# Physical Sciences and Mathematics Commons™

Articles 1 - 30 of 3285

## Full-Text Articles in Physical Sciences and Mathematics

Investigating Small-Group Cognitive Engagement In General Chemistry Learning Activities Using Qualitative Content Analysis And The Icap Framework, Safaa Y. El-Mansy, Jack Barbera, Alissa J. Hartig Nov 2022

#### Investigating Small-Group Cognitive Engagement In General Chemistry Learning Activities Using Qualitative Content Analysis And The Icap Framework, Safaa Y. El-Mansy, Jack Barbera, Alissa J. Hartig

##### Chemistry Faculty Publications and Presentations

The level of students’ engagement during active learning activities conducted in small groups is important to understanding the effectiveness of these activities. The Interactive–Constructive–Active–Passive (ICAP) framework is a way to determine the cognitive engagement of these groups by analyzing the conversations that occur while student groups work on an activity. This study used qualitative content analysis and ICAP to investigate cognitive engagement during group activities in a General Chemistry course at the question level, a finer grain size than previously studied. The analysis determined the expected engagement based on question design and the observed engagement based on ...

Quantum Key-Length Extension, Joseph Jaeger, Fang Song, Stefano Tessaro Nov 2022

#### Quantum Key-Length Extension, Joseph Jaeger, Fang Song, Stefano Tessaro

##### Computer Science Faculty Publications and Presentations

Should quantum computers become available, they will reduce the effective key length of basic secret-key primitives, such as blockciphers. To address this we will either need to use blockciphers with inherently longer keys or develop key-length extension techniques to amplify the security of a blockcipher to use longer keys.

We consider the latter approach and revisit the FX and double encryption constructions. Classically, FX was proven to be a secure key-length extension technique, while double encryption fails to be more secure than single encryption due to a meet-in-the-middle attack. In this work we provide positive results, with concrete and tight ...

Topological Anomaly Detection In Dynamic Multilayer Blockchain Networks, Dorcas Ofori-Boateng, I. Segovia Dominguez, C. Akcora, M. Kantarcioglu, Y. R. Gel Sep 2022

#### Topological Anomaly Detection In Dynamic Multilayer Blockchain Networks, Dorcas Ofori-Boateng, I. Segovia Dominguez, C. Akcora, M. Kantarcioglu, Y. R. Gel

##### Mathematics and Statistics Faculty Publications and Presentations

Motivated by the recent surge of criminal activities with cross-cryptocurrency trades, we introduce a new topological perspective to structural anomaly detection in dynamic multilayer networks. We postulate that anomalies in the underlying blockchain transaction graph that are composed of multiple layers are likely to also be manifested in anomalous patterns of the network shape properties. As such, we invoke the machinery of clique persistent homology on graphs to systematically and efficiently track evolution of the network shape and, as a result, to detect changes in the underlying network topology and geometry. We develop a new persistence summary for multilayer networks ...

Analytic Solution Of 1d Diffusion-Convection Equation With Varying Boundary Conditions, Malgorzata B. Glinowiecka-Cox Jun 2022

#### Analytic Solution Of 1d Diffusion-Convection Equation With Varying Boundary Conditions, Malgorzata B. Glinowiecka-Cox

##### University Honors Theses

A diffusion-convection equation is a partial differential equation featuring two important physical processes. In this paper, we establish the theory of solving a 1D diffusion-convection equation, subject to homogeneous Dirichlet, Robin, or Neumann boundary conditions and a general initial condition. Firstly, we transform the diffusion-convection equation into a pure diffusion equation. Secondly, using a separation of variables technique, we obtain a general solution formula for each boundary type case, subject to transformed boundary and initial conditions. While eigenvalues in the cases of Dirichlet and Neumann boundary conditions can be constructed easily, the Robin boundary condition necessitates solving a transcendental algebraic ...

