Physical Sciences and Mathematics Commons^™

Prediction And Confirmation Of A Switch-Like Region Within The N-Terminal Domain Of Hsirt1, Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig, Ningkun Wang

Faculty Research, Scholarly, and Creative Activity

Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch- like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important …

Faster Multidimensional Data Queries On Infrastructure Monitoring Systems, Yinghua Qin, Gheorghi Guzun

Faculty Research, Scholarly, and Creative Activity

The analytics in online performance monitoring systems have often been limited due to the query performance of large scale multidimensional data. In this paper, we introduce a faster query approach using the bit-sliced index (BSI). Our study covers multidimensional grouping and preference top-k queries with the BSI, algorithms design, time complexity evaluation, and the query time comparison on a real-time production performance monitoring system. Our research work extended the BSI algorithms to cover attributes filtering and multidimensional grouping. We evaluated the query time with the single attribute, multiple attributes, feature filtering, and multidimensional grouping. To compare with the existing prior …

Machine Learning To Predict Sports-Related Concussion Recovery Using Clinical Data, Yan Chu, Gregory Knell, Riley P. Brayton, Scott O. Burkhart, Xiaoqian Jiang, Shayan Shams

Faculty Research, Scholarly, and Creative Activity

Objectives
Sport-related concussions (SRCs) are a concern for high school athletes. Understanding factors contributing to SRC recovery time may improve clinical management. However, the complexity of the many clinical measures of concussion data precludes many traditional methods. This study aimed to answer the question, what is the utility of modeling clinical concussion data using machine-learning algorithms for predicting SRC recovery time and protracted recovery?
Methods
This was a retrospective case series of participants aged 8 to 18 years with a diagnosis of SRC. A 6-part measure was administered to assess pre-injury risk factors, initial injury severity, and post-concussion symptoms, including …

Building A Quantum Engineering Undergraduate Program, Abraham Asfaw, Alexandre Blais, Kenneth R. Brown, Jonathan Candelaria, Christopher Cantwell, Lincoln D. Carr, Joshua Combes, Dripto M. Debroy, John M. Donohue, Sophia E. Economou, Emily Edwards, Michael F. J. Fox, Steven M. Girvin, Alan Ho, Hilary M. Hurst, Zubin Jacob, Blake R. Johnson, Ezekiel Johnston-Halperin, Robert Joynt, Eliot Kapit, Judith Klein-Seetharaman, Martin Laforest, H. J. Lewandowski, Theresa W. Lynn, Corey Rae H. Mcrae, Celia Merzbacher, Spyridon Michalakis, Prineha Narang, William D. Oliver, Jens Palsberg, David P. Pappas, Michael G. Raymer, David J. Reilly, Mark Saffman, Thomas A. Searles, Jeffrey H. Shapiro, Chandralekha Singh

Faculty Research, Scholarly, and Creative Activity

Contribution: A roadmap is provided for building a quantum engineering education program to satisfy U.S. national and international workforce needs.

Background: The rapidly growing quantum information science and engineering (QISE) industry will require both quantum-aware and quantum-proficient engineers at the bachelor's level.

Research Question: What is the best way to provide a flexible framework that can be tailored for the full academic ecosystem?

Methodology: A workshop of 480 QISE researchers from across academia, government, industry, and national laboratories was convened to draw on best practices; representative authors developed this roadmap.

Findings: 1) For quantum-aware engineers, …

Solution-Processed Flexible Broadband Zno Photodetector Modified By Ag Nanoparticles, N. P. Klochko, K. S. Klepikova, I. V. Khrypunova, V. R. Kopach, I. I. Tyukhov, S. I. Petrushenko, S. V. Dukarov, V. M. Sukhov, M. V. Kirichenko, A. L. Khrypunova

Faculty Research, Scholarly, and Creative Activity

In this work, we present flexible broadband photodetectors (PDs) fabricated by a deposition of nanostructured zinc oxide (ZnO) films on polyimide (PI) substrates by using cheap and scalable aqueous method Successive Ionic Layer Adsorption and Reaction (SILAR). In order to increase the long-wavelength absorption of the nanostructured ZnO layer, we created its intrinsic defects, including oxygen vacancies by post-treatment at 300 °C in vacuum and thus the light-sensitive material ZnO/PI was obtained. Then we applied silver nanoparticles (Ag NPs) from a silver sol onto a nanostructured ZnO film, which were visualized using SEM in the form of spheres up to …

Proquest Tdm Studio: A Text And Data Mining Solution, Anamika Megwalu, Anne Marie Engelsen

Faculty Research, Scholarly, and Creative Activity

TDM Studio is an integrated platform offered by ProQuest for data and text mining. TDM stands for text and data mining. This cloud-based, all-in-one innovative product is designed to offer researchers a clean interface with rights-cleared content, Jupyter notebook, and data visualization tools. As a result, researchers can now search Pro-Quest databases, create large datasets, import data to Jupyter notebook for analysis, and download results within a day.

