Physical Sciences and Mathematics Commons^™

Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras

Faculty Publications

Air quality has important climate and health effects. There is a need, therefore, to monitor air quality both indoors and outdoors. Methods of measuring air quality should be cost-effective if they are to be used widely, and one such method is low-cost sensors (LCS). This study reports on the use of LCSs in Ulaanbataar, Mongolia to measure PM_2.5 concentrations inside yurts or “gers”. Some of these gers were part of a non-government agency (NGO) initiative to improve insulating properties of these housing structures. The goal of the NGO was to decrease particulate emissions inside the gers; a secondary result …

Order And Harmony: Kepler’S Guiding Forces, Dan Broadbent

Faculty Publications

Adapted from the article “Order and Harmony: Kepler’s Guiding Forces” included in “Towards Mysteries of the Cosmos with Johannes Kepler – on the 450th Anniversary of His Birth,” a commemorative volume published by the Obserwatorium Atronommiczne Krolowej Jadwigi Rzepienniku Biskupim (Queen Jadwiga Observatory of Rzepiennik Biskupi Poland) December 2021. Adapted with permission.

As the subject librarian for physics and astronomy at Brigham Young University, the author has had the privilege of handling some of Johannes Kepler’s original books preserved in the university’s archives. One of the most impressive materials in the archive is a large page from Mysterium Cosmographicum that …

Encirclement Of Moving Targets Using Noisy Range And Bearing Measurements, Cammy Peterson, Puneet Jain, Randal Beard

Faculty Publications

This paper presents theoretically justified controllers that use relative range and bearing measurements to steer a team of autonomous vehicles, operating without inertial position information, to circular trajectories around a constant-acceleration, constant-velocity, or stationary target. An extended Kalman filter is used to improve the noisy relative measurements and estimate the velocity of the moving target. These estimated values are used in the control laws to encircle constant-velocity moving targets. Lyapunov techniques are utilized to show that the vehicle will converge to the desired circular formations. Additionally, cooperating vehicles are shown to converge to a circular formation with equal temporal spacing …

Historical Milestones In Astronomy: As Shown Through The Byu Special Collections Archives, Dan Broadbent

Faculty Publications

Science Research: The “Long Conversation”

• Ideas in science can take a long time to develop.
• How do they develop?

• These books document a part of a conversation that began 447 years ago and spanned a 153 year period… documenting:
• how the overall nature of the universe was worked out,
• the establishment of the scientific method, and the boundaries of religious authority,
• and culminated in Isaac Newton’s book that presented his three laws of motion that allow us to explore the universe to this day.

Cell Velocity Is Asymptotically Independent Of Force: A Differential Equation Model With Random Switching., J. C. Dallon, Emily J. Evans, Christopher P. Grant, William V. Smith

Faculty Publications

Numerical simulations suggest that average velocity of a biological cell depends largely on attachment dynamics and less on the forces exerted by the cell. We determine the relationship between two models of cell motion, one based on finite spring constants modeling attachment properties (a randomly switched differential equation) and a limiting case (a centroid model-a generalized random walk) where spring constants are infinite. We prove the main result of this paper, the Expected Velocity Relationship theorem. This result shows that the expected value of the difference between cell locations in the differential equation model at the initial time and at …

Deciphering The Transport Of Elastic Filaments By Antagonistic Motor Proteins, Stephanie Portet, Cecil Leduc, Sandrine Etienne-Manneville, J. C. Dallon

Faculty Publications

Intermediate filaments are long elastic fibres that are transported by microtubule-associated motor proteins kinesin and dynein inside the cell. How elastic filaments are efficiently transported by antagonistic motors is not well understood and difficult to measure with current experimental techniques. Adapting the tug-of-war paradigm for vesicle-like cargos, we develop a mathematical model to describe the motion of an elastic filament punctually bound to antagonistic motors. As observed in cells, up to 3 modes of transport are obtained; dynein-driven retrograde, kinesin-driven anterograde fast motions and a slow motion. Motor properties and initial conditions that depend on intracellular context, regulate the transport …

Stochastic Modeling Reveals How Motor Protein And Filament Properties Affect Intermediate Filament Transport, J. C. Dallon, Cecil Leduc, Sandrine Etienne-Manneville, Stephanie Portet

Faculty Publications

Intermediate filaments are a key component of the cytoskeleton. Their trans- port along microtubules plays an essential role in the control of the shape and structural organization of cells. To identify the key parameters responsible for the control of intermediate filament transport, we generated a model of elastic filament transport by microtubule-associated dynein and kinesin. The model is also applicable to the transport of any elastically-coupled cargoes. We inves- tigate the effect of filament properties such as number of motor binding sites, length, and elasticity on motion of filaments. Additionally, we consider the ef- fect of motor properties, i.e. off …

