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At least 1,135 records · Page 63

Surrogate models for linear response

Linear response theory is a well-established method in physics and chemistry for exploring excitations of many-body systems. In particular, the quasiparticle random-phase approximation (QRPA) provides a powerful microscopic framework by building excitations on top of the mean-field vacuum; however, its high computational cost limits model calibration and uncertainty quantification studies. Here, we present two complementary QRPA surrogate models and apply them to study response functions of finite nuclei. One is a reduced-order model that exploits the underlying QRPA structure, while the other utilizes the recently developed parametric matrix model algorithm to construct a map between the system’s Hamiltonian and observables. Our benchmark applications, the calculation of the electric dipole polarizability of 180 Yb and the 𝛽-decay half-life of 80 Ni, show that both emulators can achieve 0.1%–1% accuracy while offering a 6–7 orders of magnitude speedup compared to state-of-the-art QRPA solvers. These results demonstrate that the developed QRPA emulators are well positioned to enable Bayesian calibration and large-scale studies of computationally expensive physics models describing the properties of many-body systems.

Beta decay↗

Rietveld Refinement for Macromolecular Powder Diffraction

Powder X-ray diffraction (PXRD) has been employed extensively for the structural characterization of materials, quantitative analysis of multicomponent mixtures, phase identification, texture, and microstructural analysis. At the heart of all those lies the Rietveld method, which has revolutionized the use of powder diffraction for materials studies. Initially applied to minerals and inorganics, the Rietveld method has progressively been used for more complex materials, for instance, zeolites and pharmaceuticals. A major advance of the method came some 20 years ago, when the first protein structure was successfully refined. Because of the sheer complexity of macromolecules, several new approaches and algorithms had to be pioneered or adapted from macromolecular single-crystal diffraction experiments, thus constituting macromolecular PXRD a quite unique field of study. This review aims to provide necessary elements of theory and application of structure solution and refinement via the Rietveld method for macromolecular PXRD data. Here, practical explanations and highlighted case studies are also presented.

36 MATERIALS SCIENCE↗

Quantitative Structure Determination from Experimental Four-Dimensional Scanning Transmission Electron Microscopy via the Scattering Matrix

Considerable inroads have recently been made on algorithms to determine the sample potential from four-dimensional scanning transmission electron microscopy data from thick samples where multiple scattering cannot be neglected. This paper further develops the scattering matrix approach to such structure determination. Through simulation, we demonstrate how this approach can be modified to better handle partial spatial coherence, unknown probe defocus, and information from the dark field region. By combining these developments we reconstruct the electrostatic potential of a monolithic SrTiO 3 crystal showing good quantitative agreement with the expected structure.

4D STEM↗

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand–maximize–compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Decomposition Algorithms for Solving NP-hard Problems on a Quantum Annealer

NP-hard problems such as the maximum clique or minimum vertex cover problems, two of Karp’s 21 NP-hard problems, have several applications in computational chemistry, biochemistry and computer network security. Adiabatic quantum annealers can search for the optimum value of such NP-hard optimization problems, given the problem can be embedded on their hardware. However, this is often not possible due to certain limitations of the hardware connectivity structure of the annealer. This paper studies a general framework for a decomposition algorithm for NP-hard graph problems aiming to identify an optimal set of vertices. Our generic algorithm allows us to recursively divide an instance until the generated subproblems can be embedded on the quantum annealer hardware and subsequently solved. Furthermore, the framework is applied to the maximum clique and minimum vertex cover problems, and we propose several pruning and reduction techniques to speed up the recursive decomposition. The performance of both algorithms is assessed in a detailed simulation study.

97 MATHEMATICS AND COMPUTING↗

Block-Iterative Methods for 3D Constant-Coefficient Stencils on GPUs and Multicore CPUs

Block iterative methods are extremely important as smoothers for multigrid methods, as preconditioners for Krylov methods, and as solvers for diagonally dominant linear systems. Developing robust and efficient smoother algorithms suitable for current and evolving GPU and multicore CPU systems is a significant challenge. We address this issue in the case of constant-coefficient stencils arising in the solution of elliptic partial differential equations on structured 3D uniform and adaptively refined block structured grids. Robust, highly parallel implementations of block Jacobi and chaotic block Gauss-Seidel algorithms with exact inversion of the blocks are developed using different parallelization techniques. Experimental results for NVIDIA Fermi/Kepler GPUs and AMD multicore systems are presented.