Informing Wetland Management With Waterfowl Movement And Sanctuary Use Responses To Human-Induced Disturbance, Fiona Mcduie, Austen A. Lorenz, Robert C. Klinger, Cory T. Overton, Cliff L. Feldheim, Joshua T. Ackerman, Michael L. Casazza

Faculty Research, Scholarly, and Creative Activity

Long-term environmental management to prevent waterfowl population declines is informed by ecology, movement behavior and habitat use patterns. Extrinsic factors, such as human-induced disturbance, can cause behavioral changes which may influence movement and resource needs, driving variation that affects management efficacy. To better understand the relationship between human-based disturbance and animal movement and habitat use, and their potential effects on management, we GPS tracked 15 dabbling ducks in California over ~4-weeks before, during and after the start of a recreational hunting season in October/November 2018. We recorded locations at 2-min intervals across three separate 24-h tracking phases: Phase 1) two …

Characterization Of Cdom In The Elkhorn Slough Estuary Using Eem Spectroscopy And Its Potential For Macrophyte Monitoring, María Vila Duplá

Faculty Research, Scholarly, and Creative Activity

The Elkhorn Slough estuary is an upwelling-influenced system located in Monterey Bay, California. It is of great ecological importance, as it provides essential habitat to over 750 species, and is one of the largest estuaries in California. The sources and distribution of chromophoric dissolved organic matter (cDOM) in Elkhorn Slough are strongly influenced by geochemical processes linked to the transition between sea and continent, and to anthropogenic activity from adjacent lands. In 2016, water samples were collected from across the Elkhorn Slough estuary to assess the sources and spatial dynamics of cDOM and its components throughout the system. Using EEM …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Computer-Aided Diagnosis Of Low Grade Endometrial Stromal Sarcoma (Lgess), Xinxin Yang, Mark Stamp

Faculty Research, Scholarly, and Creative Activity

Low grade endometrial stromal sarcoma (LGESS) accounts for about 0.2% of all uterine cancer cases. Approximately 75% of LGESS patients are initially misdiagnosed with leiomyoma, which is a type of benign tumor, also known as fibroids. In this research, uterine tissue biopsy images of potential LGESS patients are preprocessed using segmentation and stain normalization algorithms. We then apply a variety of classic machine learning and advanced deep learning models to classify tissue images as either benign or cancerous. For the classic techniques considered, the highest classification accuracy we attain is about 0.85, while our best deep learning model achieves an …

Traveling Wave Solutions For Two Species Competitive Chemotaxis Systems, T. B. Issa, R. B. Salako, W. Shen

Faculty Research, Scholarly, and Creative Activity

In this paper, we consider two species chemotaxis systems with Lotka–Volterra competition reaction terms. Under appropriate conditions on the parameters in such a system, we establish the existence of traveling wave solutions of the system connecting two spatially homogeneous equilibrium solutions with wave speed greater than some critical number c∗. We also show the non-existence of such traveling waves with speed less than some critical number c∗0 , which is independent of the chemotaxis. Moreover, under suitable hypotheses on the coefficients of the reaction terms, we obtain explicit range for the chemotaxis sensitivity coefficients ensuring c∗ = c∗0 , which …

Multifidelity Prediction In Wildfire Spread Simulation: Modeling, Uncertainty Quantification And Sensitivity Analysis, Mario Miguel Valero, Lluís Jofre, Ricardo Torres

Faculty Research, Scholarly, and Creative Activity

Wildfire behavior predictions typically suffer from significant uncertainty. However, wildfire modeling uncertainties remain largely unquantified in the literature, mainly due to computing constraints. New multifidelity techniques provide a promising opportunity to overcome these limitations. Therefore, this paper explores the applicability of multifidelity approaches to wildland fire spread prediction problems. Using a canonical simulation scenario, we assessed the performance of control variates Monte-Carlo (MC) and multilevel MC strategies, achieving speedups of up to 100x in comparison to a standard MC method. This improvement was leveraged to quantify aleatoric uncertainties and analyze the sensitivity of the fire rate of spread (RoS) to …