Y2O3 Optical Constants Between 5 Nm And 50 Nm, Joseph B. Muhlestein, Benjamin D. Smith, Margaret Miles, Stephanie M. Thomas, Anthony Willey, David D. Allred, R. Steven Turley

Faculty Publications

We report optical constants of e-beam evaporated yttrium oxide Y₂O₃ thin films as determined from angle-dependent reflectance measurements at wavelengths from 5 to 50 nm. Samples were measured using synchrotron radiation at the Advanced Light Source. The experimental reflectance data were fit to obtain values for the index of refraction and thin film roughness. We compare our computed constants with those of previous researchers and those computed using the independent atom approximation from the CXRO website. We found that the index of refraction near 36 nm is much lower than previous data from Tomiki as reported by …

Fitting Parameter Uncertainties In Least Squares Fitting, R. Steven Turley

Faculty Publications

This article review the theory and practice of computing uncertainties in the fit parameters in least squares fits. It shows how to estimate the uncertainties and gives some numerical examples in Julia of their use. Examples are given and validated for both linear and nonlinear fits.

Polynomial Fitting, R. Steven Turley

Faculty Publications

This article reviews the theory and some good practice for fitting polynomials to data. I show by theory and example why fitting using a basis of orthogonal polynomials rather than monomials is desirable. I also show how to scale the independent variable for a more stable fit. I also demonstrate how to compute the uncertainty in the fit parameters. Finally, I discuss regression analysis: how to determine whether adding an additional term to the fit is justified.

Linear Least Squares Curve Fitting, R. Steven Turley

Faculty Publications

This article is a review of the theory and practice behind linear least squares curve fitting. It outlines how to find the optimal parameters to match experimental data with theory and how to estimate the uncertainty in those parameters. The article demonstrates and validates these calculations in Excel, MATLAB, Mathematica, Python, and Julia.

Cubic Interpolation With Irregularly-Spaced Points In Julia 1.4, R. Steven Turley

Faculty Publications

This article shows how to interpolate between regularly- or irregularly-spaced points in Julia 1.4. It has derivations of the theory behind cubic splines, and piece-wise cubic hermite polynomial interpolation. The spline interpolants are continuous and have continuous first and second derivatives. The hermite polynomial interpolants are continuous and have continuous first derivatives. Three techniques are implemented to determine the slope at the data points for the interpolation (knots). One uses the average slope of the neighboring segments. Another use the quadratic polynomial passing through the point and its two neighbors. The third, PCHIP, is similar to the first method, but …

Fitting Als Reflectance Data Using Python, R. Steven Turley

Faculty Publications

This article describes how to use the python refl library in https://bitbucket.org/steve_turley/reflectance-fitting to fit thin film reflectance data from the Advanced Light Source (ALS) at Lawrence Berkeley National Labs. It uses data taken for a thin film of aluminum capped by a thin film of aluminum fluoride on a silicon nitride substrate. The single fit in the example shown here shows the importance of taking into account the oxidation of the aluminum layer as part of the fit.

Bare Aluminum Oxidation, R. Steven Turley

Faculty Publications

This paper computes the oxidation rate of bare evaporated aluminum thin films under high vacuum conditions and exposed to air.

The Human Touch: How Non-Expert Users Perceive, Interpret, And Fix Topic Models, Tak Yeon Lee, Alison Smith, Kevin Seppi, Niklas Elmqvist, Jordan Boyd-Graber, Leah Findlater

Faculty Publications

Topic modeling is a common tool for understanding large bodies of text, but is typically provided as a “take it or leave it” proposition. Incorporating human knowledge in unsupervised learning is a promising approach to create high-quality topic models. Existing interactive systems and modeling algorithms support a wide range of refinement operations to express feedback. However, these systems’ interactions are primarily driven by algorithmic convenience, ignoring users who may lack expertise in topic modeling. To better understand how non-expert users understand, assess, and refine topics, we conducted two user studies—an in-person interview study and an online crowdsourced study. These studies …

Circular Integration Region, R. Steven Turley

Faculty Publications

This report explains how to transform a singular integration over the an arc of a circle into an integration over a unit square using various coordinate transformations include a Duffy transformation. Fortran code illustrating the algorithms is included along with unit test validations.

