, optically identified galaxy clusters are prone to selection effects that can bias the weak lensing mass calibration. We investigate the selection bias of the stacked cluster lensing signal associated with optically selected clusters, using clusters identified by the redMaPPer algorithm in the Buzzard simulations as a case study. We find that at a given cluster halo mass, the residuals of redMaPPer richness and weak lensing signal are positively correlated. As a result, for a given richness selection, the stacked lensing …

Synthesis Of Metastable Ruddlesden–Popper Titanates, (ATio3)NAO, With N ≥ 20 By Molecular-Beam Epitaxy, Matthew R. Barone, Myoungho Jeong, Nicholas Parker, Jiaxin Sun, Dmitri A. Tenne, Kiyoung Lee, Darrell G. Schlom

Physics Faculty Publications and Presentations

We outline a method to synthesize (ATiO₃)_nAO Ruddlesden–Popper phases with high-n, where the A-site is a mixture of barium and strontium, by molecular-beam epitaxy. The precision and consistency of the method described is demonstrated by the growth of an unprecedented (SrTiO₃)₅₀SrO epitaxial film. We proceed to investigate barium incorporation into the Ruddlesden–Popper structure, which is limited to a few percent in bulk, and we find that the amount of barium that can be incorporated depends on both the substrate temperature and the strain state of the …

An Integral Transform For Quantum Amplitudes, Jack C. Straton

Physics Faculty Publications and Presentations

The central impediment to reducing multidimensional integrals of transition amplitudes to analytic form, or at least to a fewer number of integral dimensions, is the presence of magnitudes of coordinate vector differences (square roots of polynomials) |x1−x2|2=x21−2x1x2cosθ+x2 √ in disjoint products of functions. Fourier transforms circumvent this by introducing a three-dimensional momentum integral for each of those products, followed in many cases by another set of integral transforms to move all of the resulting denominators into a single quadratic form in one denominator whose square my be completed. Gaussian transforms introduce a one-dimensional integral for each such product while squaring …

Membrane Elasticity Modulated By Cholesterol In Model Of Porcine Eye Lens-Lipid Membrane, Nawal K. Khadka, Max-Florian Mortimer, Mason Marosvari, Raju Timsina, Laxman Mainali

Physics Faculty Publications and Presentations

Experimental evidence shows that the eye lens loses its elasticity dramatically with age. It has also been reported that the cholesterol (Chol) content in the eye lens fiber cell plasma membrane increases significantly with age. High Chol content leads to the formation of cholesterol bilayer domains (CBDs) in the lens membrane. The role of high Chol associated with lens elasticity is unclear. The purpose of this research is to investigate the membrane elasticity of the model of porcine lens-lipid (MPLL) membrane with increasing Chol content to elucidate the role of high Chol in lens membrane elasticity. In this study, we …

A Multi-City Urban Atmospheric Greenhouse Gas Measurement Data Synthesis, Logan E. Mitchell, John C. Lin, Lucy R. Hutyra, David R. Bowling, Ronald C. Cohen, Kenneth J. Davis, Elizabeth Digangi, Riley M. Duren, Andrew Rice, Multiple Additional Authors

Physics Faculty Publications and Presentations

Urban regions emit a large fraction of anthropogenic emissions of greenhouse gases (GHG) such as carbon dioxide (CO2) and methane (CH4) that contribute to modern-day climate change. As such, a growing number of urban policymakers and stakeholders are adopting emission reduction targets and implementing policies to reach those targets. Over the past two decades research teams have established urban GHG monitoring networks to determine how much, where, and why a particular city emits GHGs, and to track changes in emissions over time. Coordination among these efforts has been limited, restricting the scope of analyses and insights. Here we present a …

Alpha-Crystallin Association With The Model Of Human And Animal Eye Lens-Lipid Membranes Is Modulated By Surface Hydrophobicity Of Membranes, Raju Timsina, Geraline Trossi-Torres, Jackson Thieme, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali

Physics Faculty Publications and Presentations

Purpose

This research aims to probe the interaction of α-crystallin with a model of human, porcine, and mouse lens-lipid membranes.

Methods

Cholesterol/model of human lens-lipid (Chol/MHLL), cholesterol/model of porcine lens-lipid (Chol/MPLL), and cholesterol/model of mouse lens-lipid (Chol/MMLL) membranes with 0–60 mol% Chol were prepared using the rapid solvent exchange method and probe-tip sonication. The hydrophobicity near the surface of model lens-lipid membranes and α-crystallin association with these membranes were investigated using the electron paramagnetic resonance spin-labeling approach.