Peer Motivation: Getting Through Math Together, Jessica Mean, Wes Maciejewski

Faculty Research, Scholarly, and Creative Activity

Students have a complex relationship with mathematics. Some love it, but more often than not, the feelings are less favorable. These feelings can lead to decreased motivation which makes it difficult for students to engage with the subject as the semester progresses. Instructors also have difficulty addressing this waning motivation. In this paper, we claim peers are better able to connect with the students and this can be leveraged to better motivate students. We present an approach to having peers motivate their students. These peer interactions integrated with a mandatory mathematics course might improve students’ motivation.

Feedback Induced Magnetic Phases In Binary Bose-Einstein Condensates, Hilary M. Hurst, Shangjie Guo, I. B. Spielman

Faculty Research, Scholarly, and Creative Activity

Weak measurement in tandem with real-time feedback control is a new route toward engineering novel non-equilibrium quantum matter. Here we develop a theoretical toolbox for quantum feedback control of multicomponent Bose-Einstein condensates (BECs) using backaction-limited weak measurements in conjunction with spatially resolved feedback. Feedback in the form of a single-particle potential can introduce effective interactions that enter into the stochastic equation governing system dynamics. The effective interactions are tunable and can be made analogous to Feshbach resonances -- spin-independent and spin-dependent -- but without changing atomic scattering parameters. Feedback cooling prevents runaway heating due to measurement backaction and we present …

Non-Hermitian Topology Of One-Dimensional Spin-Torque Oscillator Arrays, Benedetta Flebus, Rembert A. Duine, Hilary M. Hurst

Faculty Research, Scholarly, and Creative Activity

Magnetic systems have been extensively studied both from a fundamental physics perspective and as building blocks for a variety of applications. Their topological properties, in particular those of excitations, remain relatively unexplored due to their inherently dissipative nature. The recent introduction of non-Hermitian topological classifications opens up new opportunities for engineering topological phases in dissipative systems. Here, we propose a magnonic realization of a non-Hermitian topological system. A crucial ingredient of our proposal is the injection of spin current into the magnetic system, which alters and can even change the sign of terms describing dissipation. We show that the magnetic …

Quantum Control With Spinor Bose-Einstein Condensates, Hilary M. Hurst

Faculty Research, Scholarly, and Creative Activity

Understanding and controlling many-body quantum systems in noisy environments is paramount to developing robust quantum technologies. An external environment can be thought of as a measurement reservoir which extracts information about the quantum system. Cold atoms are well suited to examine system-environment interaction via weak (i.e. minimally destructive) measurement techniques, wherein the measurement probe acts as the environment and also provides a noisy record of system dynamics. The measurement record can then be used in a feedback scheme, opening the door to real time control of quantum gases. In this talk I discuss our theoretical proposal to use weak measurement …

Electron-Induced Massive Dynamics Of Magnetic Domain Walls, Hilary M. Hurst, Victor Galitski, Tero T. Heikkilä

Faculty Research, Scholarly, and Creative Activity

We study the dynamics of domain walls (DWs) in a metallic, ferromagnetic nanowire. We develop a Keldysh collective coordinate technique to describe the effect of conduction electrons on rigid magnetic structures. The effective Lagrangian and Langevin equations of motion for a DW are derived. The DW dynamics is described by two collective degrees of freedom: position and tilt-angle. The coupled Langevin equations therefore involve two correlated noise sources, leading to a generalized fluctuation-dissipation theorem (FDT). The DW response kernel due to electrons contains two parts: one related to dissipation via FDT, and another `inertial' part. We prove that the latter …

Continuous Deployment Transitions At Scale, Laurie Williams, Kent Beck, Jeffrey Creasey, Andrew Glover, James Holman, Jez Humble, David Mclaughlin, John Thomas Micco, Brendan Murphy, Jason A. Cox, Vishnu Pendyala, Steven Place, Zachary T. Pritchard, Chuck Rossi, Tony Savor, Michael Stumm, Chris Parnin

