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At least 1,063 records · Page 59

Direct estimation of the density of states for fermionic systems

Simulating time evolution is one of the most natural applications of quantum computers and is thus one of the most promising prospects for achieving practical quantum advantage. Here, we develop quantum algorithms to extract thermodynamic properties by estimating the density of states (DOS), which is a central object in quantum statistical mechanics. We introduce several key innovations that significantly improve the practicality and extend the generality of previous techniques. First, our approach allows one to estimate the DOS only for a specific subspace of the full Hilbert space. This is crucial for fermionic systems, since both canonical and grand canonical ensemble thermal equilibrium properties depend on subspaces of fixed number. Second, in our approach, by time evolving very simple, random initial states, such as randomly chosen computational basis states, we can exactly recover the DOS on average. Third, due to circuit-depth limitations, we only reconstruct the DOS up to a convolution with a Gaussian window—thus all imperfections that shift the energy levels by less than the width of the convolution window will not significantly affect the estimated DOS. For these reasons, we find the approach is a promising candidate for early quantum advantage as even short-time, noisy dynamics can yield a semiquantitative reconstruction of the DOS (convolution with a broad Gaussian window), while early fault-tolerant devices will likely enable higher-resolution DOS reconstruction through longer time evolutions. We demonstrate the practicality of our approach in representative Fermi-Hubbard and spin models and indeed find that our approach is highly robust against algorithmic errors in the time evolution and against gate noise. We further demonstrate that our approach is compatible with noisy intermediate-scale quantum (NISQ) computing NISQ-friendly variational techniques, introducing and leveraging a technique for variational time evolution.

97 MATHEMATICS AND COMPUTING↗

NSE abundance data

A novel method of calculating nuclear statistical equilibrium (NSE) is presented. Basic equations are carefully solved using arbitrary precision arithmetic. A special interpolation procedure is then used to retrieve all abundances using tabulated results for neutrons and protons, together with basic nuclear data. Proton and neutron abundance tables, basic nuclear data, and partition functions for nuclides used in the calculations are provided. A simple interpolation algorithm using pre-calculated p and n abundances tabulated as functions of kT, {rho} and Y{sub e} is outlined. Unique properties of this method are: (1) ability to pick up out of NSE selected nuclei only, (2) computational time scaling linearly with number of re-calculated abundances, (3) relatively small amount of stored data: only two large tables, (4) slightly faster than solving the NSE equations using traditional Newton-Raphson methods for small networks (few tens of species); superior for huge (800-3000) networks, (5) does not require initial guess; works well on random input, (6) can be tailored to specific application, (7) ability to use third-party NSE solvers to obtain fully compatible tables, and (8) encapsulation of the NSE code for bug-free calculations. A range of applications for this approach is possible: covering tests of traditional NSE Newton-Raphson codes, generating starting values, code-to-code verification, and possible replacement of the old legacy procedures in supernova simulations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A microbenchmark characterization of the Emu chick

The Emu Chick is a prototype system designed around the concept of migratory memory-side processing. Rather than transferring large amounts of data across power-hungry, high-latency interconnects, the Emu Chick moves lightweight thread contexts to near-memory cores before the beginning of each memory read. The current prototype hardware uses FPGAs to implement cache-less “Gossamer” cores for computational work and rely on a typical stationary core (PowerPC) to run basic operating system functions and migrate threads between nodes. In this multi-node characterization of the Emu Chick, we extend an earlier single-node investigation of the the memory bandwidth characteristics of the system through benchmarks like STREAM, pointer chasing, and sparse matrix-vector multiplication. Here, we compare the Emu Chick hardware to architectural simulation and an Intel Xeon-based platform. Our results demonstrate that for many basic operations the Emu Chick can use available memory bandwidth more efficiently than a more traditional, cache-based architecture although bandwidth usage suffers for computationally intensive workloads like SpMV. Moreover, the Emu Chick provides stable, predictable performance with up to 65% of the peak bandwidth utilization on a random-access pointer chasing benchmark with weak locality.