#### Surface Plasmon Characterization In Ag Nanotriangles For Evaluation Of Fano Resonance Conditions, Nabila Islam

##### Student Research Symposium

Surface plasmon polariton (SPP) is a collective oscillation of electrons and light at the metal -dielectric interface excited by the incident radiation on metal surface through the momentum matching conditions. The properties of SPPs and the resonance conditions are highly dependent on the confining materials and geometry of the confining nanostructure. The sensitivity of the surface plasmon resonance to the property of the confining materials made Surface plasmon resonance (SPR) sensors a central tool for biosensing. However, the frequency resolution of SPR sensors is typically limited by the broad resonance of the SPR mode. The resolution can be enhanced through ...

Growing Reservoir Networks Using The Genetic Algorithm Deep Hyperneat, Nancy L. Mackenzie May 2022

#### Growing Reservoir Networks Using The Genetic Algorithm Deep Hyperneat, Nancy L. Mackenzie

##### Student Research Symposium

Typical Artificial Neural Networks (ANNs) have static architectures. The number of nodes and their organization must be chosen and tuned for each task. Choosing these values, or hyperparameters, is a bit of a guessing game, and optimizing must be repeated for each task. If the model is larger than necessary, this leads to more training time and computational cost. The goal of this project is to evolve networks that grow according to the task at hand. By gradually increasing the size and complexity of the network to the extent that the task requires, we will build networks that are more ...

#### Research Proposal For An Assessment Of The Potential For The Arbuscular Fungi “Rhizophagus Irregularis” To Aid In Corn Uptake And Availability Of Iron, Caitlin Costello

##### Student Research Symposium

Global iron deficiency is one factor contributing to malnutrition and varied health conditions. This deficiency accounts for 841,000 deaths and approximately 35,057,000 “disability-adjusted life years lost” (Stoltzfus, R. J. 2003). One way to combat this is to maintain or increase the iron uptake of the globe’s major crops. Research has shown that certain types of mycorrhizal fungi can increase the nutrient uptake of plants. To further this research, we will look at the arbuscular fungi Rhizophagus irregularis and its potential relationship with a short harvest corn variety. This type of mycorrhizal fungi improves plant nutrition including ...

Houseless Water Insecurity During Covid-19 Pandemic, Alicia N. Gamble May 2022

#### Houseless Water Insecurity During Covid-19 Pandemic, Alicia N. Gamble

##### Student Research Symposium

Water security is of the utmost importance for the houseless population. However, little is known about how the houseless population has been resilient to water barriers related to the COVID-19 pandemic. The purpose of this study is to understand houseless individuals' perceptions of public versus grassroots water sources, and the barriers and impacts of these sources. In order to understand these perceptions, individuals experiencing houselessness (e.g. living in tents, vehicles, emergency shelters, couch-surfing, or no roof) that utilize water sources in Portland, Oregon will be interviewed while walking in public areas to gain rich qualitative data, along with GPS ...

Social Capital And Cross-Boundary Collaboration In Wyoming Wildfire Management Networks, Hannah L. Spencer, Christian Heisler May 2022

#### Social Capital And Cross-Boundary Collaboration In Wyoming Wildfire Management Networks, Hannah L. Spencer, Christian Heisler

##### Student Research Symposium

Wildfire hotspots often intersect jurisdictional boundaries, so protecting human communities and restoring healthy fire regimes will require collaborative, cross-boundary action from fire managers. However, collaboration between fire management groups can have varied outcomes depending on the actors involved, all with different missions, financial obligations, and cultures. One way to conceptualize the interactions between actors is with the idea of social capital. We will investigate the following research question: how does social capital impact cross-boundary collaboration in wildfire management networks? We will survey wildfire managers in northwestern Wyoming about their collaborative actions using a snowball sampling method. Using Social Network Analysis ...