2d Surface Creation Using Intel Mkl, R. Steven Turley

Faculty Publications

This document illustrates how to use the Intel Math Kernel Library (MKL) to create surfaces with a given cut-off spatial frequency and rms surface height. They closely mimic typical surfaces our group has measured using atomic force microscopy (AFM).

A Continuous Time Model Of Centrally Controlled Motion With Random Switching Terms, J. C. Dallon, L C. Despain, E J. Evans, C P. Grant, Willaim V. Smith

Faculty Publications

This paper considers differential problems with random switching, with specific applications to the motion of cells and centrally coordinated motion. Starting with a differential-equation model of cell motion that was proposed previously, we set the relaxation time to zero and consider the simpler model that results. We prove that this model is well-posed, in the sense that it corresponds to a pure jump-type continuous time Markov process (without explosion). We then describe the model's long-time behavior, first by specifying an attracting steady-state distribution for a projection of the model, then by examining the expected location of the cell center when …

Measurement Of The Yb I 1S0-1P1 Transition Frequency At 399 Nm Using An Optical Frequency Comb, Michaela Kleinert, M. E. Gold Dahl, Scott D. Bergeson

Faculty Publications

We determine the frequency of the Yb I ¹S₀-¹P₁ transition at 399 nm using an optical frequency comb. Although this transition was measured previously using an optical transfer cavity [D. Das et al., Phys, Rev. A 72, 032506 (2005)], recent work has uncovered significant errors in that method. We compare our result of 751 526 533.49 ± 0.33 MHz for the ¹⁷⁴Yb isotope with those from the literature and discuss observed differences. We verify the correctness of our method by measuring the frequencies of well-known transitions in Rb and Cs, and by …

Improving Production Of Carbon Nanotube Composites, Dan Broadbent

Faculty Publications

Carbon nanotube (CNT) composites offer great promise for making lighter, thinner and stronger structures. Producing CNT composites, however, can be tricky. The focus of this work is to improve production yields of CNT composites by doing research and development in two areas:

• Research the relationship between ethylene gas concentrations used during CNT growth and yields of usable composite films produced.
• Develop furnace for growing larger CNT samples, which will enable larger sizes and quantities of research product.

Strongly-Coupled Plasmas Formed From Laser-Heated Solids, M. Lyon, Scott D. Bergeson, G. Hart, M. S. Murillo

Faculty Publications

We present an analysis of ion temperatures in laser-produced plasmas formed from solids with different initial lattice structures. We show that the equilibrium ion temperature is limited by a mismatch between the initial crystallographic configuration and the close-packed configuration of a strongly-coupled plasma, similar to experiments in ultracold neutral plasmas. We propose experiments to demonstrate and exploit this crystallographic heating in order to produce a strongly coupled plasma with a coupling parameter of several hundred.

Using Higher Ionization States To Increase Coulomb Coupling In An Ultracold Neutral Plasma, M. Lyon, Scott D. Bergeson, A. Diaw, M. S. Murillo

Faculty Publications

We report measurements and simulations of the time-evolving rms velocity distribution in an ultracold neutral plasma. A strongly coupled ultracold neutral Ca⁺ plasma is generated by photoionizing laser-cooled atoms close to threshold. A fraction of these ions is then promoted to the second ionization state to form a mixed Ca⁺-Ca²⁺ plasma. By varying the time delay between the first and the second ionization events, a minimum in ion heating is achieved. We show that the Coulomb strong-coupling parameter Γ increases by a factor of 1.4 to a maximum value of 3.6. A pure Ca²⁺ plasma …

Instrument For Precision Long-Term Ss-Decay Rate Measurements, M. J. Ware, Scott D. Bergeson, J. E. Ellsworth, M. Groesbeck, J. E. Hansen, D. Pace, J. Peatross

Faculty Publications

We describe an experimental setup for making precision measurements of relative ß-decay rates of ²²Na, ³⁶Cl, ⁵⁴Mn, ⁶⁰Co, ⁹⁰Sr, ¹³³Ba, ¹³⁷Cs, ¹⁵²Eu, and ¹⁵⁴Eu. The radioactive samples are mounted in two automated sample changers that sequentially position the samples with high spatial precision in front of sets of detectors. The set of detectors for one sample changer consists of four Geiger-Müller (GM) tubes and the other set of detectors consists of two NaI scintillators. The statistical uncertainty in the count rate is few times 0.01% per day for the GM …

How Well Does Multiple Ocr Error Correction Generalize?, William B. Lund, Eric K. Ringger, Daniel D. Walker