97 MATHEMATICS AND COMPUTING↗

Estimating contact rates at a mass gathering by using video analysis: a proof-of-concept project

Current approaches for estimating social mixing patterns and infectious disease transmission at mass gatherings have been limited by various constraints, including low participation rates for volunteer-based research projects and challenges in quantifying spatially and temporally accurate person-to-person interactions. We developed a proof-of-concept project to assess the use of automated video analysis for estimating contact rates of attendees of the GameFest 2013 event at Rensselaer Polytechnic Institute (RPI) in Troy, New York. Video tracking and analysis algorithms were used to estimate the number and duration of contacts for 5 attendees during a 3-minute clip from the RPI video. Attendees were considered to have a contact event if the distance between them and another person was ≤1 meter. Contact duration was estimated in seconds. We also simulated 50 attendees assuming random mixing using a geospatially accurate representation of the same GameFest location. The 5 attendees had an overall median of 2 contact events during the 3-minute video clip (range: 0 6). Contact events varied from less than 5 seconds to the full duration of the 3- minute clip. The random mixing simulation was visualized and presented as a contrasting example. We were able to estimate the number and duration of contacts for five GameFest attendees from a 3-minute video clip that can be compared to a random mixing simulation model at the same location. In conclusion, the next phase will involve scaling the system for simultaneous analysis of mixing patterns from hours-long videos and comparing our results with other approaches for collecting contact data from mass gathering attendees.

59 BASIC BIOLOGICAL SCIENCES↗

OPERA models for predicting physicochemical properties and environmental fate endpoints

The collection of chemical structure information and associated experimental data for quantitative structure–activity/ property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public databases containing large amounts of useful data. However, the performance of QSAR models highly depends on the quality of the data and modeling methodology used. This study aims to develop robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes. This study primarily uses data from the publicly available PHYSPROP database consisting of a set of 13 common physicochemical and environmental fate properties. These datasets have undergone extensive curation using an automated workflow to select only high-quality data, and the chemical structures were standardized prior to calculation of the molecular descriptors. The modeling procedure was developed based on the five Organization for Economic Cooperation and Development (OECD) principles for QSAR models. A weighted k-nearest neighbor approach was adopted using a minimum number of required descriptors calculated using PaDEL, an open-source software. The genetic algorithms selected only the most pertinent and mechanistically interpretable descriptors (2–15, with an average of 11 descriptors). The sizes of the modeled datasets varied from 150 chemicals for biodegradability half-life to 14,050 chemicals for logP, with an average of 3222 chemicals across all endpoints. The optimal models were built on randomly selected training sets (75%) and validated using fivefold cross-validation (CV) and test sets (25%). The CV Q2 of the models varied from 0.72 to 0.95, with an average of 0.86 and an R2 test value from 0.71 to 0.96, with an average of 0.82. Modeling and performance details are described in QSAR model reporting format and were validated by the European Commission’s Joint Research Center to be OECD compliant. All models are freely available as an open-source, command-line application called OPEn structure–activity/property Relationship App (OPERA). OPERA models were applied to more than 750,000 chemicals to produce freely available predicted data on the U.S. Environmental Protection Agency’s CompTox Chemistry Dashboard.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sparse Bayesian Regression with Integrated Feature Selection for Nuclear Reactor Analysis

High-dimensional, nonlinear function estimation using large datasets is a current area of interest in the machine learning community, and applications may be found throughout the analytical sciences, where ever-growing datasets are making more information available to the analyst. In this paper, we leverage the existing relevance vector machine, a sparse Bayesian version of the well-studied support vector machine, and expand the method to include integrated feature selection and automatic function shaping. These innovations produce an algorithm that is able to distinguish variables that are useful for making predictions of a response from variables that are unrelated or confusing. We test the technology using synthetic data, conduct initial performance studies, and develop a model capable of making position-independent predictions of the coreaveraged burnup using a single specimen drawn randomly from a nuclear reactor core.