Results

With increased Chol content, the hydrophobicity near the surface of Chol/MHLL, Chol/MPLL, and Chol/MMLL membranes, the maximum percentage of membrane surface occupied …

Experimental Investigations On The Conductance Of Lipid Membranes Under Differential Hydrostatic Pressure, Rose Whiting, Pangaea W. Finn, Andrew Bogard, Fulton Mckinney, Dallin Pankratz, Aviana R. Smith, Elen A. Gardner, Daniel Fologea

Physics Faculty Publications and Presentations

The unassisted transport of inorganic ions through lipid membranes has become increasingly relevant to an expansive range of biological phenomena. Recent simulations indicate a strong influence of a lipid membrane’s curvature on its permeability, which may be part of the overall cell sensitivity to mechanical stimulation. However, most ionic permeability experiments employ a flat, uncurved lipid membrane, which disregards the physiological relevance of curvature on such investigations. To fill this gap in our knowledge, we adapted a traditional experimental system consisting of a planar lipid membrane, which we exposed to a controlled, differential hydrostatic pressure. Our electrophysiology experiments indicate a …

An Afm Approach Applied In A Study Of Α-Crystallin Membrane Association: New Insights Into Lens Hardening And Presbyopia Development, Nawal K. Khadka, Raju Timsina, Laxman Mainali

Physics Faculty Publications and Presentations

The lens of the eye loses elasticity with age, while α-crystallin association with the lens membrane increases with age. It is unclear whether there is any correlation between α-crystallin association with the lens membrane and loss in lens elasticity. This research investigated α-crystallin membrane association using atomic force microscopy (AFM) for the first time to study topographical images and mechanical properties (breakthrough force and membrane area compressibility modulus (K_A), as measures of elasticity) of the membrane. α-Crystallin extracted from the bovine lens cortex was incubated with a supported lipid membrane (SLM) prepared on a flat mica surface. The …

Objective Crystallographic Symmetry Classifications Of A Noisy Crystal Pattern With Strong Fedorov-Type Pseudo­Symmetries And Its Optimal Image-Quality Enhancement, Peter Moeck

Physics Faculty Publications and Presentations

Statistically sound crystallographic symmetry classifications are obtained with information-theory-based methods in the presence of approximately Gaussian distributed noise. A set of three synthetic patterns with strong Fedorov-type pseudo­symmetries and varying amounts of noise serve as examples. Contrary to traditional crystallographic symmetry classifications with an image processing program such as CRISP, the classification process does not need to be supervised by a human being and is free of any subjectively set thresholds in the geometric model selection process. This enables crystallographic symmetry classification of digital images that are more or less periodic in two dimensions (2D), also known as crystal …

Alpha-Crystallin-Membrane Association Modulated By Phospholipid Acyl Chain Length And Degree Of Unsaturation, Geraline Trossi-Torres, Raju Timsina, Laxman Mainali

Physics Faculty Publications and Presentations

α-crystallin-membrane association increases with age and cataracts, with the primary association site of α-crystallin being phospholipids. However, it is unclear if phospholipids’ acyl chain length and degree of unsaturation influence α-crystallin association. We used the electron paramagnetic resonance approach to investigate the association of α-crystallin with phosphatidylcholine (PC) membranes of different acyl chain lengths and degrees of unsaturation and with and without cholesterol (Chol). The association constant (K_a) of α-crystallin follows the trends, i.e., K_a (14:0–14:0 PC) > K_a (18:0–18:1 PC) > K_a (18:1–18:1 PC) ≈ K_a (16:0–20:4 PC) where the presence of Chol decreases K …

Quantification Of Motility In Bacillus Subtilis At Temperatures Up To 84°C Using A Submersible Volumetric Microscope And Automated Tracking, Megan M. Dubay, Nikki Johnston, Mark Wronkiewicz, Jake Lee, Chris Lindensmith, Jay Nadeau

Physics Faculty Publications and Presentations

We describe a system for high-temperature investigations of bacterial motility using a digital holographic microscope completely submerged in heated water. Temperatures above 90°C could be achieved, with a constant 5°C offset between the sample temperature and the surrounding water bath. Using this system, we observed active motility in Bacillus subtilis up to 66°C. As temperatures rose, most cells became immobilized on the surface, but a fraction of cells remained highly motile at distances of >100 μm above the surface. Suspended non-motile cells showed Brownian motion that scaled consistently with temperature and viscosity. A novel open-source automated tracking package was used …

Coil-To-Bridge Transitions Of Self-Assembled Water Chains Observed In A Nanoscopic Meniscus, Byung I. Kim, Ryan D. Boehm, Harrison Agrusa