Faculty Research, Scholarly, and Creative Activity

Predictable, rapid, and data-driven feature rollout; lightning-fast; and automated fix deployment are some of the benefits most large software organizations worldwide are striving for. In the process, they are transitioning toward the use of continuous deployment practices. Continuous deployment enables companies to make hundreds or thousands of software changes to live computing infrastructure every day while maintaining service to millions of customers. Such ultra-fast changes create a new reality in software development. Over the past four years, the Continuous Deployment Summit, hosted at Facebook, Netflix, Google, and Twitter has been held. Representatives from companies like Cisco, Facebook, Google, IBM, Microsoft, …

Evolution Of Integration, Build, Test, And Release Engineering Into Devops And To Devsecops, Vishnu Pendyala

Faculty Research, Scholarly, and Creative Activity

Software engineering operations in large organizations are primarily comprised of integrating code from multiple branches, building, testing the build, and releasing it. Agile and related methodologies accelerated the software development activities. Realizing the importance of the development and operations teams working closely with each other, the set of practices that automated the engineering processes of software development evolved into DevOps, signifying the close collaboration of both development and operations teams. With the advent of cloud computing and the opening up of firewalls, the security aspects of software started moving into the applications leading to DevSecOps. This chapter traces the journey …

Near-Bottom Currents At Station M In The Northeast Pacific, Thomas Connolly, Paul Mcgill, Richard Henthorn, Drew Burrier, Cynthia Michaud

Faculty Research, Scholarly, and Creative Activity

No abstract provided.

A Case Study Of Stratospheric Ozone Transport To The Northern San Francisco Bay Area And Sacramento Valley During Cabots 2016, Jodie Clark, Sen Chiao

Faculty Research, Scholarly, and Creative Activity

The California Baseline Ozone Transport Study (CABOTS) was a major air quality study that collected ozone measurements aloft between mid-May and mid-August of 2016. Aircraft measurements, ground-based lidar measurements, and balloon-borne ozonesondes collected precise upper-air ozone measurements across the central and Southern California valley. Utilizing daily ozonesonde data from Bodega Bay, California, and Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2), reanalysis data for 25 July to 14 August 2016, three stratospheric intrusion events are identified over Northern California influencing air masses above Bodega Bay and Sacramento simultaneously. Calculated percent daily changes in afternoon ozonesonde observations indicate increasing …

Blockchain In Libraries, Michael Meth

Faculty Research, Scholarly, and Creative Activity

This issue of Library Technology Reports (vol. 55, no. 8), “Blockchain in Libraries,” examines the application of blockchain in libraries. Blockchain technology has the ability to transform how libraries provide services and organize information. To date, most of these applications are still in the conceptual stage. However, sooner or later, development and implementation will follow. This report is intended to provide a primer on the technology and some thought starters. In chapter 2, the concept of blockchain is explained. Chapter 3 provides eight thought and conversation starters that look at how blockchain could be applied in libraries. Chapter 4 looks …

Transport Signatures Of Dirac States In Topological Insulator - Ferromagnet Heterostructures, Hilary M. Hurst

Faculty Research, Scholarly, and Creative Activity

No abstract provided.

Lanczos-Boosted Numerical Linked-Cluster Expansion For Quantum Lattice Models, Krishnakumar Bhattaram, Ehsan Khatami

Faculty Research, Scholarly, and Creative Activity

Numerical linked-cluster expansions allow one to calculate finite-temperature properties of quantum lattice models directly in the thermodynamic limit through exact solutions of small clusters. However, full diagonalization is often the limiting factor for these calculations. Here we show that a partial diagonalization of the largest clusters in the expansion using the Lanczos algorithm can be as useful as full diagonalization for the method while mitigating some of the time and memory issues. As test cases, we consider the frustrated Heisenberg model on the checkerboard lattice and the Fermi-Hubbard model on the square lattice. We find that our approach can surpass …

Physical Factors Influencing Phytoplankton Abundance In Southern Monterey Bay, C. Ryan Manzer, Thomas Connolly, Erika Mcphee-Shaw, G. Smith

Faculty Research, Scholarly, and Creative Activity

As the base of almost all marine food webs, phytoplankton play a dominant role in determining the productivity of marine ecosystems. Recent studies have highlighted the dynamic variability of phytoplankton abundance in nearshore ecosystems over synoptic time scales. Therefore, a greater understanding of the physical mechanisms that contribute to this variability is required to assess impacts of current as well as future weather patterns on these ecosystems. In this study, chlorophyll fluorescence data from a nearshore location in southern Monterey Bay was used to identify the timing and duration of increases in phytoplankton concentrations. Regional physical parameters, including wind stress, …

