Physics Commons^™

Buzzard To Cardinal: Improved Mock Catalogs For Large Galaxy Surveys, Chun-Hao To, Joseph Derose, Risa H. Wechsler, Eli Rykoff, Hao-Yi Wu, Susmita Adhikari, Elisabeth Krause, Eduardo Rozo, David H. Weinberg

Physics Faculty Publications and Presentations

We present the Cardinal mock galaxy catalogs, a new version of the Buzzard simulation that has been updated to support ongoing and future cosmological surveys, including the Dark Energy Survey (DES), DESI, and LSST. These catalogs are based on a one-quarter sky simulation populated with galaxies out to a redshift of z = 2.35 to a depth of m_r = 27. Compared to the Buzzard mocks, the Cardinal mocks include an updated subhalo abundance matching model that considers orphan galaxies and includes mass-dependent scatter between galaxy luminosity and halo properties. This model can simultaneously fit galaxy clustering and group–galaxy …

The Dynamic Universe: Realizing The Potential Of Classical Time Domain And Multimessenger Astrophysics, Steve B. Howell, D. Andrew Howell, R. A. Street, Melinda Soares-Furtado, Brian Jackson, Thomas P. Greene

Physics Faculty Publications and Presentations

In parallel with the multi-messenger revolution, major advances in time-domain astronomy across multiple science disciplines relevant to astrophysics are becoming more urgent to address. Aside from electromagnetic observations of gravitational wave events and explosive counterparts, there are a number of “classical” astrophysical areas that require new thinking for proper exploration in the time domain. How NASA, NSF, ESA, and ESO consider the 2020 USA Decadal Survey within the astronomy community, as well as the worldwide call to support and expand time domain and multi-messenger astrophysics, it is crucial that all areas of astrophysics, including stellar, galactic, Solar System, and exoplanetary …

Electromagnetic Fields And Radiation From Localized Current Source Interacting With A Cosmic Axion Field In The Context Of Massive Axion Electrodynamics, Railing Chang, P. T. Leung

Physics Faculty Publications and Presentations

Electromagnetic fields from localized current source interacting with an oscillatory cosmic axion field are studied, accounting for the possibility of a finite photon mass. In particular, focus will be on the dipole radiation from static current sources. The Proca theory is generalized to include the axion field and solutions to the modified EM field equations are obtained to first order in the axion coupling parameter. Analysis of the interplay between the two vanishingly small parameters – the axion mass (via the coupling constant and the oscillating frequency) and the photon mass – is carried out with reference to possible future …

The Use Of Fluorescence Lifetime Imaging (Flim) For In Situ Microbial Detection In Complex Mineral Substrates, Yekaterina G. Chmykh, Jay Nadeau

Physics Faculty Publications and Presentations

The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging. It was found that FLIM …

The Influence Of Subhaloes On Host Halo Properties, Lorena Mezini, Catherine E. Fielder, Andrew R. Zentner, Yao-Yuan Mao, Kuan Wang, Hao-Yi Wu

Physics Faculty Publications and Presentations

Within the ΛCDM cosmology, dark matter haloes are composed of both a smooth component and a population of smaller gravitationally bound subhaloes. These components are often treated as a single halo when properties, such as density profiles, are extracted from simulations. Recent work has shown that density profiles change substantially when subhalo mass is excluded. In this paper, we expand on this result by analysing three specific host halo properties – concentration (c_NFW), spin (λ_B), and shape (c/a) – when calculated only from the smooth component of the halo. This analysis …

Interaction Of ΒL- And Γ-Crystallin With Phospholipid Membrane Using Atomic Force Microscopy, Nawal K. Khadka, Preston Hazen, Dieter Haemmerle, Laxman Mainali

Physics Faculty Publications and Presentations

Highly concentrated lens proteins, mostly β- and γ-crystallin, are responsible for maintaining the structure and refractivity of the eye lens. However, with aging and cataract formation, β- and γ-crystallin are associated with the lens membrane or other lens proteins forming high-molecular-weight proteins, which further associate with the lens membrane, leading to light scattering and cataract development. The mechanism by which β- and γ-crystallin are associated with the lens membrane is unknown. This work aims to study the interaction of β- and γ-crystallin with the phospholipid membrane with and without cholesterol (Chol) with the overall goal of understanding the role of …