Physics Faculty Publications and Presentations

Ten downward portions in the large oscillatory force–distance curve reported earlier are analyzed to understand a nanoscale water meniscus confined between a sharp probe and a flat substrate in air. The sigmoidal shape of each portion leads to the assumption that the meniscus is made up of n independent transitions of two states: one for a coil state and the other for a bridge state. The analysis reveals that each downward portion occurs due to a coil-to-bridge transition of n self-assembled water chains whose length ranges between 197 and 383 chain units. The transition provides novel insights into water’s unique …

Exploiting Non-Linear Scales In Galaxy–Galaxy Lensing And Galaxy Clustering: A Forecast For The Dark Energy Survey, Andrés N. Salcedo, David H. Weinberg, Hao-Yi Wu, Benjamin D. Wibking

Physics Faculty Publications and Presentations

No abstract provided.

Maximum Entropy And Constraints In Composite Systems, John D. Ramshaw

Physics Faculty Publications and Presentations

The principle of maximum entropy (PME), as expounded by Jaynes, is based on the maximization of the Boltzmann-Gibbs-Shannon (BGS) entropy subject to linear constraints. The resulting probability distributions are of canonical (exponential) form. However, the rationale for linear constraints is nebulous, and probability distributions are not always canonical. Here we show that the correct noncanonical distribution for a system in equilibrium with a finite heat bath is implied by the unconstrained maximization of the total BGS entropy of the system and bath together. This procedure is shown to be equivalent to maximizing the BGS entropy of the system alone subject …

Effect Of As Flux On Inas Submonolayer Quantum Dot Formation For Infrared Photodetectors, K. D. Vallejo, P. J. Simmonds

Physics Faculty Publications and Presentations

The performance of infrared photodetectors based on submonolayer quantum dots was investigated as a function of the arsenic flux. All the devices showed similar figures of merit and a very high specific detectivity above 1 × 10¹¹ cm Hz^1/2/W at 12 K, despite the fact that cross-sectional scanning tunneling microscopy images pointed out a strong reduction in the density of such nanostructures with decreasing arsenic flux. This contrast is a consequence of the small size and low In content of the submonolayer quantum dots that lead to a strong delocalization of the electrons wave function and, therefore, …

Vortices And Dust Devils As Observed By The Mars Environmental Dynamics Analyzer Instruments On Board The Mars 2020 Perseverance Rover, Brian Jackson

Physics Faculty Publications and Presentations

An important and perhaps dominant source of dust in the Martian atmosphere, dust devils play a key role in Mars' climate. Data sets from previous landed missions have revealed dust devil activity, constrained their structures, and elucidated their dust-lifting capacities. However, each landing site and observational season exhibits unique meteorological properties that shape dust devil activity and illuminate their dependence on ambient conditions. The recent release of data from the Mars Environmental Dynamics Analyzer (MEDA) instrument suite on board the Mars 2020 Perseverance rover promises a new treasure trove for dust devil studies. In this study, we sift the time …

Clmm: A Lsst-Desc Cluster Weak Lensing Mass Modeling Library For Cosmology, H. Wu

Physics Faculty Publications and Presentations

We present the v1.0 release of CLMM, an open source PYTHON library for the estimation of the weak lensing masses of clusters of galaxies. CLMM is designed as a stand-alone toolkit of building blocks to enable end-to-end analysis pipeline validation for upcoming cluster cosmology analyses such as the ones that will be performed by the Vera C. Rubin Legacy Survey of Space and Time-Dark Energy Science Collaboration (LSST-DESC). Its purpose is to serve as a flexible, easy-to-install, and easy-to-use interface for both weak lensing simulators and observers and can be applied to real and mock data to study the systematics …

2d Vs 3d Tracking In Bacterial Motility Analysis, Jacqueline Acres, Jay Nadeau

Physics Faculty Publications and Presentations

Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the …

The Ionic Selectivity Of Lysenin Channels In Open And Sub-Conducting States, Andrew Bogard, Pangaea W. Finn, Fulton Mckinney, Ilinca M. Flacau, Aviana R. Smith, Rosey Whiting, Daniel Fologea

Physics Faculty Publications and Presentations

The electrochemical gradients established across cell membranes are paramount for the execution of biological functions. Besides ion channels, other transporters, such as exogenous pore-forming toxins, may present ionic selectivity upon reconstitution in natural and artificial lipid membranes and contribute to the electrochemical gradients. In this context, we utilized electrophysiology approaches to assess the ionic selectivity of the pore-forming toxin lysenin reconstituted in planar bilayer lipid membranes. The membrane voltages were determined from the reversal potentials recorded upon channel exposure to asymmetrical ionic conditions, and the permeability ratios were calculated from the fit with the Goldman–Hodgkin–Katz equation. Our work shows that …