97 MATHEMATICS AND COMPUTING↗

Machine Learning Classical Interatomic Potentials for Molecular Dynamics from First-Principles Training Data

The ever-increasing power of modern super-computers, along with the availability of highly scalable atomistic simulation codes, has begun to revolutionize predictive modeling of materials. In particular, molecular dynamics (MD) has led to breakthrough advances in diverse fields, including tribology, catalysis, sensing, and nanoparticle self-assembly. Furthermore, recent integration of MD simulations with X-ray characterization has demonstrated promise in real-time 3-D characterization of materials on the atomic scale. The popularity of MD is driven by its applicability at disparate length/time scales, ranging from ab initio MD (hundreds of atoms and tens of picoseconds) to all-atom classical MD (millions of atoms over microseconds), and coarse-grained (CG) models (micrometers and tens of microseconds). Nevertheless, a substantial gap persists between AIMD, which is highly accurate but restricted to extremely small sizes, and those based on classical force fields (atomistic and CG) with limited accuracy but access to larger length/time scales. The accuracy and predictive power of classical MD simulations is dictated by the empirical force fields, and their capability to capture the relevant physics. Here, we discuss some of our recent work on the use of machine learning (ML) to combine the accuracy and flexibility of electronic structure calculations with the speed of classical potentials. Our ML framework attempts to bridge the significant gulf that exists between the handful of research groups that develop new interatomic potential models (often requiring several years of effort), and the increasingly large user community from academia and industry that applies these models. Our data-driven approach represents significant departure from the status quo and involves several steps including generation and manipulation of extensive training data sets through electronic structure calculations, defining novel potential functional forms, employing state-of-the-art ML algorithms to formulate highly optimized training procedures, and subsequently developing user-friendly workflow tools integrating these algorithms on high-performance computers (HPCs). Our ML approach shows marked success in developing force fields for a wide range of materials from metals, oxides, nitrides, and heterointerfaces to two-dimensional (2D) materials.

Chan, Henry↗

Composable Programming of Hybrid Workflows for Quantum Simulation

We present a composable design scheme for the development of hybrid quantum/classical algorithms and workflows for applications of quantum simulation. Our object-oriented approach is based on constructing an expressive set of common data structures and methods that enable programming of a broad variety of complex hybrid quantum simulation applications. The abstract core of our scheme is distilled from the analysis of the current quantum simulation algorithms. Subsequently, it allows a synthesis of new hybrid algorithms and workflows via the extension, specialization, and dynamic customization of the abstract core classes defined by our design. We implement our design scheme using the hardware-agnostic programming language QCOR into the QuaSiMo library. To validate our implementation, we test and show its utility on commercial quantum processors from IBM, running some prototypical quantum simulations.

97 MATHEMATICS AND COMPUTING↗

Disentangling error structures of precipitation datasets using decision trees

Characterizing error structures in precipitation products not only facilitates their proper applications for scientific and practical purposes but also helps improve their retrieval algorithms and processing methods. Despite the fact that multiple precipitation products have been assessed in the literature, factors that affect their error structures remain inadequately addressed. By interpreting 60 binary decision trees, this study disentangles the error characteristics of precipitation products in terms of their spatiotemporal patterns and geographical factors. Three independent precipitation products - two satellite-based and one reanalysis datasets: the Integrated Multi-satellitE Retrievals for GPM (Global Precipitation Measurement) late run (IMERG-L), Soil Moisture to Rain-Advanced SCATterometer (SM2RAIN-ASCAT), and the Modern-Era Retrospective analysis for Research and Applications, Version 2 uncorrected precipitation output (MERRA2-UC), are evaluated across the contiguous United States from 2010 to 2019. Here, the ground-based Stage IV precipitation dataset is used as the ground truth. Results indicate that the MERRA2-UC outperforms the IMERG-L and SM2RAIN-ASCAT with higher accuracy and more stable interannual patterns for the analysis period. Decision trees cross-assess three spatiotemporal factors and find that the underestimation of MERRA2-UC occurs in the east of the Rocky Mountains, and SM2RAIN-ASCAT underestimates precipitation over high latitudes, especially in winter. Additionally, the decision tree method ascribes system errors to nine different geographical characteristics, of which the distance to the coast, soil type, and DEM are the three dominant features. On the other hand, the land cover type, topography position index, and aspect are three relatively weak factors.

54 ENVIRONMENTAL SCIENCES↗

SU-F-T-187: Quantifying Normal Tissue Sparing with 4D Robust Optimization of Intensity Modulated Proton Therapy

Purpose: To report an approach to quantify the normal tissue sparing for 4D robustly-optimized versus PTV-optimized IMPT plans. Methods: We generated two sets of 90 DVHs from a patient’s 10-phase 4D CT set; one by conventional PTV-based optimization done in the Eclipse treatment planning system, and the other by an in-house robust optimization algorithm. The 90 DVHs were created for the following scenarios in each of the ten phases of the 4DCT: ± 5mm shift along x, y, z; ± 3.5% range uncertainty and a nominal scenario. A Matlab function written by Gay and Niemierko was modified to calculate EUD for each DVH for the following structures: esophagus, heart, ipsilateral lung and spinal cord. An F-test determined whether or not the variances of each structure’s DVHs were statistically different. Then a t-test determined if the average EUDs for each optimization algorithm were statistically significantly different. Results: T-test results showed each structure had a statistically significant difference in average EUD when comparing robust optimization versus PTV-based optimization. Under robust optimization all structures except the spinal cord received lower EUDs than PTV-based optimization. Using robust optimization the average EUDs decreased 1.45% for the esophagus, 1.54% for the heart and 5.45% for the ipsilateral lung. The average EUD to the spinal cord increased 24.86% but was still well below tolerance. Conclusion: This work has helped quantify a qualitative relationship noted earlier in our work: that robust optimization leads to plans with greater normal tissue sparing compared to PTV-based optimization. Except in the case of the spinal cord all structures received a lower EUD under robust optimization and these results are statistically significant. While the average EUD to the spinal cord increased to 25.06 Gy under robust optimization it is still well under the TD50 value of 66.5 Gy from Emami et al. Supported in part by the NCI U19 CA021239.