Quantum Criticality At Cryogenic Melting Of Polar Bubble Lattices, Wei Luo, Alireza Akbarzadeh, Yousra Nahas, Sergei Prokhorenko, Laurent Bellaiche

Physics Faculty Publications and Presentations

Quantum fluctuations (QFs) caused by zero-point phonon vibrations (ZPPVs) are known to prevent the occurrence of polar phases in bulk incipient ferroelectrics down to 0 K. On the other hand, little is known about the effects of QFs on the recently discovered topological patterns in ferroelectric nanostructures. Here, by using an atomistic effective Hamiltonian within classical Monte Carlo (CMC) and path integral quantum Monte Carlo (PI-QMC), we unveil how QFs affect the topology of several dipolar phases in ultrathin Pb(Zr_0.4Ti_0.6)O₃ (PZT) films. In particular, our PI-QMC simulations show that the ZPPVs do not suppress polar …

Extended Planar Defects Of Oxygen Vacancies In Ferroelectric Batio3 And Impact On Ferroelectricity, Shaohui Qiu, Huaxiang Fu

Physics Faculty Publications and Presentations

Extended defects of vacancies in ferroelectrics (FE), where vacancies spread over an extended space, are of critical importance in terms of understanding the long-standing problems such as polarization fatigue and aging. However, extended defects in FEs are poorly understood. Here we investigate the extended planar oxygen vacancies in ferroelectric BaTiO₃ using density functional theory and the modern theory of polarization. Oxygen vacancies of different charge states, namely V ²⁺_O , V ¹⁺_O , and V ⁰_O , are studied. We obtain interesting results such as: (i) The formation energy of planar V ²⁺_O vacancies can …

Luminous Radio Emission From The Superluminous Supernova 2017ens At 3.3 Yr After Explosion, Raffaella Margutti, J. S. Bright, D. J. Matthews, D. L. Coppejans, K. D. Alexander, E. Berger, M. Bietenholz, R. Chornock, L. Demarchi, M. R. Drout, T. Eftekhari, W. V. Jacobson-Galán, T. Laskar, D. Milisavljevic, K. Murase, M. Nicholl, C. M. B. Omand, M. Stroh, G. Terreran, B. A. Vanderley

Physics Faculty Publications and Presentations

We present the results from a multiyear radio campaign of the superluminous supernova (SLSN) SN 2017ens, which yielded the earliest radio detection of an SLSN to date at the age of ∼3.3 yr after explosion. SN 2017ens was not detected at radio frequencies in the first ∼300 days but reached L_ν ≈ 10²⁸ erg s⁻¹ cm⁻² Hz⁻¹ at ν ∼ 6 GHz, ∼1250 days post explosion. Interpreting the radio observations in the context of synchrotron radiation from the supernova shock interaction with the circumstellar medium (CSM), we infer an effective mass-loss rate Ṁ ≈ 10 …

Binding Of ΒL-Crystallin With Models Of Animal And Human Eye Lens-Lipid Membrane, Preston Hazen, Geraline Trossi-Torres, Nawal K. Khadka, Raju Timsina, Laxman Mainali

Physics Faculty Publications and Presentations

Several discoveries show that with age and cataract formation, β-crystallin binds with the lens membrane or associates with other lens proteins, which bind with the fiber cell plasma membrane, accompanied by light scattering and cataract formation. However, how lipids (phospholipids and sphingolipids) and cholesterol (Chol) influence β-crystallin binding to the membrane is unclear. This research aims to elucidate the role of lipids and Chol in the binding of β-crystallin to the membrane and the membrane’s physical properties (mobility, order, and hydrophobicity) with β-crystallin binding. We used electron paramagnetic resonance (EPR) spin-labeling methods to investigate the binding of β_L-crystallin …

Modelling Galaxy Cluster Triaxiality In Stacked Cluster Weak Lensing Analyses, Hao-Yi Wu