Measurement-Induced Dynamics And Stabilization Of Spinor-Condensate Domain Walls, Hilary M. Hurst, I. B. Spielman

Faculty Research, Scholarly, and Creative Activity

Weakly measuring many-body systems and allowing for feedback in real-time can simultaneously create and measure new phenomena in strongly correlated quantum systems. We study the dynamics of a continuously measured two-component Bose-Einstein condensate (BEC) potentially containing a domain wall, and focus on the trade-off between usable information obtained from measurement and quantum backaction. Each weakly measured system yields a measurement record from which we extract real-time dynamics of the domain wall. We show that quantum backaction due to measurement causes two primary effects: domain wall diffusion and overall heating. The system dynamics and signal-to-noise ratio depend on the choice of …

Induced Quantum Dot Probe For Material Characterization, Yun-Pil Shim, Rusko Ruskov, Hilary M. Hurst, Charles Tahan

Faculty Research, Scholarly, and Creative Activity

We propose a non-destructive means of characterizing a semiconductor wafer via measuring parameters of an induced quantum dot on the material system of interest with a separate probe chip that can also house the measurement circuitry. We show that a single wire can create the dot, determine if an electron is present, and be used to measure critical device parameters. Adding more wires enables more complicated (potentially multi-dot) systems and measurements. As one application for this concept we consider silicon metal-oxide-semiconductor and silicon/silicon-germanium quantum dot qubits relevant to quantum computing and show how to measure low-lying excited states (so-called "valley" …

Gelatinous Zooplankton Abundance And Benthic Boundary Layer Currents In The Abyssal Northeast Pacific: A 3-Yr Time Series Study, Kenneth Smith, Christine Huffard, Paul Mcgill, Alana Sherman, Thomas Connolly, Susan Von Thun, Linda Kuhnz

Faculty Research, Scholarly, and Creative Activity

Gelatinous zooplankton are prominent fauna in the deep ocean, especially in the water column associated with the sea floor. This interface zone, the benthic boundary layer, is critical to biogeochemical exchanges between pelagic and benthic communities. A conspicuous member of this benthic boundary layer community in the abyssal Northeast Pacific (Sta. M; 4000 m depth) is the hydrozoan medusa, Benthocodon pedunculata. A 3-year time-series study was conducted of B. pedunculata from October 2014 to November 2017 using an autonomous time-lapse camera system and acoustic current meter deployed on the sea floor. Remotely operated vehicle benthic video transects and collections were …

Observing Change In Students’ Attitudes Towards Mathematics: Contrasting Quantitative And Qualitative Approaches, Wes Maciejewski

Faculty Research, Scholarly, and Creative Activity

A student’s attitude towards mathematics affects how they learn and perform in mathematics. What exactly is meant by attitude and how this interacts with mathematics education is a current debate in the mathematics education research community. Regardless, practitioners often acknowledge a consideration of improving students’ attitudes towards mathematics in their course design. This creates an impetus to study attitudes towards mathematics in a way that lends itself to observing changes over a course in mathematics. The current study draws on two approaches to observing and measuring attitudes towards mathematics in an effort to contrast disparate approaches and deepen an investigation …

The Extended Planetary Nebula Spectrograph (Epn.S) Early-Type Galaxy Survey: The Kinematic Diversity Of Stellar Halos And The Relation Between Halo Transition Scale And Stellar Mass, C. Pulsoni, O. Gerhard, M. Arnaboldi, L. Coccato, A. Longobardi, N. Napolitano, E. Moylan, C. Narayan, V. Gupta, A. Burkert, M. Capaccioli, A. Chies-Santos, A. Cortesi, K. Freeman, K. Kuijken, M. Merrifield, Aaron Romanowsky, C. Tortora

Faculty Research, Scholarly, and Creative Activity

Context. In the hierarchical two-phase formation scenario, the halos of early type galaxies (ETGs) are expected to have different physical properties from the galaxies’ central regions.Aims. The ePN.S survey characterizes the kinematic properties of ETG halos using planetary nebulae (PNe) as tracers, overcoming the limitations of absorption line spectroscopy at low surface brightness.Methods. We present two-dimensional velocity and velocity dispersion fields for 33 ETGs, including fast (FRs) and slow rotators (SRs). The velocity fields were reconstructed from the measured PN velocities using an adaptive kernel procedure validated with simulations, and extend to a median of 5.6 effective radii (Re). We …