Inferring Vortex And Dust Devil Statistics From Insight, Brian Jackson, Justin Crevier, Michelle Szurgot, Ryan Battin, Clément Perrin, Sébastien Rodriguez

Physics Faculty Publications and Presentations

The InSight mission has operated on the surface of Mars for nearly two Earth years, returning detections of the first marsquakes. The lander also deployed a meteorological instrument package and cameras to monitor local surface activity. These instruments have detected boundary layer phenomena, including small-scale vortices. These vortices register as short-lived, negative pressure excursions and closely resemble those that could generate dust devils. Although our analysis shows that InSight encountered more than 900 vortices and collected more than 1000 images of the Martian surface, no active dust devils were imaged. In spite of the lack of dust devil detections, we …

Phosphine Generation Pathways On Rocky Planets, Arthur Omran, Christopher Oze, Brian Jackson, Chris Mehta, Laura M. Barge, Jeffrey Bada, Matthew A. Pasek

Physics Faculty Publications and Presentations

The possibility of life in the venusian clouds was proposed in the 1960s, and recently this hypothesis has been revived with the potential detection of phosphine (PH₃) in Venus' atmosphere. These observations may have detected ∼5–20 ppb phosphine on Venus (Greaves et al., 2020), which raises questions about venusian atmospheric/geochemical processes and suggests that this phosphine could possibly be generated by biological processes. In such a claim, it is essential to understand the abiotic phosphorus chemistry that may occur under Venus-relevant conditions, particularly those processes that may result in phosphine generation. Here, we discuss two related abiotic …

Microscopic Object Classification Through Passive Motion Observations With Holographic Microscopy, Christian Lindensmith, Jay Nadeau, Manuel Bedrossian, Louis Sumrall, J. Kent Wallace, Eugene Serabyn

Physics Faculty Publications and Presentations

Digital holographic microscopy provides the ability to observe throughout a volume that is large compared to its resolution element without the need to refocus through the volume. This capability enables simultaneous observations of large numbers of small objects within such a volume. We have constructed a microscope that can observe a volume 0.4 x 0.4 x 1.0 μm with submicrometer resolution for observation of microorganisms and minerals in liquid environments in earth and on potential planetary missions. Because environmental samples are likely to contain mixtures of inorganics and microorganisms that are of comparable sizes near the resolution limit of the …

Mechanical Properties Of The High Cholesterol-Containing Membrane: An Afm Study, Nawal K. Khadka, Raju Timsina, Erica L. Rowe, Matthew O'Dell, Laxman Mainali

Physics Faculty Publications and Presentations

Cholesterol (Chol) content in most cellular membranes does not exceed 50 mol%, only in the eye lens’s fiber cell plasma membrane, its content surpasses 50 mol%. At this high concentration, Chol induces the formation of pure cholesterol bilayer domains (CBDs), which coexist with the surrounding phospholipid-cholesterol domain (PCD). Here, we applied atomic force microscopy to study the mechanical properties of Chol/phosphatidylcholine membranes where the Chol content was increased from 0 to 75 mol%, relevant to eye lens membranes. The surface roughness of the membrane decreases with an increase of Chol content until it reaches 60 mol%, and roughness increases with …

Association Of Alpha-Crystallin With Fiber Cell Plasma Membrane Of The Eye Lens Accompanied By Light Scattering And Cataract Formation, Raju Timsina, Laxman Mainali

Physics Faculty Publications and Presentations

α-crystallin is a major protein found in the mammalian eye lens that works as a molecular chaperone by preventing the aggregation of proteins and providing tolerance to stress in the eye lens. These functions of α-crystallin are significant for maintaining lens transparency. However, with age and cataract formation, the concentration of α-crystallin in the eye lens cytoplasm decreases with a corresponding increase in the membrane-bound α-crystallin, accompanied by increased light scattering. The purpose of this review is to summarize previous and recent findings of the role of the: (1) lens membrane components, i.e., the major phospholipids (PLs) and sphingolipids, cholesterol …

Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea

Physics Faculty Publications and Presentations

Liposomes are spherical-shaped vesicles that enclose an aqueous milieu surrounded by bilayer or multilayer membranes formed by self-assembly of lipid molecules. They are intensively exploited as either model membranes for fundamental studies or as vehicles for delivery of active substances in vivo and in vitro. Irrespective of the method adopted for production of loaded liposomes, obtaining the final purified product is often achieved by employing multiple, time consuming steps. To alleviate this problem, we propose a simplified approach for concomitant production and purification of loaded liposomes by exploiting the Electrodialysis-Driven Depletion of charged molecules from solutions. Our investigations show that …