Physics Faculty Publications and Presentations

Counts of galaxy clusters offer a high-precision probe of cosmology, but control of systematic errors will determine the accuracy of this measurement. Using Buzzard simulations, we quantify one such systematic, the triaxiality distribution of clusters identified with the redMaPPer optical cluster finding algorithm, which was used in the Dark Energy Survey Year-1 (DES Y1) cluster cosmology analysis. We test whether redMaPPer selection biases the clusters’ shape and orientation and find that it only biases orientation, preferentially selecting clusters with their major axes oriented along the line of sight. Modelling the richness–mass relation as log-linear, we find that the log-richness amplitude …

Modulation Of Voltage-Gating And Hysteresis Of Lysenin Channels By Cu2+ Ions, Andrew Bogard, Pangaea W. Finn, Aviana R. Smith, Ilinca M. Flacau, Rose Whiting, Daniel Fologea

Physics Faculty Publications and Presentations

The intricate voltage regulation presented by lysenin channels reconstituted in artificial lipid membranes leads to a strong hysteresis in conductance, bistability, and memory. Prior investigations on lysenin channels indicate that the hysteresis is modulated by multivalent cations which are also capable of eliciting single-step conformational changes and transitions to stable closed or sub-conducting states. However, the influence on voltage regulation of Cu²⁺ ions, capable of completely closing the lysenin channels in a two-step process, was not sufficiently addressed. In this respect, we employed electrophysiology approaches to investigate the response of lysenin channels to variable voltage stimuli in the presence …

Self-Calibrating Optical Galaxy Cluster Selection Bias Using Cluster, Galaxy, And Shear Cross-Correlations, Chenxiao Zeng, Andrés N. Salcedo, Hao-Yi Wu, Christopher M. Hirata

Physics Faculty Publications and Presentations

The clustering signals of galaxy clusters are powerful tools for self-calibrating the mass–observable relation and are complementary to cluster abundance and lensing. In this work, we explore the possibility of combining three correlation functions – cluster lensing, the cluster–galaxy cross-correlation function, and the galaxy autocorrelation function – to self-calibrate optical cluster selection bias, the boosted clustering and lensing signals in a richness-selected sample mainly caused by projection effects. We develop mock catalogues of redMaGiC-like galaxies and redMaPPer-like clusters by applying halo occupation distribution models to N-body simulations and using counts-in-cylinders around massive haloes as a richness proxy. In addition …

Hypo-Osmotic Stress And Pore-Forming Toxins Adjust The Lipid Order In Sheep Red Blood Cell Membranes, Rose Whiting, Sevio Stanton, Maryna Kucheriava, Aviana R. Smith, Matt Pitts, Daniel Robertson, Jacob Kammer, Zhiyu Li, Daniel Fologea

Physics Faculty Publications and Presentations

Lipid ordering in cell membranes has been increasingly recognized as an important factor in establishing and regulating a large variety of biological functions. Multiple investigations into lipid organization focused on assessing ordering from temperature-induced phase transitions, which are often well outside the physiological range. However, particular stresses elicited by environmental factors, such as hypo-osmotic stress or protein insertion into membranes, with respect to changes in lipid status and ordering at constant temperature are insufficiently described. To fill these gaps in our knowledge, we exploited the well-established ability of environmentally sensitive membrane probes to detect intramembrane changes at the molecular level. …

Freestanding Graphene Heat Engine Analyzed Using Stochastic Thermodynamics, J. Durbin, J. M. Mangum, M. N. Gikunda, F. Harerimana, P. Kumar, L. L. Bonilla, P. M. Thibado

Physics Faculty Publications and Presentations

We present an Ito-Langevin model for freestanding graphene connected to an electrical circuit. The graphene is treated as a Brownian particle in a double-well potential and is adjacent to a fixed electrode to form a variable capacitor. The capacitor is connected in series with a battery and a load resistor. The capacitor and resistor are given separate thermal reservoirs. We have solved the coupled Ito-Langevin equations for a broad range of temperature differences between the two reservoirs. Using ensemble averages, we report the rate of change in energy, heat, and work using stochastic thermodynamics. When the resistor is held at …

