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At least 253 records · Page 14

Discrimination of Mild Cognitive Impairment and Alzheimer′s Disease Using Transfer Entropy Measures of Scalp EEG

Mild cognitive impairment (MCI) is a neurological condition related to early stages of dementia including Alzheimer′s disease (AD). This study investigates the potential of measures of transfer entropy in scalp EEG for effectively discriminating between normal aging, MCI, and AD participants. Resting EEG records from 48 age‐matched participants (mean age 75.7 years)—15 normal controls, 16 MCI, and 17 early AD—are examined. The mean temporal delays corresponding to peaks in inter‐regional transfer entropy are computed and used as features to discriminate between the three groups of participants. Three‐way classification schemes based on binary support vector machine models demonstrate overall discrimination accuracies of 91.7— 93.8%, depending on the protocol condition. These results demonstrate the potential for EEG transfer entropy measures as biomarkers in identifying early MCI and AD. Moreover, the analyses based on short data segments (two minutes) render the method practical for a primary care setting.

McBride, Joseph↗

Molecular fluctuations inhibit intermittency in compressible turbulence

In the standard picture of fully developed turbulence, highly intermittent hydrodynamic fields are nonlinearly coupled across scales, where local energy cascades from large scales into dissipative vortices and large density gradients. Microscopically, however, constituent fluid molecules are in constant thermal (Brownian) motion, but the role of molecular fluctuations in large-scale turbulence is largely unknown, and with rare exceptions, it has historically been considered irrelevant at scales larger than the molecular mean free path. Recent theoretical and computational investigations have shown that molecular fluctuations can impact energy cascade at Kolmogorov length scales. Here, we show that molecular fluctuations not only modify energy spectrum at wavelengths larger than the Kolmogorov length in compressible turbulence, but also significantly inhibit spatio-temporal intermittency across the entire dissipation range. Using large-scale direct numerical simulations of computational fluctuating hydrodynamics, we demonstrate that the extreme intermittency characteristic of turbulence models is replaced by nearly Gaussian statistics in the dissipation range. These results demonstrate that the compressible Navier–Stokes equations should be augmented with molecular fluctuations to accurately predict turbulence statistics across the dissipation range. Our findings have significant consequences for turbulence modelling in applications such as astrophysics, reactive flows and hypersonic aerodynamics, where dissipation-range turbulence is approximated by closure models.

compressible turbulence↗

Temporal regulation of cold transcriptional response in switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis- regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k -mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k -mers, referred to as putative cis -regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

60 APPLIED LIFE SCIENCES↗

Spatio-Temporal Data Analysis at Scale Using Models Based on Gaussian Processes

Gaussian processes are the most commonly used statistical model for spatial and spatio-temporal processes that vary continuously. They are broadly applicable in the physical sciences and engineering and are also frequently used to approximate the output of complex computer models, deterministic or stochastic. We undertook research related to theory, computation, and applications of Gaussian processes as well as some work on estimating extremes of distributions for which a Gaussian process assumption might be inappropriate. Our theoretical contributions include the development of new classes of spatial-temporal covariance functions with desirable properties and new results showing that certain covariance models lead to predictions with undesirable properties. To understand how Gaussian process models behave when applied to deterministic computer models, we derived what we believe to be the first significant results on the large sample properties of estimators of parameters of Gaussian processes when the actual process is a simple deterministic function. Finally, we investigated some theoretical issues related to maxima of observations with varying upper bounds and found that, depending on the circumstances, standard large sample results for maxima may or may not hold. Our computational innovations include methods for analyzing large spatial datasets when observations fall on a partially observed grid and methods for estimating parameters of a Gaussian process model from observations taken by a polar-orbiting satellite. In our application of Gaussian process models to deterministic computer experiments, we carried out some matrix computations that would have been infeasible using even extended precision arithmetic by focusing on special cases in which all elements of the matrices under study are rational and using exact arithmetic. The applications we studied include total column ozone as measured from a polar-orbiting satellite, sea surface temperatures over the Pacific Ocean, and annual temperature extremes at a site in New York City. In each of these applications, our theoretical and computational innovations were directly motivated by the challenges posed by analyzing these and similar types of data.