Using Digital Holographic Microscopy To Characterize Vibrio's Chemotaxis, Jacqueline Acres, Eric Valentino May 2022

#### Using Digital Holographic Microscopy To Characterize Vibrio's Chemotaxis, Jacqueline Acres, Eric Valentino

##### Student Research Symposium

Vibrio alginolyticus is a marine bacterium that displays distinctive chemotactic behavior. Chemotaxis is the ability to move in response to a concentration gradient, either in the direction of nutrients or away from repellants. Vibrio's single, polar flagellum allows it to form a tight cloud in the presence of a chemoattractant. In this work, we experimentally characterize cloud sizes after both normal culture conditions and simulated microgravity using digital holographic microscopy or DHM. DHM allows visualization of volumetric samples by recording x,y,z and t information in holograms. Plane-by-plane reconstruction retrieves the z-plane information which can then by stitched ...

The Power Of The Collective: A Multi Agent-Based Modeling Approach To Nuclear Radiation Localization, Benjamin Totten, Christof Teuscher May 2022

#### The Power Of The Collective: A Multi Agent-Based Modeling Approach To Nuclear Radiation Localization, Benjamin Totten, Christof Teuscher

##### Student Research Symposium

Gamma radiation is a very high frequency, very dangerous electromagnetic wave that has a chance of being emitted after radioactive decay. Radiation source localization, or locating the previously unknown source of nuclear radiation, in a rapid and efficient manner is critically important, but challenging. We aim to create an architecture for multiple, fully independent agents that cooperate to localize sources faster than existing single-agent architectures, without compromising accuracy. Using Agent-Based Modeling and Deep Reinforcement Learning, agents are enabled to make decisions based on other agents' behaviors while maintaining programmatic autonomy. We hypothesize that radiation sources can be localized faster using ...

#### Comparison Of Heavy Metals In Spinach Grown On The Roof Ground Location At Portland State University, Tyler A. Robin

##### Student Research Symposium

As a result of urbanization, fresh, healthy food can be expensive and easily contaminated but space for local farming is limited. Roofs can be underutilized in densely populated cities and can offer a space for local fresh farming. The purpose of this study is to continue a previous study done in 2021, to find if growing leafy vegetables on the roof can limit heavy metal exposure from air pollutants. This study compares spinach grown on the roof in 2021, 2019 and spinach bought from stores around the Portland State University campus and the heavy metals found in these greens. The ...

#### Mapping Ecosystem Service Flows Of Estuary Restoration Projects On The Oregon Coast To Identify Impacted Stakeholders, Shersten Finley

##### Student Research Symposium

Restoration of largely depleted estuarine systems is increasingly recognized as key to solving a variety of problems coastal communities face currently. Many of these issues will become more acute with climate change and sea level rise. Historic losses of estuary area, and recognition of the ecosystem services provided by functioning estuary ecosystems have resulted in current impetus to pursue estuary restoration. By mapping the flows of ecosystem services using three ecosystem service ‘scorecard’ categories pertaining to coastal resource management: recreation, aesthetics, and cultural/historical/spiritual, we gain a better understanding of the populations impacted by the changes in flows of ...

Computational Investigation Of The Mechanism Of An Octahedral Ni(Ii) Proton Reduction Catalyst And Importance Of Intramolecular Hydrogen Bonding, Avik Bhattacharjee, Dayalis S.V. Brown, Carolyn N. Virca, Trent E. Ethridge, Oreana Mendez Galue, Uyen T. Pham, Theresa M. Mccormick May 2022

#### Computational Investigation Of The Mechanism Of An Octahedral Ni(Ii) Proton Reduction Catalyst And Importance Of Intramolecular Hydrogen Bonding, Avik Bhattacharjee, Dayalis S.V. Brown, Carolyn N. Virca, Trent E. Ethridge, Oreana Mendez Galue, Uyen T. Pham, Theresa M. Mccormick

##### Student Research Symposium

Water-splitting to make hydrogen gas is of extreme importance in the field of alternative energy research. Transition-metal complexes are capable of catalyzing the conversion of water to hydrogen at higher pH, with low overpotential. Our research focuses on the importance of intramolecular hydrogen bonding (H-bonding) on the pKa and thermodynamic stability of the catalytic intermediates of a well-known proton-reduction catalyst, nickel (II) tris-pyridinethiolate. Density Functional Theory (DFT) calculations on the parent catalyst and eleven derivatives demonstrate geometric isomer formation after the protonation step of catalysis. These isomers differ in the relative thermodynamic stabilities and pKa values, which can be attributed ...

