Physical Sciences and Mathematics Commons^™

Atomistic Simulations And Network-Based Modeling Of The Hsp90-Cdc37 Chaperone Binding With Cdk4 Client Protein: A Mechanism Of Chaperoning Kinase Clients By Exploiting Weak Spots Of Intrinsically Dynamic Kinase Domains, John Czemeres, Kurt Buse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37- Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic …

Virtual Reality As A Training Tool To Treat Physical Inactivity In Children, Adam W. Kiefer, David Pincus, Michael J. Richardson, Gregory D. Myer

Psychology Faculty Articles and Research

Lack of adequate physical activity in children is an epidemic that can result in obesity and other poor health outcomes across the lifespan. Physical activity interventions focused on motor skill competence continue to be developed, but some interventions, such as neuromuscular training (NMT), may be limited in how early they can be implemented due to dependence on the child’s level of cognitive and perceptual-motor development. Early implementation of motor-rich activities that support motor skill development in children is critical for the development of healthy levels of physical activity that carry through into adulthood. Virtual reality (VR) training may be beneficial …

Interaction-Free Effects Between Distant Atoms, Yakir Aharonov, Eliahu Cohen, Avshalom C. Elitzur, Lee Smolin

Mathematics, Physics, and Computer Science Faculty Articles and Research

A Gedanken experiment is presented where an excited and a ground-state atom are positioned such that, within the former’s half-life time, they exchange a photonwith 50% probability.Ameasurement of their energy statewill therefore indicate in 50% of the cases that no photon was exchanged. Yet other measurements would reveal that, by the mere possibility of exchange, the two atoms have become entangled. Consequently, the “no exchange” result, apparently precluding entanglement, is non-locally established between the atoms by this very entanglement. This quantum-mechanical version of the ancient Liar Paradox can be realized with already existing transmission schemes, with the addition of Bell’s …

Past Observable Dynamics Of A Continuously Monitored Qubit, Luis Pedro García-Pinto, Justin Dressel

Mathematics, Physics, and Computer Science Faculty Articles and Research

Monitoring a quantum observable continuously in time produces a stochastic measurement record that noisily tracks the observable. For a classical process, such noise may be reduced to recover an average signal by minimizing the mean squared error between the noisy record and a smooth dynamical estimate. We show that for a monitored qubit, this usual procedure returns unusual results. While the record seems centered on the expectation value of the observable during causal generation, examining the collected past record reveals that it better approximates a moving-mean Gaussian stochastic process centered at a distinct (smoothed) observable estimate. We show that this …

How Is Your Productivity Affected Based On Your App Usage?, Colette Noghreian

Student Scholar Symposium Abstracts and Posters

As technology becomes more prominent in society, it is crucial to investigate its effect on day to day life. The purpose of this study is to determine how the amount of time spent on iPhone applications affects how productive students feel in the span of one week. Results are tested through a survey which first determines general information about the student, and then guides students to navigate their phone settings and record the battery usage of the top three applications which use up the most battery. It is hypothesized that productivity decreases as battery usage increases due to the substantial …

A Cluster Analysis Of Challenging Behaviors In Autism Spectrum Disorder, Elizabeth Stevens, Abigail Atchison, Laura Stevens, Esther Hong, Doreen Granpeesheh, Dennis Dixon, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

We apply cluster analysis to a sample of 2,116 children with Autism Spectrum Disorder in order to identify patterns of challenging behaviors observed in home and centerbased clinical settings. The largest study of this type to date, and the first to employ machine learning, our results indicate that while the presence of multiple challenging behaviors is common, in most cases a dominant behavior emerges. Furthermore, the trend is also observed when we train our cluster models on the male and female samples separately. This work provides a basis for future studies to understand the relationship of challenging behavior profiles to …

Arrow Of Time For Continuous Quantum Measurement, Justin Dressel, Areeya Chantasri, Andrew N. Jordan, Alexander N. Korotkov

Mathematics, Physics, and Computer Science Faculty Articles and Research

We investigate the statistical arrow of time for a quantum system being monitored by a sequence of measurements. For a continuous qubit measurement example, we demonstrate that time-reversed evolution is always physically possible, provided that the measurement record is also negated. Despite this restoration of dynamical reversibility, a statistical arrow of time emerges, and may be quantified by the log-likelihood difference between forward and backward propagation hypotheses. We then show that such reversibility is a universal feature of nonprojective measurements, with forward or backward Janus measurement sequences that are time-reversed inverses of each other.