97 MATHEMATICS AND COMPUTING↗

Topological terms with qubit regularization and relativistic quantum circuits

Qubit regularization provides a rich framework to explore quantum field theories. The freedom to choose how the important symmetries of the theory are embedded in the qubit regularization scheme allows us to construct new lattice models with rich phase diagrams. Some of the phases can contain topological terms which lead to critical phases. In this work we introduce and study the SU(3)-F qubit regularization scheme to embed the SO(3) spin-symmetry. We argue that qubit models in this regularization scheme contain several phases including a critical phase which describes the k = 1 Wess-Zumino-Witten (WZW) conformal field theory (CFT) at long distances, and two massive phases one of which is trvially gapped and the other which breaks the lattice translation symmetry. We construct a simple space-time Euclidean lattice model with a single coupling U and study it using the Monte Carlo method. We show the model has a critical phase at small U and a trivially massive phase at large U with a first order transition separating the two. Another feature of our model is that it is symmetric under space-time rotations, which means the temporal and spatial lattice spacing are connected to each other. The unitary time evolution operator obtained by a Wick rotation of the transfer matrix of our model can help us compute the physics of the k = 1 WZW CFT in real time without the need for tuning the temporal lattice spacing to zero. We use this idea to introduce the concept of a relativistic quantum circuit on a discrete space-time lattice.

Bhattacharya, Tanmoy↗

Apparatus for characterizing the temporo-spatial properties of a dynamic fluid front and method thereof

Methods and apparatus are described for characterizing the temporal-spatial properties of a dynamic fluid front within a mold space while the mold space is being filled with fluid. A method includes providing a mold defining a mold space and having one or more openings into the mold space; heating a plurality of temperature sensors that extend into the mold space; injecting a fluid into th emold space through the openings, the fluid experiencing a dynamic fluid front while filling the mold space with a fluid; and characterizing temporal-spatial properties of the dynamic fluid front by monitoring a termperature of each of the plurality of heated temperature sensors while the mold space is being filled with the fluid. An apparatus includes a mold defining a mold space; one or more openings for introducing a fluid into th emold space and filling the mold space with the fluid, the fluid experiencing a dynamic fluid front while filling the mold space; a plurality of heated temperature sensors extending into the mold space; and a computer coupled to the plurality of heated temperature sensors for characterizing the temporal-spatial properties of the dynamic fluid front.

47 OTHER INSTRUMENTATION↗

Covering Resilience: A Recent Development for Binomial Checkpointing

In terms of computing time, adjoint methods offer a very attractive alternative to compute gradient information, required, e.g., for optimization purposes. However, together with this very favorable temporal complexity result comes a memory requirement that is in essence proportional with the operation count of the underlying function, e.g., if algorithmic differentiation is used to provide the adjoints. For this reason, checkpointing approaches in many variants have become popular. This paper analyzes an extension of the so-called binomial approach to cover also possible failures of the computing systems. Such a measure of precaution is of special interest for massive parallel simulations and adjoint calculations where the mean time between failure of the large scale computing system is smaller than the time needed to complete the calculation of the adjoint information. We describe the extensions of standard checkpointing approaches required for such resilience, provide a corresponding implementation and discuss first numerical results.

Walther, Andrea↗

Spatially Resolving Lithiation in Silicon–Graphite Composite Electrodes via in Situ High-Energy X-ray Diffraction Computed Tomography

Optimizing the chemical and morphological parameters of lithium-ion (Li-ion) electrodes is extremely challenging, due in part to the absence of techniques to construct spatial and temporal descriptions of chemical and morphological heterogeneities. We present the first demonstration of combined high-speed X-ray diffraction (XRD) and XRD computed tomography (XRD-CT) to probe, in 3D, crystallographic heterogeneities within Li-ion electrodes with a spatial resolution of 1 um. The local charge-transfer mechanism within and between individual particles was investigated in a silicon(Si)-graphite composite electrode. Here, high-speed XRD revealed charge balancing kinetics between the graphite and Si during the minutes following the transition from operation to open circuit. Subparticle lithiation heterogeneities in both Si and graphite were observed using XRD-CT, where the core and shell structures were segmented, and their respective diffraction patterns were characterized.

36 MATERIALS SCIENCE↗

Boson sampling with Gaussian input states: Toward efficient scaling and certification

A universal quantum computer of large scale is not available yet, however, intermediate models of quantum computation would still permit demonstrations of a quantum computational advantage over classical computing and could challenge the Extended Church-Turing Thesis. One of these models based on single photons interacting via linear optics is called Boson Sampling. Although Boson Sampling was demonstrated and the threshold to claim quantum computational advantage was achieved, the question of how to scale up Boson Sampling experiments remains. To make progress with this problem, here we present a practically achievable pathway to scale Boson Sampling experiments by combining continuous-variable quantum information and temporal encoding. Here, we propose the combination of switchable dual-homodyne and single-photon detections, the temporal loop technique, and scattershot-based Boson Sampling. We detail the required assumptions for concluding computational hardness for this configuration. Furthermore, this particular combination of techniques moves towards an efficient scaling and certification of Boson Sampling, all in a single experimental setup.