Stakeholder Perceptions Of Microplastics Management In Oregon, Maya A. Hurst-Mayr May 2022

#### Stakeholder Perceptions Of Microplastics Management In Oregon, Maya A. Hurst-Mayr

##### Student Research Symposium

There is currently no federal policy in the United States that specifically addresses microplastics (MPs) pollution. However, states are beginning to act on this issue; California’s SB 1422 initiates measurement of MPs in drinking water resources and Senate Bill 1263 requires the state to adopt a strategy to reduce the ecological impact of MPs in marine ecosystems. Other West Coast states like Oregon and Washington are expected to follow California’s example. It is important to know what the actors who are a part of shaping MPs policy in Oregon would see as barriers and opportunities to doing so ...

Analysis Of Aftershock Parameters For The Alaskan Subduction Zone Tectonic Region, Gabrielle M. Paris (They/Them), Richard C. Hugo, Andrew J. Michael May 2022

#### Analysis Of Aftershock Parameters For The Alaskan Subduction Zone Tectonic Region, Gabrielle M. Paris (They/Them), Richard C. Hugo, Andrew J. Michael

##### Student Research Symposium

On 29 July 2021, a magnitude 8.2 earthquake was felt by over 200 people near Perryville, Alaska. The early aftershock forecasts issued by the USGS use default parameters based on expected productivity within a given tectonic region. These forecasts predicted a slower decrease in aftershock activity than what was observed. Even after the USGS adjusted the aftershock forecast parameters, the forecasts did not improve in the long term. Accurate aftershock predictions are important for maintaining public confidence in disaster alert systems. The question I want to explore is: are the generic parameters used in aftershock forecasting accurately describing the ...

May 2022

#### Extending Tensor Virtual Machine To Support Deep-Learning Accelerators With Convolution Cores, Yanzhao Wang, Fei Xie

##### Computer Science Faculty Publications and Presentations

Deep-learning accelerators are increasingly popular. There are two prevalent accelerator architectures: one based on general matrix multiplication units and the other on convolution cores. However, Tensor Virtual Machine (TVM), a widely used deep-learning compiler stack, does not support the latter. This paper proposes a general framework for extending TVM to support deep-learning accelerators with convolution cores. We have applied it to two well-known accelerators: Nvidia's NVDLA and Bitmain's BM1880 successfully. Deep-learning workloads can now be readily deployed to these accelerators through TVM and executed efficiently. This framework can extend TVM to other accelerators with minimum effort.

Spatial And Temporal Variations Of Microplastic Concentrations In Portland's Freshwater Ecosystems, Rebecca Talbot, Elise F. Granek, Heejun Chang, Rosemary Wood, Susanne Brander Apr 2022

#### Spatial And Temporal Variations Of Microplastic Concentrations In Portland's Freshwater Ecosystems, Rebecca Talbot, Elise F. Granek, Heejun Chang, Rosemary Wood, Susanne Brander

##### Geography Faculty Publications and Presentations

While microplastics are a pollutant of growing concern in various environmental compartments, less is known regarding the sources and delivery pathways of microplastics in urban rivers. We investigated the relationship between microplastic concentrations and various spatiotemporal factors (e.g., land use, arterial road length, water velocity, precipitation) in two watersheds along an urban-rural gradient in the Portland metropolitan area. Samples were collected in August, September, and February and were analyzed for total microplastic count and type. Nonparametric statistics were used to evaluate potential relationships with the explanatory variables, derived at both the subwatershed and near stream scales. In August, microplastic ...