Stability Of Retinol In Liposomes As Measured By Fluorescence Lifetime Spectroscopy And Flim, Louis Sumrall, L. Smith, Elmukhtar Ehmed Alhatmi, Yekaterina G. Chmykh, D. Mitchell, Jay Nadeau

Physics Faculty Publications and Presentations

Retinol shows complex photophysical properties that make it potentially useful as an exogenous or endogenous probe of membrane microenvironment, but it has not been fully explored. In this study, we use bulk fluorescence lifetime measurements and fluorescence lifetime imaging microscopy (FLIM) to examine the stability of retinol in phosphatidylcholine (PC) multilamellar and unilamellar vesicles with and without cholesterol. We find that both light and exposure to ambient temperature and oxygen contribute to retinol degradation, with the addition of an antioxidant such as butylated hydroxytoluene (BHT) essential to provide stability, especially in the absence of cholesterol. With exposure to ultraviolet light …

A Simple In Situ Method For Optimizing Settings For The Einzel Lens Elements In A Focused Ion Beam, Rich Swinford, Erik Sanchez

Physics Faculty Publications and Presentations

Ion beams have had an incredible impact on research in the past couple of decades. One major reason for this is the continued development of systems having optimal beam currents that allows one to image more clearly at different spot sizes to include higher currents that allow for faster milling. The advancements for Focused ion beam (FIB) columns have developed rapidly due to the computational optimization of lens designs. However, once a system has been produced, the optimal column settings for these lenses may change or simply become obscure. Our work involves regaining this optimization with the newly applied values …

Designing Polar Textures With Ultrafast Neuromorphic Features From Atomistic Simulations, Sergey Prosandeev, Sergei Prokhorenko, Yousra Nahas, Yali Yang, Changsong Xu, Julie Grollier, Diyar Talbayev, Brahim Dkhil, L. Bellaiche

Physics Faculty Publications and Presentations

This review summarizes recent works, all using a specific atomistic approach, that predict and explain the occurrence of key features for neuromorphic computing in three archetypical dipolar materials, when they are subject to THz excitations. The main ideas behind such atomistic approach are provided, and illustration of model relaxor ferroelectrics, antiferroelectrics, and normal ferroelectrics are given, highlighting the important potential of polar materials as candidates for neuromorphic computing. Some peculiar emphases are made in this Review, such as the connection between neuromorphic features and percolation theory, local minima in energy path, topological transitions and/or anharmonic oscillator model, depending on the …

Microbial Motility At The Bottom Of North America: Digital Holographic Microscopy And Genomic Motility Signatures In Badwater Spring, Death Valley National Park, Carl Snyder, Jakob P. Centlvre, Shrikant Bhute, Jay Nadeau, Multiple Additional Authors

Physics Faculty Publications and Presentations

Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon …

Thin Film Deposition Of Mop, A Topological Semimetal, Robert Browning, Paul Plachinda, Raj Solanki

Physics Faculty Publications and Presentations

MoP is a topological semimetal which has drawn attention due to its unique electrical and optical properties resulting from massless electrons. In order to utilize these properties for practical applications, it is necessary to develop a technique to produce high-quality, large-scale thin films of this 2D material. We report below our initial results of growth of MoP thin films using atomic layer deposition (ALD), where the film grows layer-by-layer. These films were grown on 5 cm × 5 cm silicon oxide coated Si wafers. Resistivity versus temperature measurements show that these films are metallic and includes a partial superconducting phase. …

Quantification Of Age-Related Changes In The Lateral Organization Of The Lipid Portion Of The Intact Membranes Isolated From The Left And Right Eye Lenses Of The Same Human Donor, Laxman Mainali, Marija Raguz, Witold Karol Subczynski