79 ASTRONOMY AND ASTROPHYSICS↗

A general spatial-temporal framework for short-term building temperature forecasting at arbitrary locations with crowdsourcing weather data

Weather forecasting has been a critical component to predict and control building energy consumption for better building energy management. Without accessibility to other data sources, the onsite observed temperatures or the airport temperatures are used in forecast models. In this paper, we present a novel approach by utilizing the crowdsourcing weather data from neighboring personal weather stations (PWS) to improve the weather forecast accuracy around buildings using a general spatial-temporal modeling framework. The final forecast is based on the ensemble of local forecasts for the target location using neighboring PWSs. Our approach is distinguished from existing literature in various aspects. First, we leverage the crowdsourcing weather data from PWS in addition to public data sources. In this way, the data is at much finer time resolution (e.g., at 5-minute frequency) and spatial resolution (e.g., arbitrary location vs grid). Second, our proposed model incorporates spatial-temporal correlation information of weather variables between the target building and a set of neighboring PWSs so that underlying correlations can be effectively captured to improve forecasting performance. Here, we demonstrate the performance of the proposed framework by comparing to the benchmark models on temperature forecasting for a building located at an arbitrary location at San Antonio, Texas, USA. In general, the proposed model framework equipped with machine learning technique such as Random Forest can improve forecasting by 50% compares with persistent model and has 90% chance to outperform airport forecast in short-term forecasting. In a real-time setting, the proposed model framework can provide more accurate temperature forecasting results compared with using airport temperature forecast for most forecast horizon. Moreover, we analyze the sensitivity of model parameters to gain insights on how crowdsourcing data from the neighboring personal weather stations impacts forecasting performance. Finally, we implement our model in other cities such as Syracuse and Chicago to test the model's performance in different landforms and climate types.

54 ENVIRONMENTAL SCIENCES↗

AN OVERVIEW OF REDUCED ORDER MODELING TECHNIQUES FOR SAFETY APPLICATIONS

The RISMC project is developing new advanced simulation-based tools to perform Computational Risk Analysis (CRA) for the existing fleet of U.S. nuclear power plants (NPPs). These tools numerically model not only the thermal-hydraulic behavior of the reactors primary and secondary systems, but also external event temporal evolution and component/system ageing. Thus, this is not only a multi-physics problem being addressed, but also a multi-scale problem (both spatial, µm-mm-m, and temporal, seconds-hours-years). As part of the RISMC CRA approach, a large amount of computationally-expensive simulation runs may be required. An important aspect is that even though computational power is growing, the overall computational cost of a RISMC analysis using brute-force methods may be not viable for certain cases. A solution that is being evaluated to assist the computational issue is the use of reduced order modeling techniques. During the FY2015, we investigated and applied reduced order modeling techniques to decrease the RISMC analysis computational cost by decreasing the number of simulation runs; for this analysis improvement we used surrogate models instead of the actual simulation codes. This article focuses on the use of reduced order modeling techniques that can be applied to RISMC analyses in order to generate, analyze, and visualize data. In particular, we focus on surrogate models that approximate the simulation results but in a much faster time (microseconds instead of hours/days).

97 MATHEMATICS AND COMPUTING↗

A semiparametric latent factor model for large scale temporal data with heteroscedasticity

Large scale temporal data have flourished in a vast array of applications, and their sophisticated structures, especially the heteroscedasticity among subjects with inter- and intra-temporal dependence, have fueled a great demand for new statistical models. In this paper, with covariate information, we consider a flexible model for large scale temporal data with subject-specific heteroscedasticity. Formally, the model employs latent semiparametric factors to simultaneously account for the subject-specific heteroscedasticity and the contemporaneous and/or serial correlations. The subject-specific heteroscedasticity is modeled as the product of the unobserved factor process and subject’s covariate effect, which is further characterized via additive models. For estimation, we propose a two-step procedure. First, the latent factor process and nonparametric loading are recovered through projection-based methods, and following, we estimate the regression components by approaches motivated from the generalized least squares. By scrupulously examining the non-asymptotic rates for recovering the factor process and its loading, we show the consistency and efficiency of estimated regression coefficients in the absence of prior knowledge of latent factor process and subject’s covariate effect. Here, the statistical guarantees remain valid even for finite time points that makes our method particularly appealing when the subjects significantly outnumber the observation time points. Using comprehensive simulations, we demonstrate the finite sample performance of our method, which corroborates the theoretical findings. Finally, we apply our method to a data set of air quality and energy consumption collected at 129 monitoring sites in the United States in 2015.