Dayman, Ken J↗

Generalized master equation for particle transport in binary random media with renewal statistics

Particle transport in binary stochastic mixtures is classically modeled assuming Markovian or exponential mixing statistics but in many applications material memory invalidates the Markov assumption. For non-Markovian mixing characterized by alternating renewal processes, a transport-theoretic framework is presented that provides an exact description of transport in nonscattering random binary media with general non-exponential statistics. Our approach is to Markovianize the problem by augmenting the {material type, particle flux} state space with the age or distance from the last interface. A Chapman-Kolmogorov equation is formulated for the joint probability density of the material type, particle flux, and age, and subsequently reduced to a generalized Master equation (GME) in differential form. This constitutes the primary result of this work. A state-updating Monte Carlo algorithm consistent with the GME is developed and benchmarked against analytical solutions for multiple chord-length laws. For purely absorbing renewal statistical media, the GME reproduces analytical benchmarks for the equilibrium age distribution, interior mean/variance of material-conditioned fluxes, and boundary transmittance. Simulations further demonstrate that a Markov (exponential) approximation of non-exponential statistics can introduce large errors in transmittance and interior flux profiles. Lastly, the reintroduction of memory due to scattering is briefly addressed through heuristic considerations.

Fluctuations & noise↗

Short-Depth QAOA circuits and Quantum Annealing on Higher-Order Ising Models (Rev.2)

The Quantum Alternating Operator Ansatz (QAOA) and Quantum Annealing (QA) are quantum algorithms that are both based on the adiabatic theorem and both have the goal of sampling the optimal solution(s) of combinatorial optimization problems. Quantum annealing has been physically instantiated on D-Wave devices using superconducting flux qubits, and QAOA can be programmed on digital gate-model quantum computers such as the programmable superconducting transmon qubits devices of the IBMQ series, for instance ibm washington. QAOA and QA address the same types of problems, but it is unclear how they will scale to large problem sizes and to larger and higher-fidelity quantum computers. In this article, we present a direct comparison between QAOA, one and two rounds, run on all 127 qubits of ibm washington and QA run on D-Wave Advantage system4.1 and Advantage system6.1. The problems which allow for this comparison are random Ising model problems whose connectivity matches the heavy hexagonal lattice topology of ibm washington and the Pegasus graph connectivity of the two D-Wave devices. We create two classes of problem instances for this comparison: one with higher order terms (ZZZ variable interactions), linear terms, and quadratic terms, and a separate problem type with only linear and quadratic terms. Our QAOA circuits are novel and extremely short depth, with a CNOT depth of 6 per round, which allows whole chip usage of ibm washington’s heavy hexagonal lattice and can be applied to future heavy-hex chips. We also test the effectiveness of the error suppression technique digital dynamical decoupling on the QAOA circuits. The QAOA circuits compiled to ibm washington are composed of several thousand circuit instructions, approximately 3, 000 depending on the details of the circuit, making these some the largest quantum circuits ever executed on a digital quantum processor. QAOA and QA are compared against the classical heuristic algorithm of simulated annealing and all problem instances are exactly solved using CPLEX in order to evaluate which samplers, if any, correctly found the ground state solution(s) of the problem instances. We find that (i) QA outperforms QAOA on all problem instances, (ii) QAOA samples the problems better than random sampling, and (iii) QAOA angle computation exhibits clear parameter concentration across the ensemble of Ising models.