Physics Faculty Publications and Presentations

The continuous wave EPR spin-labeling method was used to evaluate age-related changes in the amounts of phospholipids (PLs) and cholesterol (Chol) in domains present in intact, cortical, and nuclear fiber cell plasma membranes isolated separately from the left and right eye lenses of the same human donor. The relative amounts of boundary plus trapped PLs were evaluated with the PL analog 12-doxylstearic acid spin label (12-SASL) and the relative amounts of trapped Chol with the Chol analog androstane spin label (ASL). The donors ranged in age from 15 to 70 years. Both the left and right eye lenses from donors …

Recent Advances In Experimental Design And Data Analysis To Characterize Prokaryotic Motility, Megan M. Dubay, Jacqueline Acres, Max Riekeles, Jay Nadeau

Physics Faculty Publications and Presentations

Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying …

Electromagnetic Radiation From A Spherical Static Current Source Coupled To Harmonic Axion Field, Railing Chang, Huai-Yi Xie, P. T. Leung

Physics Faculty Publications and Presentations

The electromagnetic fields generated from a static current source on a spherical surface are calculated in the framework of axion electrodynamics to first order in the coupling parameter. Comparisons of the results are made with reference to various results obtained in conventional Maxwell electrodynamics, as well as previous results obtained for point magnetic dipole source coupled to harmonic axion fields. Distinct features from the results so obtained are highlighted for possible experimental probing of the axions via electromagnetic interactions. In particular, electromagnetic radiation from sources with strong magnetic field is studied which may enable the detection of a cosmic …

Atomic Force Microscopy Cantilever-Based Nanoindentation: Mechanical Property Measurements At The Nanoscale In Air And Fluid, Ashton E. Enrriques, Sean Howard, Raju Timsina, Nawal K. Khadka, Amber N. Hoover, Allison E. Ray, Ling Ding, Chioma Onwumelu, Stephan Nordeng, Laxman Mainali, Gunes Uzer, Paul H. Davis

Physics Faculty Publications and Presentations

An atomic force microscope (AFM) fundamentally measures the interaction between a nanoscale AFM probe tip and the sample surface. If the force applied by the probe tip and its contact area with the sample can be quantified, it is possible to determine the nanoscale mechanical properties (e.g., elastic or Young's modulus) of the surface being probed. A detailed procedure for performing quantitative AFM cantilever-based nanoindentation experiments is provided here, with representative examples of how the technique can be applied to determine the elastic moduli of a wide variety of sample types, ranging from kPa to GPa. These include live mesenchymal …

A Multi-Modal Volumetric Microscope With Automated Sample Handling For Surveying Microbial Life In Liquid Samples, Nathan Oborny, Eugene Serabyn, J. Kent Wallace, Kurt Liewer, Manuel Bedrossian, Stephanie Rider, Chris Lindensmith, Jay Nadeau, Multiple Additional Authors

Physics Faculty Publications and Presentations

In the study of microbial life, microscopy plays a unique role due to its ability to detect ordered structure, motility, and fluorescence signals. As such it has also recently gained attention in the context of searching for extant life on distant Solar System bodies bearing liquid water. In this paper we introduce a multimodal volumetric microscopy system for potential future spaceflight missions that combines digital holographic microscopy (DHM) and volume fluorescence imager (VFI), which are volumetric imaging methods that provide highresolution, high-throughput examination of liquid samples. DHM provides information on the absorption, morphology, and motility of imaged objects without requiring …

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 …

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 …

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 …

Spirality: A Novel Way To Measure Spiral Arm Pitch Angle, Deanna Shields, Benjamin Boe, Casey Pfountz, Benjamin L. Davis, Matthew Hartley, Ryan Miller, Zac Slade, M. Shameer Abdeen, Daniel Kennefick, Julia Kennefick

Physics Faculty Publications and Presentations

We present the MATLAB code Spirality, a novel method for measuring spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. Computation time is typically on the order of 2 min per galaxy, assuming 8 GB of working memory. We tested the code using 117 synthetic spiral images with known pitches, varying both the spiral properties and the input parameters. The code yielded correct results for all synthetic spirals with galaxy-like properties. We also compared the code’s results to two-dimensional Fast Fourier Transform (2DFFT) measurements for the sample of nearby galaxies defined by DMS PPak. Spirality’s …