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 …

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 …

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 …

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 …

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.

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.

“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 …

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 …

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.

Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury

Mathematics, Physics, and Computer Science Faculty Articles and Research

Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …

Estimation Of The Virtual Water Content Of Main Crops On The Korean Peninsula Using Multiple Regional Climate Models And Evapotranspiration Methods, Chul-Hee Lim, Seung Hee Kim, Yuyoung Choi, Menas Kafatos, Woo-Kyun Lee

Mathematics, Physics, and Computer Science Faculty Articles and Research

Sustainable agriculture in the era of climate change needs to find solutions for the retention and proper utilization of water. This study proposes an ensemble approach for identifying the virtual water content (VWC) of main crops on the Korean Peninsula in past and future climates. Ensemble results with low uncertainty were obtained using three regional climate models, five potential evapotranspiration methods, and the Environmental Policy Integrated Climate (EPIC) crop model. The productivity results of major crops (rice and maize) under climate change are likely to increase more than in the past based on the ensemble results. The ensemble VWC is …

Multi-Type Display Calculus For Semi-De Morgan Logic, Giuseppe Greco, Fei Liang, M. Andrew Moshier, Alessandra Palmigiano

Mathematics, Physics, and Computer Science Faculty Articles and Research

We introduce a proper multi-type display calculus for semi De Morgan logic which is sound, complete, conservative, and enjoys cut-elimination and subformula property. Our proposal builds on an algebraic analysis of semi De Morgan algebras and applies the guidelines of the multi-type methodology in the design of display calculi.

Satellite Observation Of Ch4 And Co Anomalies Associated With The Wenchuan Ms 8.0 And Lushan Ms 7.0 Earthquakes In China, Y. Cui, Dimitar Ouzounov, N. Hatzopoulos, K. Sun, Z. Zou, J. Du

Mathematics, Physics, and Computer Science Faculty Articles and Research

Spatial and temporal variations of total column of CH4 and CO (TotCH4 and TotCO) associated with the 12 May 2008 Wenchuan and 20 April 2013 Lushan earthquakes in western Sichuan, China were investigated using satellite data from AQUA AIRS in order to understand the lithospheric and atmospheric interactions during the seismic activity. The Wenchuan MS 8.0 and Lushan MS7.0 earthquakes occurred in the Longmenshan fault zone. It was observed that large amounts of gases emitted from the earth's crust into the atmosphere before, during and after the earthquakes. The anomalies of TotCH4 and TotCO occurred along the …

Is A Time Symmetric Interpretation Of Quantum Theory Possible Without Retrocausality?, Matthew S. Leifer, Matthew F. Pusey

Mathematics, Physics, and Computer Science Faculty Articles and Research

Huw Price has proposed an argument that suggests a time symmetric ontology for quantum theory must necessarily be retrocausal, i.e. it must involve influences that travel backwards in time. One of Price's assumptions is that the quantum state is a state of reality. However, one of the reasons for exploring retrocausality is that it offers the potential for evading the consequences of no-go theorems, including recent proofs of the reality of the quantum state. Here, we show that this assumption can be replaced by a different assumption, called λ-mediation, that plausibly holds independently of the status of the quantum …

Ultrasensitive Inverse Weak-Value Tilt Meter, Julián Martínez-Rincón, Christopher A. Mullarkey, Gerardo I. Viza, Wei-Tao Liu, John C. Howell

Mathematics, Physics, and Computer Science Faculty Articles and Research

We present an interferometric technique for measuring ultrasmall tilts. The information of a tilt in one of the mirrors of a modified Sagnac interferometer is carried by the phase difference between the counter-propagating laser beams. Using a small misalignment of the interferometer, orthogonal to the plane of the tilt, a bimodal (or two-fringe) pattern is induced in the beam’s transverse power distribution. By tracking the mean of such a distribution, using a split detector, a sensitive measurement of the phase is performed. With 1.2 mW of continuous-wave laser power, the technique has a shot noise limited sensitivity of 56 frad/Hz−−−√ …

The Spatiotemporal Distribution Of Air Pollutants And Their Relationship With Land-Use Patterns In Hangzhou City, China, Sheng Zheng, Xueyuan Zhou, Ramesh Singh, Yuzhe Wu, Yanmei Ye, Cifang Wu