Environmental Decision Support Systems As A Service: Demonstration On Ce-Qual-W2 Model, Yoav Bornstein, Ben Dayan, Amir Cahn, Scott A. Wells Apr 2022

#### Environmental Decision Support Systems As A Service: Demonstration On Ce-Qual-W2 Model, Yoav Bornstein, Ben Dayan, Amir Cahn, Scott A. Wells

##### Civil and Environmental Engineering Faculty Publications and Presentations

An environmental decision support system (EDSS) can be used as an important tool for the rehabilitation and preservation of ecosystems. Nonetheless, high assimilation costs (both money and time) are one of the main reasons these tools are not widely adopted in practice. This work presents a low-cost paradigm of “EDSS as a Service.” This paradigm is demonstrated for developing a water quality EDSS as a service that utilizes the well-known CE-QUAL-W2 model as a kernel for deriving optimized decisions. The paradigm is leveraging new open-source technologies in software development (e.g., Docker, Kubernetes, and Helm) with cloud computing to significantly ...

Extreme Winds Alter Influence Of Fuels And Topography On Megafire Burn Severity In Seasonal Temperate Rainforests Under Record Fuel Aridity, Cody Evers, Andres Holz, Sebastian Upton Busby, Max Nielsen-Pincus Apr 2022

#### Extreme Winds Alter Influence Of Fuels And Topography On Megafire Burn Severity In Seasonal Temperate Rainforests Under Record Fuel Aridity, Cody Evers, Andres Holz, Sebastian Upton Busby, Max Nielsen-Pincus

##### Environmental Science and Management Faculty Publications and Presentations

Nearly 0.8 million hectares of land were burned in the North American Pacific Northwest (PNW) over two weeks under record-breaking fuel aridity and winds during the extraordinary 2020 fire season, representing a rare example of megafires in forests west of the Cascade Mountains. We quantified the relative influence of weather, vegetation, and topography on patterns of high burn severity (>75% tree mortality) among five synchronous megafires in the western Cascade Mountains. Despite the conventional wisdom in climate-limited fire regimes that regional drivers (e.g., extreme aridity, and synoptic winds) overwhelm local controls on vegetation mortality patterns (e.g., vegetation ...

Black Carbon Dominated Dust In Recent Radiative Forcing On Rocky Mountain Snowpacks, Kelly E. Gleason, Joseph R. Mcconnell, Monica M. Arienzo, Graham Sexstone, Stefan Rahimi Apr 2022

#### Black Carbon Dominated Dust In Recent Radiative Forcing On Rocky Mountain Snowpacks, Kelly E. Gleason, Joseph R. Mcconnell, Monica M. Arienzo, Graham Sexstone, Stefan Rahimi

##### Environmental Science and Management Faculty Publications and Presentations

The vast majority of surface water resources in the semi-arid western United States start as winter snowpack. Solar radiation is a primary driver of snowmelt, making snowpack water resources especially sensitive to even small increases in concentrations of light absorbing particles such as mineral dust and combustion-related black carbon (BC). Here we show, using fresh snow measurements and snowpack modeling at 51 widely distributed sites in the Rocky Mountain region, that BC dominated impurity-driven radiative forcing in 2018. BC contributed three times more radiative forcing on average than dust, and up to 17 times more at individual locations. Evaluation of ...

Gps-Derived Interseismic Fault Locking Along The Jalisco–Colima Segment Of The Mexico Subduction Zone, Beatriz Cosenza-Muralles, Charles Demets, B. Márquez-Azúa, O. Sánchez, J. Stock, Enrique Cabral-Cano, Robert Mccaffrey Apr 2022

#### Gps-Derived Interseismic Fault Locking Along The Jalisco–Colima Segment Of The Mexico Subduction Zone, Beatriz Cosenza-Muralles, Charles Demets, B. Márquez-Azúa, O. Sánchez, J. Stock, Enrique Cabral-Cano, Robert Mccaffrey

##### Geology Faculty Publications and Presentations

Northeastward subduction of the oceanic Rivera and Cocos plates in western Mexico poses a poorly understood seismic hazard to the overlying areas of the North America plate. We estimate the magnitude and distribution of interseismic locking along the northern ∼500 km of the Mexico subduction zone, with a series of elastic half-space inversions that optimize the fits to the velocities of 57 GPS stations in western Mexico. All velocities were corrected for the co-seismic, afterslip and viscoelastic rebound effects of the 1995 Colima–Jalisco and 2003 Tecomán earthquakes. We explore the robustness of interseismic locking estimates to a variety of ...