127 Qubits↗

Error Convergence Characterization for Stochastic Transport Methods

There has been increased interest in reliably and efficiently solving engineering systems involving uncertainty in recent years. Characterization of the convergence of errors within the problem, including statistical and bias errors, increases confidence that chosen solution methods are appropriate for a particular problem and quantity of interest (QoI), that implementation errors have not been made, and can aid users or algorithms in solving problems within a tolerance efficiently. We demonstrate a method for characterizing error convergence in a simple stochastic transport problem. Though the approach is applicable to problems with more complicated physics, our simple problem enables analytic QoI solutions so that error convergence behavior and the identification of limiting errors can be presented with high precision. A one-dimensional, two-material, neutral-particle, and absorption-only transport problem involving uniformly distributed uncertain total cross sections is presented. Random sampling (RS) and stochastic collocation (SC) are used as stochastic solvers which sample from the uncertain space and Monte Carlo (MC) transport is employed to solve transport results on the resulting realizations. Probability density functions (PDFs) are created using either RS solutions or samples taken from a polynomial chaos expansion (PCE) constructed with SC solutions. The convergence of each solver is characterized with respect to the QoI against analytic solutions, convergence behavior is used to efficiently solve a QoI within a tolerance, and convergence plots are used to identify dominant solution errors.

42 ENGINEERING↗

Combinatorial theory of the semiclassical evaluation of transport moments II: Algorithmic approach for moment generating functions

Electronic transport through chaotic quantum dots exhibits universal behaviour which can be understood through the semiclassical approximation. Within the approximation, calculation of transport moments reduces to codifying classical correlations between scattering trajectories. These can be represented as ribbon graphs and we develop an algorithmic combinatorial method to generate all such graphs with a given genus. This provides an expansion of the linear transport moments for systems both with and without time reversal symmetry. The computational implementation is then able to progress several orders further than previous semiclassical formulae as well as those derived from an asymptotic expansion of random matrix results. The patterns observed also suggest a general form for the higher orders.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Image-based model of the spectrin cytoskeleton for red blood cell simulation

We simulate deformable red blood cells in the microcirculation using the immersed boundary method with a cytoskeletal model that incorporates structural details revealed by tomographic images. The elasticity of red blood cells is known to be supplied by both their lipid bilayer membranes, which resist bending and local changes in area, and their cytoskeletons, which resist in-plane shear. The cytoskeleton consists of spectrin tetramers that are tethered to the lipid bilayer by ankyrin and by actin-based junctional complexes. We model the cytoskeleton as a random geometric graph, with nodes corresponding to junctional complexes and with edges corresponding to spectrin tetramers such that the edge lengths are given by the end-to-end distances between nodes. The statistical properties of this graph are based on distributions gathered from three-dimensional tomographic images of the cytoskeleton by a segmentation algorithm. We show that the elastic response of our model cytoskeleton, in which the spectrin polymers are treated as entropic springs, is in good agreement with the experimentally measured shear modulus. By simulating red blood cells in flow with the immersed boundary method, we compare this discrete cytoskeletal model to an existing continuum model and predict the extent to which dynamic spectrin network connectivity can protect against failure in the case of a red cell subjected to an applied strain. As a result, the methods presented here could form the basis of disease- and patient-specific computational studies of hereditary diseases affecting the red cell cytoskeleton.

59 BASIC BIOLOGICAL SCIENCES↗

Peak Rain Rate Sensitivity to Observed Cloud Condensation Nuclei and Turbulence in Continental Warm Shallow Clouds During CACTI

Abstract Warm clouds strongly affect Earth's energy budget but remain imperfectly represented in climate models, partly due to the complexity and covariability of relevant processes influencing warm rain. This work presents a detailed analysis of different factors affecting rain rate peak intensity (RR) in continental warm clouds. Clouds were identified with vertically pointing radar and lidar observations and categorized via a temperature‐based cloud type classification algorithm from which warm clouds were isolated. Observations and retrievals of liquid water path (LWP), cloud condensation nuclei concentration (N CCN ), cloud depth, and cloud duration of more than 3,000 separate warm clouds sampled during the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign are analyzed in this work. Multiple linear regression (MLR) and random forest (RF) models are applied to assess the relative impact of these variables on RR. Overall, RR tends to increase as cloud depth, LWP, and cloud duration increase, or N CCN decreases. Cloud depth affects RR the most while N CCN impacts it the least. When considering over 170 warm clouds observed at least 1 hr in which in‐cloud turbulence is retrieved, the effect of N CCN on RR remains most likely suppressive, but it is not significant at a 75% level for MLR and is highly uncertain for RF. The impact of in‐cloud turbulence depends on the moment and location it is sampled. Cloud base turbulence around the time of RR suppresses RR, while cloud top turbulence effects are inconclusive. Possible difficulties in isolating robust CCN and turbulence effects on RR are discussed.