Mathematics, Physics, and Computer Science Faculty Articles and Research

Air pollution contributes to a large fraction of the total mortality estimated under the global burden of disease project (GBD) of the World Health Organization (WHO). This paper discusses an integrated study to obtain the spatiotemporal characteristics of particulate matter (PM10 and PM2.5) and trace gases (O3, SO2, NO2, and CO) pollutants in Hangzhou City (China) for the years 2014–2016. Our detailed analysis shows a relationship between air pollutants and land-use/land-cover change. Air quality parameters (PM2.5 and PM10) and trace gases (SO2, NO2, and CO) show strong monthly variations in the months of January (higher values) and July (lower values). …

Practical Advantages Of Almost-Balanced-Weak-Value Metrological Techniques, Julián Martínez-Rincón, Zekai Chen, John C. Howell

Mathematics, Physics, and Computer Science Faculty Articles and Research

Precision measurements of ultrasmall linear velocities of one of the mirrors in a Michelson interferometer are performed using two different weak-value techniques. We show that the technique of almost-balanced weak values (ABWV) offers practical advantages over the technique of weak-value amplification, resulting in larger signal-to-noise ratios and the possibility of longer integration times due to robustness to slow drifts. As an example of the performance of the ABWV protocol we report a velocity sensitivity of 60 fm/s after 40 h of integration time. The sensitivity of the Doppler shift due to the moving mirror is 150 nHz.

On Tarski's Axiomatic Foundations Of The Calculus Of Relations, Hajnal Andréka, Steven Givant, Peter Jipsen, István Németi

Mathematics, Physics, and Computer Science Faculty Articles and Research

It is shown that Tarski’s set of ten axioms for the calculus of relations is independent in the sense that no axiom can be derived from the remaining axioms. It is also shown that by modifying one of Tarski’s axioms slightly, and in fact by replacing the right-hand distributive law for relative multiplication with its left-hand version, we arrive at an equivalent set of axioms which is redundant in the sense that one of the axioms, namely the second involution law, is derivable from the other axioms. The set of remaining axioms is independent. Finally, it is shown that if …

Beurling-Lax Type Theorems In The Complex And Quaternionic Setting, Daniel Alpay, Irene Sabadini

Mathematics, Physics, and Computer Science Faculty Articles and Research

We give a generalization of the Beurling–Lax theorem both in the complex and quaternionic settings. We consider in the first case functions meromorphic in the right complex half-plane, and functions slice hypermeromorphic in the right quaternionic half-space in the second case. In both settings we also discuss a unified framework, which includes both the disk and the half-plane for the complex case and the open unit ball and the half-space in the quaternionic setting.

Relation Algebras, Idempotent Semirings And Generalized Bunched Implication Algebras, Peter Jipsen

Mathematics, Physics, and Computer Science Faculty Articles and Research

This paper investigates connections between algebraic structures that are common in theoretical computer science and algebraic logic. Idempotent semirings are the basis of Kleene algebras, relation algebras, residuated lattices and bunched implication algebras. Extending a result of Chajda and Länger, we show that involutive residuated lattices are determined by a pair of dually isomorphic idempotent semirings on the same set, and this result also applies to relation algebras. Generalized bunched implication algebras (GBI-algebras for short) are residuated lattices expanded with a Heyting implication. We construct bounded cyclic involutive GBI-algebras from so-called weakening relations, and prove that the class of weakening …

The Case Of The Disappearing (And Re-Appearing) Particle, Yakir Aharonov, Eliahu Cohen, Ariel Landau, Avshalom C. Elitzur

Mathematics, Physics, and Computer Science Faculty Articles and Research

A novel prediction is derived by the Two-State-Vector-Formalism (TSVF) for a particle superposed over three boxes. Under appropriate pre- and post-selections, and with tunneling enabled between two of the boxes, it is possible to derive not only one, but three predictions for three different times within the intermediate interval. These predictions are moreover contradictory. The particle (when looked for using a projective measurement) seems to disappear from the first box where it would have been previously found with certainty, appearing instead within the third box, to which no tunneling is possible, and later re-appearing within the second. It turns out …