Mar 2022

#### Mass Capacity Analysis Of Stormwater Control Measures Using Synthetic Stormwater With Silica, Organic And Hydrocarbon Constituents, Craig Michael Fairbaugh

##### Dissertations and Theses

Stormwater control measure (SCM) performance is well studied regarding solids removal; however, analysis of mass loading capacity, long-term performance, and maintenance demands are challenging due to the variability and multiple constituents inherent in urban stormwater. This research examines the long-term water quality performance and sediment mass capacity of two common SCMs: high rate biofiltration (HRBF) and conventional bioretention (BRT). Pollutant removal trials were conducted in a laboratory setting per the New Jersey Department of Environmental Protection (NJDEP) filtration protocol in two phases: the first using inorganic sediment per the NJDEP protocol, the second phase with the addition of organic sediment ...

Mar 2022

#### Characterization Of High Mobility Channels For Use In Quantum Computing Devices, Payam Amin

##### Dissertations and Theses

Quantum computing promises computation that is fundamentally beyond the reach of classical computers. For the realization of a full-scale quantum computer, millions of quantum bits need to be fabricated on an integrated circuit and operated at cryogenic temperatures. Silicon and silicon-germanium based electron spin quantum bits have the advantage of leveraging decades of semiconductor industry knowledge for high volume manufacturability.

During the process development of any semiconductor device, material characterization is essential to understand and improve the process. Transmission electron microscopy is the only technique that could offer localized high spatial resolution characterization. In this work we have introduced two ...

Dependence Comparisons Of Order Statistics In The Proportional Hazards Model, Subhash C. Kochar Mar 2022

#### Dependence Comparisons Of Order Statistics In The Proportional Hazards Model, Subhash C. Kochar

##### Mathematics and Statistics Faculty Publications and Presentations

Let X1,…,Xn be mutually independent exponential random variables with distinct hazard rates λ1,…,λn > 0 and let Y1,…,Yn be a random sample from the exponential distribution with hazard rate $\bar \lmd = \sum_{i=1}^n \lmd_i/n$. Also let X1:n < ⋯ < Xn:n and Y1:n < ⋯ < Yn:n be their associated order statistics. It is shown that for 1 i < j n, the generalized spacing Xj:n - X i:n is more dispersed than Yj:n− Yi:n according to dispersive ordering. This result is used to ...

Fenchel-Rockafellar Theorem In Infinite Dimensions Via Generalized Relative Interiors, Dang Van Cuong, Mau Nam Nguyen, B. S. Mordukhovich, G. Sandine Mar 2022

#### Fenchel-Rockafellar Theorem In Infinite Dimensions Via Generalized Relative Interiors, Dang Van Cuong, Mau Nam Nguyen, B. S. Mordukhovich, G. Sandine

##### Mathematics and Statistics Faculty Publications and Presentations

In this paper we provide further studies of the Fenchel duality theory in the general framework of locally convex topological vector (LCTV) spaces. We prove the validity of the Fenchel strong duality under some qualification conditions via generalized relative interiors imposed on the epigraphs and the domains of the functions involved. Our results directly generalize the classical Fenchel-Rockafellar theorem on strong duality from finite dimensions to LCTV spaces.