54 ENVIRONMENTAL SCIENCES↗

Cache Locality Optimization for Recursive Programs

We present an approach to optimize the cache locality for recursive programs by dynamically splicing--recursively interleaving--the execution of distinct function invocations. By utilizing data effect annotations, we identify concurrency and data reuse opportunities across function invocations and interleave them to reduce reuse distance. We present algorithms that efficiently track effects in recursive programs, detect interference and dependencies, and interleave execution of function invocations using user-level (non-kernel) lightweight threads. To enable multi-core execution, a program is parallelized using a nested fork/join programming model. Our cache optimization strategy is designed to work in the context of a random work stealing scheduler. We present an implementation using the MIT Cilk framework that demonstrates significant improvements in sequential and parallel performance, competitive with a state-of-the-art compile-time optimizer for loop programs and a domain- specific optimizer for stencil programs.

Lifflander, Jonathan↗

CosTuuM: Polarized Thermal Dust Emission by Magnetically Oriented Spheroidal Grains

We present the new open-source C++-based Python library CosTuuM that can be used to generate infrared absorption and emission coefficients for arbitrary mixtures of spheroidal dust grains that are (partially) aligned with a magnetic field. We outline the algorithms underlying the software, demonstrate the accuracy of our results using benchmarks from literature, and use our tool to investigate some commonly used approximative recipes. We find that the linear polarization fraction for a partially aligned dust grain mixture can be accurately represented by an appropriate linear combination of perfectly aligned grains and grains that are randomly oriented, but that the commonly used picket fence alignment breaks down for short wavelengths. We also find that for a fixed dust grain size, the absorption coefficients and linear polarization fraction for a realistic mixture of grains with various shapes cannot both be accurately represented by a single representative grain with a fixed shape, but that instead an average over an appropriate shape distribution should be used. Insufficient knowledge of an appropriate shape distribution is the main obstacle in obtaining accurate optical properties. CosTuuM is available as a standalone Python library and can be used to generate optical properties to be used in radiative transfer applications.

79 ASTRONOMY AND ASTROPHYSICS↗

Performance of Replica-Exchange Wang-Landau Sampling for the 2D Ising Model: A Brief Survey

We report a brief performance study of the replica-exchange Wang-Landau algorithm, a recently proposed parallel realization of Wang-Landau sampling, using the 2D Ising model as a test case. The simulation time is found to scale inversely with the square root of the number of subwindows (and thus number of processors) used to span the global parameter space. We also investigate the time profiles for random walkers in dierent subwindows to complete iterations, which will aid the development of and adaptive load-balancing scheme.

Zhao, Yiwei↗

Karhunen-Loeve expansion analysis of uncertainties in cloud microphysical property retrievals

Here, this study proposes a methodology of quantifying uncertainties for cloud retrievals on model resolution to facilitate the comparison with model outputs. Primary component analysis is applied to reduce the dimension of random variables (up to a factor of 50) and reveal the cross correlations in the input data, making large sampling computationally feasible and uncertainty quantification accurate and reliable. Our approach has the capability of parameterizing input uncertainties and attributing the uncertainties in the retrieval output to each individual source, which allows sensitivity analysis of cloud retrieval algorithms and provides directions for improving observation instruments as well as strategies. We applied the method to characterize uncertainties in cloud ice water content (IWC) retrieved from the DOE Atmospheric Radiation Measurement (ARM) programs baseline cloud microphysical retrieval algorithm (MICROBASE). We test it with a selected ice cloud case observed on 9 March 2000 at the ARM Southern Great Plains site during its 2000 cloud intensive observing period. The test results indicate that (1) uncertainties in the output retrieved by MICROBASE are comparable amongst different retrievals; (2) The mean values obtained by our UQ method are closer to the aircraft data with less errors compared to the direct ensemble average; (3) Ice water path (IWP) generally incurred larger uncertainty in optically thin ice clouds and there was more variability in vertical in the retrieved IWC; and (4) Uncertainties in the output are mainly due to the interactions among different modes of ARM radar pro files.