Weak-Value Amplification And Optimal Parameter Estimation In The Presence Of Correlated Noise, Josiah Sinclair, Matin Hallaji, Aephraim M. Steinberg, Jeff Tollaksen, Andrew N. Jordan

Mathematics, Physics, and Computer Science Faculty Articles and Research

We analytically and numerically investigate the performance of weak-value amplification (WVA) and related parameter estimation methods in the presence of temporally correlated noise. WVA is a special instance of a general measurement strategy that involves sorting data into separate subsets based on the outcome of a second “partitioning” measurement. Using a simplified correlated noise model that can be analyzed exactly together with optimal statistical estimators, we compare WVA to a conventional measurement method. We find that WVA indeed yields a much lower variance of the parameter of interest than the conventional technique does, optimized in the absence of any partitioning …

No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands store roughly one-third of the terrestrial soil carbon and release the potent greenhouse gas methane (CH₄) to the atmosphere, making these wetlands among the most important ecosystems in the global carbon cycle. Despite their importance, the controls of anaerobic decomposition of organic matter to carbon dioxide (CO₂) and CH₄ within peatlands are not well understood. It is known, however, that the enzymes responsible for CH₄ production require cobalt, iron and nickel, and there is a growing appreciation for the potential role of trace metal limitation in anaerobic decomposition. To explore the possibility of …

Ensemble-Based Modeling And Rigidity Decomposition Of Allosteric Interaction Networks And Communication Pathways In Cyclin-Dependent Kinases: Differentiating Kinase Clients Of The Hsp90-Cdc37 Chaperone, Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK …

Responsive Nanogel Probe For Ratiometric Fluorescent Sensing Of Ph And Strain In Hydrogels, Mingning Zhu, Dongdong Lu, Shanglin Wu, Qing Lian, Wenkai Wang, Amir H. Milani, Zhengxing Cui, Nam T. Nguyen, Mu Chen, L. Andrew Lyon, Daman J. Adlam, Anthony J. Freemont, Judith A. Hoyland, Brian R. Saunders

Engineering Faculty Articles and Research

In this study a new pH-responsive nanogel probe containing a complementary nonradiative resonance energy transfer (NRET) fluorophore pair is investigated and its ability to act as a versatile probe of network-related changes in three hydrogels demonstrated. Fluorescent sensing using NRET is a powerful method for studying relationships between Angstrom length-scale structure and macroscopic properties of soft matter. Unfortunately, inclusion of NRET fluorophores into such materials requires material-specific chemistry. Here, low concentrations of preformed nanogel probes were included into hydrogel hosts. Ratiometric photoluminescence (PL) data for the gels labeled with the nanogel probes enabled pH-triggered swelling and deswelling to be studied …

Critical Digital Literacies Across Scales And Beneath The Screen, Noah Asher Golden

Education Faculty Articles and Research

Digital technologies and education scholarship tend to focus on either individual creative design or analysis of the political economy. To better understand how ideologies travel across networks, critical digital literacies must focus on enactments beneath the screen, as the linguistic constructs known as software can enact interests across scales of activity to “disembed” local actions and meaning. Investigations of these mobilities and disembedding effects challenge popular notions of digital technologies as neutral, rendering overt the ways that algorithms can naturalize manifestations of power and social arrangements. Such a framework allows for descriptive analyses of the ways hegemonic discourses are enacted …

Knotty Inflation And The Dimensionality Of Spacetime, Arjun Berera, Roman V. Buniy, Thomas W. Kephart, Heinrich Päs, João G. Rosa

Mathematics, Physics, and Computer Science Faculty Articles and Research

We suggest a structure for the vacuum comprised of a network of tightly knotted/linked flux tubes formed in a QCD-like cosmological phase transition and show that such a network can drive cosmological inflation. As the network can be topologically stable only in three space dimensions, this scenario provides a dynamical explanation for the existence of exactly three large spatial dimensions in our Universe.