97 MATHEMATICS AND COMPUTING↗

Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection

A key question in SARS-CoV-2 infection is why viral loads and patient outcomes vary dramatically across individuals. Because spatial-temporal dynamics of viral spread and immune response are challenging to study in vivo, we developed Spatial Immune Model of Coronavirus (SIMCoV), a scalable computational model that simulates hundreds of millions of lung cells, including respiratory epithelial cells and T cells. SIMCoV replicates viral growth dynamics observed in patients and shows how spatially dispersed infections can lead to increased viral loads. The model also shows how the timing and strength of the T cell response can affect viral persistence, oscillations, and control. By incorporating spatial interactions, SIMCoV provides a parsimonious explanation for the dramatically different viral load trajectories among patients by varying only the number of initial sites of infection and the magnitude and timing of the T cell immune response. When the branching airway structure of the lung is explicitly represented, we find that virus spreads faster than in a 2D layer of epithelial cells, but much more slowly than in an undifferentiated 3D grid or in a well-mixed differential equation model. These results illustrate how realistic, spatially explicit computational models can improve understanding of within-host dynamics of SARS-CoV-2 infection.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient Space–Time Reduced Order Model for Linear Dynamical Systems in Python Using Less than 120 Lines of Code

A classical reduced order model (ROM) for dynamical problems typically involves only the spatial reduction of a given problem. Recently, a novel space–time ROM for linear dynamical problems has been developed [Choi et al., Space–tume reduced order model for large-scale linear dynamical systems with application to Boltzmann transport problems, Journal of Computational Physics, 2020], which further reduces the problem size by introducing a temporal reduction in addition to a spatial reduction without much loss in accuracy. The authors show an order of a thousand speed-up with a relative error of less than 10−5 for a large-scale Boltzmann transport problem. In this work, we present for the first time the derivation of the space–time least-squares Petrov–Galerkin (LSPG) projection for linear dynamical systems and its corresponding block structures. Utilizing these block structures, we demonstrate the ease of construction of the space–time ROM method with two model problems: 2D diffusion and 2D convection diffusion, with and without a linear source term. For each problem, we demonstrate the entire process of generating the full order model (FOM) data, constructing the space–time ROM, and predicting the reduced-order solutions, all in less than 120 lines of Python code. We compare our LSPG method with the traditional Galerkin method and show that the space–time ROMs can achieve O(10−3) to O(10−4) relative errors for these problems. Depending on parameter–separability, online speed-ups may or may not be achieved. For the FOMs with parameter–separability, the space–time ROMs can achieve O(10) online speed-ups. Finally, we present an error analysis for the space–time LSPG projection and derive an error bound, which shows an improvement compared to traditional spatial Galerkin ROM methods.

97 MATHEMATICS AND COMPUTING↗

Modeling the impact of bubbling bed hydrodynamics on tar yield and its fluctuations during biomass fast pyrolysis

The impact of bubbling bed hydrodynamics on temporal variations in the exit tar yield for biomass fast pyrolysis was investigated using computational simulations of an experimental laboratory-scale reactor. A multi-fluid computational fluid dynamics model was employed to simulate the differential conservation equations in the reactor, and this was combined with a multi-component, multi-step pyrolysis kinetics scheme for biomass to account for chemical reactions. The predicted mean tar yields at the reactor exit appear to match corresponding experimental observations. Parametric studies predicted that increasing the fluidization velocity should improve the mean tar yield but increase its temporal variations. Increases in the mean tar yield coincide with reducing the diameter of sand particles or increasing the initial sand bed height. However, trends in tar yield variability are more complex than the trends in mean yield. The standard deviation in tar yield reaches a maximum with changes in sand particle size. As a result, the standard deviation in tar yield increases with the increases in initial bed height in freely bubbling state, while reaches a maximum in slugging state.