54 ENVIRONMENTAL SCIENCES↗

Six Machine-Learning Methods for Predicting Hospital-Stay Duration for Patients with Sepsis: A Comparative Study

Sepsis is a life-threatening medical condition that, if not treated promptly, can result in tissue damage, organ failure, and death. According to the Centers for Disease Control, about 270,000 individuals die of sepsis in the US each year. Further, sepsis expenditures accounted for 13% of total US hospital costs in 2013, totaling more than $24 billion. Our project objectives were to determine if Machine Learning algorithms could reliably predict hospital stay duration for patients with sepsis. The data set we used has been de-identified and is freely available through the BupaR package. The data includes 1050 cases, 15214 events, and 16 types of actions related to sepsis patient care. First, we used process mining to determine how long each patient was in the hospital. Using BupaR’s functions, we created several process model graphs. These process models depict the movement of patients at a hospital and provide duration data for each patent case. Second, we identified outlier data and created two dataset versions: one with and one without outliers. We then applied the following analysis methods: Linear Regression, Random Forest, K-Nearest Neighbors, Neural Networks, XGBoost, and lightGBM. We compared the model validations for the six machine learning models using the same data-splitting method. We found that the XGBoost model had the best prediction accuracy of 73.9 percent for cases with outliers, and 79 percent for cases without outliers. We also found that the lightGBM model had the lowest mean absolute error between prediction and actual duration in days with 3.66 days for the case with outliers, and 2.4 days for the case without outliers. These two models outperformed the other four models. This work will be enhanced in the future by exploring new prediction algorithms and comparing them with the results of this study.

Chen, Lingtao↗

A Fano cavity test for Monte Carlo proton transport algorithms

Purpose: In the scope of reference dosimetry of radiotherapy beams, Monte Carlo (MC) simulations are widely used to compute ionization chamber dose response accurately. Uncertainties related to the transport algorithm can be verified performing self-consistency tests, i.e., the so-called “Fano cavity test.” The Fano cavity test is based on the Fano theorem, which states that under charged particle equilibrium conditions, the charged particle fluence is independent of the mass density of the media as long as the cross-sections are uniform. Such tests have not been performed yet for MC codes simulating proton transport. The objectives of this study are to design a new Fano cavity test for proton MC and to implement the methodology in two MC codes: Geant4 and PENELOPE extended to protons (PENH). Methods: The new Fano test is designed to evaluate the accuracy of proton transport. Virtual particles with an energy ofE{sub 0} and a mass macroscopic cross section of (Σ)/(ρ) are transported, having the ability to generate protons with kinetic energy E{sub 0} and to be restored after each interaction, thus providing proton equilibrium. To perform the test, the authors use a simplified simulation model and rigorously demonstrate that the computed cavity dose per incident fluence must equal (ΣE{sub 0})/(ρ) , as expected in classic Fano tests. The implementation of the test is performed in Geant4 and PENH. The geometry used for testing is a 10 × 10 cm{sup 2} parallel virtual field and a cavity (2 × 2 × 0.2 cm{sup 3} size) in a water phantom with dimensions large enough to ensure proton equilibrium. Results: For conservative user-defined simulation parameters (leading to small step sizes), both Geant4 and PENH pass the Fano cavity test within 0.1%. However, differences of 0.6% and 0.7% were observed for PENH and Geant4, respectively, using larger step sizes. For PENH, the difference is attributed to the random-hinge method that introduces an artificial energy straggling if step size is not small enough. Conclusions: Using conservative user-defined simulation parameters, both PENH and Geant4 pass the Fano cavity test for proton transport. Our methodology is applicable to any kind of charged particle, provided that the considered MC code is able to track the charged particle considered.

62 RADIOLOGY AND NUCLEAR MEDICINE↗