Using Tablet Technologies To Engage And Motivate Urban High School Students, Nicol R. Howard, Keith Howard

Education Faculty Articles and Research

In this two-year study, researchers examined the impact of using tablet technologies across content areas in an urban high school setting. Class observations provided notable examples of how student motivation and learning appeared to be enhanced by use of the iPads in conjunction with opportunities to collaborate and be creative in the context of their learning. Interviews from a set of teachers with a range of classroom teaching experience provided multiple perspectives of the program’s impact. The opportunity for teachers and students to have the flexibility to select the apps they believe achieve curricular and/or learning goals supports the shift …

What Controls Variation In Carbon Use Efficiency Among Amazonian Tropical Forests?, Christopher E. Doughty, Gregory R. Goldsmith, Nicolas Raab, Cecile A. J. Girardin, Filio Farfan-Amezquita, Walter Huaraca-Huasco, Javier E. Silva-Espejo, Alejandro Araujo-Murakami, Antonio C. L. Da Costa, Wanderley Rocha, David Galbraith, Patrick Meir, Dan B. Metcalfe, Yadvinder Malhi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Why do some forests produce biomass more efficiently than others? Variations in Carbon Use Efficiency (CUE: total Net Primary Production (NPP)/ Gross Primary Production (GPP)) may be due to changes in wood residence time (Biomass/NPP_wood), temperature, or soil nutrient status. We tested these hypotheses in 14, one ha plots across Amazonian and Andean forests where we measured most key components of net primary production (NPP: wood, fine roots, and leaves) and autotrophic respiration (R_a; wood, rhizosphere, and leaf respiration). We found that lower fertility sites were less efficient at producing biomass and had higher rhizosphere respiration, …

Distributive Residuated Frames And Generalized Bunched Implication Algebras, Nikolaos Galatos, Peter Jipsen

Mathematics, Physics, and Computer Science Faculty Articles and Research

We show that all extensions of the (non-associative) Gentzen system for distributive full Lambek calculus by simple structural rules have the cut elimination property. Also, extensions by such rules that do not increase complexity have the finite model property, hence many subvarieties of the variety of distributive residuated lattices have decidable equational theories. For some other extensions, we prove the finite embeddability property, which implies the decidability of the universal theory, and we show that our results also apply to generalized bunched implication algebras. Our analysis is conducted in the general setting of residuated frames.

Phase Behavior Of Binary And Polydisperse Suspensions Of Compressible Microgels Controlled By Selective Particle Deswelling, A. Scotti, U. Gasser, E. S. Herman, Jun Han, A. Menzel, L. Andrew Lyon, A. Fernandez-Nieves

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We investigate the phase behavior of suspensions of poly(N-isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions.We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest …

“Wrong” Side Interpolation By Positive Real Rational Functions, Daniel Alpay, Izchak Lewkowicz

Mathematics, Physics, and Computer Science Faculty Articles and Research

Using polynomial interpolation, along with structural properties of the family of rational positive real functions, we here show that a set of m nodes in the open left half of the complex plane, can always be mapped to anywhere in the complex plane by rational positive real functions whose degree is at most m. Moreover we introduce an easy-to-find parametrization in R2m+3 of a large subset of these interpolating functions.

An Evaluation Of The Effects Of Intensity And Duration On Outcomes Across Treatment Domains For Children With Autism Spectrum Disorder, Erik J. Linstead, D. R. Dixon, E. Hong, C. O. Burns, Ryan French, M. N. Novack, D. Granpeesheh

Mathematics, Physics, and Computer Science Faculty Articles and Research

Applied behavior analysis (ABA) is considered an effective treatment for individuals with autism spectrum disorder (ASD), and many researchers have further investigated factors associated with treatment outcomes. However, few studies have focused on whether treatment intensity and duration have differential influences on separate skills. The aim of the current study was to investigate how treatment intensity and duration impact learning across different treatment domains, including academic, adaptive, cognitive, executive function, language, motor, play, and social. Separate multiple linear regression analyses were used to evaluate these relationships. Participants included 1468 children with ASD, ages 18 months to 12 years old, M= …

Evolution Of Superoscillations For Schrödinger Equation In A Uniform Magnetic Field, Fabrizio Colombo, Jonathan Gantner, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

Aharonov-Berry superoscillations are band-limited functions that oscillate faster than their fastest Fourier component. Superoscillations appear in several fields of science and technology, such as Aharonov’s weak measurement in quantum mechanics, in optics, and in signal processing. An important issue is the study of the evolution of superoscillations using the Schrödinger equation when the initial datum is a weak value. Some superoscillatory functions are not square integrable, but they are real analytic functions that can be extended to entire holomorphic functions. This fact leads to the study of the continuity of a class of convolution operators acting on suitable spaces of …

Sheaf Theoretic Formulation For Consciousness And Qualia And Relationship To The Idealism Of Non-Dual Philosophies, Menas Kafatos, Goro Kato