09 BIOMASS FUELS↗

Arithmetic Primitives for Efficient Neuromorphic Computing

Neuromorphic computing is steadily gaining popularity in many scientific and engineering disciplines. However, one of the biggest problems that has prevented widespread usage of neuromorphic computing is the lack of efficient encoding methods. Traditional encoding methods such as binning, rate encoding, and temporal encoding are based on unary encoding and generate a large number of spikes for certain applications, making them less energy efficient. Lack of better encoding methods has also prevented preprocessing operations from being carried out on neuromorphic computers. As a result, over 99% of the time can be spent on data preprocessing and data transfer operations in some cases, leading to an inefficient workflow. In this paper, we present preliminary results that would enable us to efficiently encode data and perform basic arithmetic operations on neuromorphic computers. First, we present a neuromorphic approach for the two’s complement encoding of numbers and leverage it to devise addition and multiplication circuits, which could be used in preprocessing operations on neuromorphic computers. We test our approach on the SuperNeuroMAT simulator. Our results indicate that two’s complement is a highly efficient encoding method in terms of time, space, and energy complexity and that the addition and multiplication circuits produce accurate results on two numbers having arbitrary precision.

Wurm, Ahna↗

Space-Time Quantum Information from the Entangled States of Magnetic Molecule (STI Product)

This collaborative project combines synthesis, measurement, and theory by three faculty members at the Eddleman Quantum Institute of UC Irvine to effectively investigate the quantum properties of molecules in the space, time, and frequency domains. Through synthetic chemistry, molecules are tailored for their magnetic and coherent properties. By combining femtosecond (fs) terahertz (THz) light and a continuous wave (cw) THz laser with a low temperature scanning tunneling microscope (STM), quantum phenomena are probed with simultaneous femtosecond temporal and atomic-scale spatial resolution. In particular, the invention of the quantum superposition microscope (QSM) advances quantum sensing for enhanced spectroscopy and imaging capabilities. Coupling theory to the experimental efforts offers a deeper understanding and predictive power for the molecular systems. The phenomena of superposition, entanglement, and coherence is central to quantum information science and can be realized in qubit states. Many systems can be modeled by a double-well potential in which two levels are formed in the two lowest energy states interacting with the environment and external radiation. In focusing on molecules as two-level systems, the underlying expectation is that their tunable composition and structure allows an effective parameter space to optimize their use as qubits for quantum sensing and computing. The THz radiation induces the superposition between the two states, appearing as temporal oscillations that damp in amplitude. Enhanced spectroscopy and imaging in the time and frequency domains is achieved through the extreme sensitivity of the frequency and damping of coherence of two-level systems to its environment. A single hydrogen molecule trapped in the STM tunneling gap experiences a double-well potential and absorption of THz femtosecond pulses of light creates the superposition of its two levels, appearing as damped oscillations in the light induced direct current (DC). The oscillation frequency depends sensitively on the electric field distribution of the copper nitride (Cu 2 N) surface, through the Stark effect, and associated with the different charge distributions at the copper and nitrogen sites and in between. This QSM can resolve variation in the surface electric field with 0.02 nanometer resolution. In addition, the single hydrogen molecule entaes with nearby hydrogen molecules as seen in the avoided level crossings of energy (oscillation frequency) versus the voltage across the tunneling gap. Thus, the first application of the QSM senses and images the surface electric field at the atomic scale. Results from this project advance fundamental understanding of quantum phenomena, develop novel synthesis, measurement, and theory, provide the knowledge foundation for molecule-based qubits and sensing that enable the development of the QSM and emergent technologies. This project trained researchers in quantum information science, extended knowledge in classrooms, and outreached to the community.

47 OTHER INSTRUMENTATION↗

A second-order-in-time, explicit approach addressing the redundancy in the low-Mach, variable-density Navier-Stokes equations

A novel algorithm for explicit temporal discretization of the variable-density, low-Mach Navier-Stokes equations is presented here in this study. Recognizing there is a redundancy between the mass conservation equation, the equation of state, and the transport equation(s) for the scalar(s) which characterize the thermochemical state, and that it destabilizes explicit methods, we demonstrate how to analytically eliminate the redundancy and propose an iterative scheme to solve the resulting transformed scalar equations. The method obtains second-order accuracy in time regardless of the number of iterations, so one can terminate this subproblem once stability is achieved. Hence, flows with larger density ratios can be simulated while still retaining the efficiency, low cost, and parallelizability of an explicit scheme. The temporal discretization algorithm is used within a pseudospectral direct numerical simulation which extends the method of Kim, Moin, and Moser for incompressible flow to the variable-density, low-Mach setting, where we demonstrate stability for density ratios up to ~25.7.

97 MATHEMATICS AND COMPUTING↗