Faculty Publications

As the digitization of historical documents, such as newspapers, becomes more common, the need of the archive patron for accurate digital text from those documents increases. Building on our earlier work, the contributions of this paper are: 1. in demonstrating the applicability of novel methods for correcting optical character recognition (OCR) on disparate data sets, including a new synthetic training set, 2. enhancing the correction algorithm with novel features, and 3. assessing the data requirements of the correction learning method. First, we correct errors using conditional random fields (CRF) trained on synthetic training data sets in order to demonstrate the …

A Mathematical Model Of Collagen Lattice Contraction, J. C. Dallon, Emily J. Evans, H Paul Erhlich

Faculty Publications

Two mathematical models for fibroblast-collagen interaction are proposed which reproduce qualitative features of fibroblast populated collagen lattice contraction in time. Both models are force based and model the cells as individual entities with discrete attachment sites however the collagen lattice is modeled differently for each model. In the collagen lattice model the lattice is more interconnected and formed by triangulating nodes to form the fibrous structure. In the collagen fiber model the nodes are not triangulated, are less interconnected, and the collagen fibers are modeled as a string of nodes. Both models suggest that the overall increase in stress of …

A Force Based Model Of Individual Cell Migration With Discrete Attachment Sites And Random Switching Terms, J. C. Dallon, Matthew Scott, William V. Smith

Faculty Publications

A force based model of cell migration is presented which gives new insight into the importance of the dynamics of cell binding to the substrate. The main features of the model are the focus on discrete attachment dynamics, the treatment of the cellular forces as springs, and an incorporation of the stochastic nature of the attachment sites. One goal of the model is to capture the effect of the random binding and unbinding of cell attachments on global cell motion. Simulations reveal one of the most important factor influencing cell speed is the duration of the attachment to the substrate. …

Versatile Rb Vapor Cells With Long Lifetimes, John F. Hulbert, Matthieu Giraud-Carrier, Tom Wall, Aaron R. Hawkins, Scott D. Bergeson, Jennifer Black, Holger Schmidt

Faculty Publications

The authors report on an approach to the construction of long-lasting rubidium atomic vapor cells. The method uses pinch-off copper cold-welds, low temperature solders, and electroplated copper to create long-lasting hermetic seals between containment chambers of dissimilar geometries and materials. High temperature epoxy, eutectic lead/tin solder, and indium solder were considered as sealing materials. These seals were analyzed using accelerated lifetime testing techniques. Vapor cells with epoxy and bare metal solder seals had a decrease in the rubidium atomic density within days after being heated to elevated temperatures. They also exhibited broadened spectra as a result of rubidium reacting with …

Cell Speed Is Independent Of Force In A Mathematical Model Of Amoeboidal Cell Motion With Random Switching Terms., J. C. Dallon, Emily J. Evans, Christopher Grant, William V. Smith

Faculty Publications

In this paper the motion of a single cell is modeled as a nucleus and multiple integrin based adhesion sites. Numerical simulations and analysis of the model indicate that when the stochastic nature of the adhesion sites is a memoryless and force independent random process, the cell speed is independent of the force these adhesion sites exert on the cell. Furthermore, understanding the dynamics of the attachment and detachment of the adhesion sites is key to predicting cell speed. We introduce a differential equation describing the cell motion and then introduce a conjecture about the expected drift of the cell, …

Limit Of Strong Ion Coupling Due To Electron Shielding, M. Lyon, Scott D. Bergeson, M. S. Murillo

Faculty Publications

We show that strong coupling between ions in an ultracold neutral plasma is limited by electron screening. While electron screening reduces the quasiequilibrium ion temperature, it also reduces the ion-ion electrical potential energy. The net result is that the ratio of nearest-neighbor potential energy to kinetic energy in quasiequilibrium is constant and limited to approximately 1 unless the electrons are heated by some external source. We support these conclusions by reporting measurements of the ion velocity distribution in an ultracold neutral calcium plasma. These results match previously reported simulations of Yukawa systems. Theoretical considerations are used to determine the screened …

A Comparison Of Boltzmann And Gibbs Definitions Of Microcanonical Entropy For Small Systems, Randall B. Shirts

Faculty Publications

Two different definitions of entropy, S= klnW, in the microcanonical ensemble have been competing for over 100 years. The Boltzmann/Planck definition is that W is the number of states accessible to the system at its energy E (also called the surface entropy). The Gibbs/Hertz definition is that W is the number of states of the system up to the energy E (also called the volume entropy). These two definitions agree for large systems but differ by terms of order N^-1 for small systems, where N is the number of particles in the system. For three analytical …