Mathematics, Physics, and Computer Science Faculty Articles and Research

Questions about the nature of reality, whether Consciousness is the fundamental reality in the universe, and what is Consciousness itself, have no answer in systems that assume an external reality independent of Consciousness. Ultimately, the ontological foundation of such systems is the absolute division of subject and object. We advocate instead what we consider to be an approach that is in agreement with the foundation of quantum reality, which is based on Rāmānuja’s version of Vedanta philosophy and non-dual Kashmir Śaivism. Quantum mechanics opened the door to consciousness, but it cannot account for consciousness. However, the quantum measurement problem implies …

Thermal Radiation Anomalies Associated With Major Earthquakes, Dimitar Ouzounov, Sergey Pulinets, Menas Kafatos, Patrick Taylor

Mathematics, Physics, and Computer Science Faculty Articles and Research

Recent developments of remote sensing methods for Earth satellite data analysis contribute to our understanding of earthquake related thermal anomalies. It was realized that the thermal heat fluxes over areas of earthquake preparation is a result of air ionization by radon (and other gases) and consequent water vapor condensation on newly formed ions. Latent heat (LH) is released as a result of this process and leads to the formation of local thermal radiation anomalies (TRA) known as OLR (outgoing Longwave radiation, Ouzounov et al, 2007). We compare the LH energy, obtained by integrating surface latent heat flux (SLHF) over the …

Nonlinear Oscillatory Dynamics Of The Hardening Of Calcium Phosphate Bone Cements, Vuk Uskoković, Julietta V. Rau

Pharmacy Faculty Articles and Research

Here we report on the nonlinear, oscillatory dynamics detected in the evolution of phase composition during the setting of different calcium phosphate cements, two of which evolved toward brushite and one toward hydroxyapatite as the final product. Whereas both brushite-forming cements contained iondoped b-tricalcium phosphate as the initial phase, the zinc-containing one yielded scholzite as an additional phase during setting and the oscillations between these two products were pronounced throughout the entire 80 h setting period, long after the hardening processes was over from the mechanical standpoint. Oscillations in the copper-containing system involved the amount of brushite as the main …

T-Time: A Data Repository Of T Cell And Calcium Release-Activated Calcium Channel Activation Imagery, Cody Arbuckle, Milton L. Greenberg, Adrienne Bergh, Rene German, Nick Sirago, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

BACKGROUND: A fundamental understanding of live-cell dynamics is necessary in order to advance scientific techniques and personalized medicine. For this understanding to be possible, image processing techniques, probes, tracking algorithms and many other methodologies must be improved. Currently there are no large open-source datasets containing live-cell imaging to act as a standard for the community. As a result, researchers cannot evaluate their methodologies on an independent benchmark or leverage such a dataset to formulate scientific questions.

FINDINGS: Here we present T-Time, the largest free and publicly available data set of T cell phase contrast imagery designed with the …

Linear Feedback Stabilization Of A Dispersively Monitored Qubit, Taylor Lee Patti, Areeya Chantasri, Luis Pedro García-Pintos, Andrew N. Jordan, Justin Dressel

Mathematics, Physics, and Computer Science Faculty Articles and Research

The state of a continuously monitored qubit evolves stochastically, exhibiting competition between coherent Hamiltonian dynamics and diffusive partial collapse dynamics that follow the measurement record. We couple these distinct types of dynamics together by linearly feeding the collected record for dispersive energy measurements directly back into a coherent Rabi drive amplitude. Such feedback turns the competition cooperative and effectively stabilizes the qubit state near a target state. We derive the conditions for obtaining such dispersive state stabilization and verify the stabilization conditions numerically.We include common experimental nonidealities, such as energy decay, environmental dephasing, detector efficiency, and feedback delay, and show …

Traceable Peo-Poly(Ester) Micelles For Breast Cancer Targeting: The Effect Of Core Structure And Targeting Peptide On Micellar Tumor Accumulation, Shyam M. Garg, Igor M. Paiva, Mohammad R. Vakili, Rania Soudy, Kate Agopsowicz, Amir H. Soleimani, Mary Hitt, Kamaljit Kaur, Afsaneh Lavasanifar