#### Using Intrinsically-Typed Definitional Interpreters To Verify Compiler Optimizations In A Monadic Intermediate Language, Dani Barrack

##### Dissertations and Theses

Compiler optimizations are critical to the efficiency of modern functional programs. At the same time, optimizations that unintentionally change the semantics of programs can systematically introduce errors into programs that pass through them. The question of how to best verify that optimizations and other program transformations preserve semantics is an important one, given the potential for error introduction. Dependent types allow us to prove that properties about our programs are correct, as well as to design data types and interpreters in such a way that they are correct-by-construction. In this thesis, we explore the use of dependent types and intrinsically-typed ...

Cetacean Strandings In The Us Pacific Northwest 2000–2019 Reveal Potential Linkages To Oceanographic Variability, Amanda J. Warlick, Jessica L. Huggins, Dyanna M. Lambourn, Deborah A. Duffield, Dalin Nichole D'Alessandro, James M. Rice, John Calambokidis, M. Bradley Hanson, Joseph K. Gaydos, Multiple Additional Authors Mar 2022

#### Cetacean Strandings In The Us Pacific Northwest 2000–2019 Reveal Potential Linkages To Oceanographic Variability, Amanda J. Warlick, Jessica L. Huggins, Dyanna M. Lambourn, Deborah A. Duffield, Dalin Nichole D'Alessandro, James M. Rice, John Calambokidis, M. Bradley Hanson, Joseph K. Gaydos, Multiple Additional Authors

##### Biology Faculty Publications and Presentations

Studying patterns in marine mammal stranding cases can provide insight into changes in population health, abundance, and distribution. Cetaceans along the United States West coast strand for a wide variety of reasons, including disease, injury, and poor nutritional status, all of which may be caused by both natural and anthropogenic factors. Examining the potential drivers of these stranding cases can reveal how populations respond to changes in their habitat, notably oceanographic variability and anthropogenic activities. In this study, we aim to synthesize recent patterns in 1,819 cetacean strandings across 26 species in the Pacific Northwest from 2000 to 2019 ...

Continuum Dynamics And Statistical Correction Of Compositional Heterogeneity In Multivalent Idp Oligomers Resolved By Single-Particle Em, Barmak Mostofian, Russell Mcfarland, Aiden Estelle, Jesse Howe, Elisar J. Barbar, Steve L. Reichow, Daniel M. Zuckerman Mar 2022

#### Continuum Dynamics And Statistical Correction Of Compositional Heterogeneity In Multivalent Idp Oligomers Resolved By Single-Particle Em, Barmak Mostofian, Russell Mcfarland, Aiden Estelle, Jesse Howe, Elisar J. Barbar, Steve L. Reichow, Daniel M. Zuckerman

##### Chemistry Faculty Publications and Presentations

Multivalent intrinsically disordered protein (IDP) complexes are prevalent in biology and act in regulation of diverse processes, including transcription, signaling events, and the assembly and disassembly of complex macromolecular architectures. These systems pose significant challenges to structural investigation, due to continuum dynamics imparted by the IDP and compositional heterogeneity resulting from characteristic low-affinity interactions. Here, we developed a modular pipeline for automated single-particle electron microscopy (EM) distribution analysis of common but relatively understudied semi-ordered systems: 'beads-on-a-string' assemblies, composed of IDPs bound at multivalent sites to the ubiquitous ∼20kDacross-linking hub protein LC8. This approach quantifies conformational geometries and compositional heterogeneity on ...

An Algorithm For Identifying Eigenvectors Exhibiting Strong Spatial Localization, Jeffrey S. Ovall, Lisa Zurk Mar 2022

#### An Algorithm For Identifying Eigenvectors Exhibiting Strong Spatial Localization, Jeffrey S. Ovall, Lisa Zurk

##### Mathematics and Statistics Faculty Publications and Presentations

We introduce an approach for exploring eigenvector localization phenomena for a class of (unbounded) selfadjoint operators. More specifically, given a target region and a tolerance, the algorithm identifies candidate eigenpairs for which the eigenvector is expected to be localized in the target region to within that tolerance. Theoretical results, together with detailed numerical illustrations of them, are provided that support our algorithm. A partial realization of the algorithm is described and tested, providing a proof of concept for the approach.