Pharmacy Faculty Articles and Research

Traceable poly(ethylene oxide)-poly(ester) micelles were developed through chemical conjugation of a near-infrared (NIR) dye to the poly(ester) end by click chemistry. This strategy was tried for micelles with poly(ε-caprolactone) (PCL) or poly(α-benzyl carboxylate-ε-caprolactone) (PBCL) cores. The surface of both micelles was also modified with the breast cancer targeting peptide, P18-4. The results showed the positive contribution of PBCL over PCL core on micellar thermodynamic and kinetic stability as well as accumulation in primary orthotopic MDA-MB-231 tumors within 4–96 h following intravenous administration in mice. This was in contrast to in vitro studies where better uptake of PEO-PCL versus PEO-PBCL micelles …

Responses Of Agroecosystems To Climate Change: Specifics Of Resilience In The Mid-Latitude Region, Menas Kafatos, Seung Hee Kim, Chul-Hee Lim, Jinwon Kim, Woo-Kyun Lee

Mathematics, Physics, and Computer Science Faculty Articles and Research

This study examines the productivity and resilience of agroecosystems in the Korean Peninsula. Having learned valuable lessons from a Chapman University project funded by the United States Department of Agriculture which concentrated on the semi-arid region of southwestern United States, our joint Korea—Chapman University team has applied similar methodologies to the Korean Peninsula, which is itself an interesting study case in the mid-latitude region. In particular, the Korean Peninsula has unique agricultural environments due to differences in political and socioeconomic systems between South Korea and North Korea. Specifically, North Korea has been suffering from food shortages due to natural disasters, …

Synergistic Use Of Remote Sensing And Modeling To Assess An Anomalously High Chlorophyll-A Event During Summer 2015 In The South Central Red Sea, Wenzhao Li, Hesham El-Askary, K. P. Manikandan, Mohamed A. Qurban, Michael J. Garay, Olga V. Kalishnikova

Mathematics, Physics, and Computer Science Faculty Articles and Research

An anomalously high chlorophyll-a (Chl-a) event (>2 mg/m3) during June 2015 in the South Central Red Sea (17.5° to 22°N, 37° to 42°E) was observed using Moderate Resolution Imaging Spectroradiometer (MODIS) data from the Terra and Aqua satellite platforms. This differs from the low Chl-a values (<0.5 mg/m3) usually encountered over the same region during summertime. To assess this anomaly and possible causes, we used a wide range of oceanographical and meteorological datasets, including Chl-a concentrations, sea surface temperature (SST), sea surface height (SSH), mixed layer depth (MLD), ocean current velocity and aerosol optical depth (AOD) obtained from different sensors and models. Findings confirmed this anomalous behavior in the spatial domain using Hovmöller data analysis techniques, while a time series analysis addressed monthly and daily variability. Our analysis suggests that a combination of factors controlling nutrient supply contributed to the anomalous phytoplankton growth. These factors include horizontal transfer of upwelling water through eddy circulation and possible mineral fertilization from atmospheric dust deposition. Coral reefs might have provided extra nutrient supply, yet this is out of the scope of our analysis. We thought that dust deposition from a coastal dust jet event in late June, coinciding with the phytoplankton blooms in the area under investigation, might have also contributed as shown by our AOD findings. However, a lag cross correlation showed a two- month lag between strong dust outbreak and the high Chl-a anomaly. The high Chl-a concentration at the edge of the eddy emphasizes the importance of horizontal advection in fertilizing oligotrophic (nutrient poor) Red Sea waters.

Estimation Of Bubble-Mediated Air–Sea Gas Exchange From Concurrent Dms And Co2 Transfer Velocities At Intermediate–High Wind Speeds, Thomas G. Bell, Sebastian Landwehr, Scott D. Miller, Warren J. De Bruyn, Adrian H. Callaghan, Brian Scanlon, Brian Ward, Mingxi Yang, Eric S. Saltzman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Simultaneous air–sea fluxes and concentration differences of dimethylsulfide (DMS) and carbon dioxide (CO2/ were measured during a summertime North Atlantic cruise in 2011. This data set reveals significant differences between the gas transfer velocities of these two gases (1kw/ over a range of wind speeds up to 21ms􀀀1. These differences occur at and above the approximate wind speed threshold when waves begin breaking. Whitecap fraction (a proxy for bubbles) was also measured and has a positive relationship with 1kw, consistent with enhanced bubble-mediated transfer of the less soluble CO2 relative to that of the more soluble DMS. However, the correlation …

Oligo(Ethylene Glycol)-Sidechain Microgels Prepared In Absence Of Cross-Linking Agent: Polymerization, Characterization And Variation Of Particle Deformability, Nicole Welsch, L. Andrew Lyon

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network. Moreover, AFM …