60 APPLIED LIFE SCIENCES↗

Uncertainty-Aware, Structure-Preserving Machine Learning Approach for Domain Shift Detection From Nonlinear Dynamic Responses of Structural Systems

Complex structural systems deployed for aerospace, civil, or mechanical applications must operate reliably under varying operational conditions. Structural health monitoring (SHM) systems help ensure the reliability of these systems by providing continuous monitoring of the state of the structure. SHM relies on synthesizing measured data with a predictive model to make informed decisions about structural states. However, these models—which may be thought of as a form of a digital twin—need to be updated continuously as structural changes (e.g., due to damage) arise. We propose an uncertainty-aware machine learning model that enforces distance preservation of the original input state space and then encodes a distance-aware mechanism via a Gaussian process (GP) kernel. The proposed approach leverages the spectral-normalized neural GP algorithm to combine the flexibility of neural networks with the advantages of GP, subjected to structure-preserving constraints, to produce an uncertainty-aware model. This model is used to detect domain shift due to structural changes that cannot be observed directly because they may be spatially isolated (e.g., inside a joint or localized damage). This work leverages detection theory to detect domain shift systematically given statistical features of the prediction variance produced by the model. The proposed approach is demonstrated on a nonlinear structure being subjected to damage conditions. In conclusion, it is shown that the proposed approach is able to rely on distances of the transformed input state space to predict increased variance in shifted domains while being robust to normative changes.

Algorithms↗

Progress toward favorable landscapes in quantum combinatorial optimization

The performance of variational quantum algorithms relies on the success of using quantum and classical computing resources in tandem. Here, we study how these quantum and classical components interrelate. In particular, we focus on algorithms for solving the combinatorial optimization problem MaxCut, and study how the structure of the classical optimization landscape relates to the quantum circuit used to evaluate the MaxCut objective function. In order to analytically characterize the impact of quantum features on the critical points of the landscape, we consider a family of quantum circuit ansätze composed of mutually commuting elements. We identify multiqubit operations as a key resource and show that overparameterization allows for obtaining favorable landscapes. Namely, we prove that an ansatz from this family containing exponentially many variational parameters yields a landscape free of local optima for generic graphs. However, we further prove that these ansätze do not offer superpolynomial advantages over purely classical MaxCut algorithms. Here, we then present a series of numerical experiments illustrating that noncommutativity and entanglement are important features for improving algorithm performance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discovery that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.

97 MATHEMATICS AND COMPUTING↗

GASP: Gradient-Aware Shortest Path Algorithm for Boundary-Confined 2-Manifold Reeb Graph Visualization

Reeb graphs are an important tool for abstracting and representing the topological structure of a function defined on a manifold. We have identified three properties for faithfully representing Reeb graphs in a visualization: they should be constrained to the boundary, compact, and aligned with the function gradient. Existing algorithms for drawing Reeb graphs are agnostic to or violate these properties. In this paper, we introduce an algorithm to generate Reeb graph visualizations, called GASP, that is cognizant of these properties, thereby producing visualizations that are more representative of the underlying data. To demonstrate the improvements, the resulting Reeb graphs are evaluated both qualitatively and quantitatively against the geometric barycenter algorithm, using its implementation available in the Topology ToolKit (TTK), a widely adopted tool for calculating and visualizing Reeb graphs.

Rahman, Sefat [University of Utah]↗

SU-E-J-114: A Practical Hybrid Method for Improving the Quality of CT-CBCT Deformable Image Registration for Head and Neck Radiotherapy

Purpose: Accurate deformable image registration (DIR) between CT and CBCT in H&N is challenging. In this study, we propose a practical hybrid method that uses not only the pixel intensities but also organ physical properties, structure volume of interest (VOI), and interactive local registrations. Methods: Five oropharyngeal cancer patients were selected retrospectively. For each patient, the planning CT was registered to the last fraction CBCT, where the anatomy difference was largest. A three step registration strategy was tested; Step1) DIR using pixel intensity only, Step2) DIR with additional use of structure VOI and rigidity penalty, and Step3) interactive local correction. For Step1, a public-domain open-source DIR algorithm was used (cubic B-spline, mutual information, steepest gradient optimization, and 4-level multi-resolution). For Step2, rigidity penalty was applied on bony anatomies and brain, and a structure VOI was used to handle the body truncation such as the shoulder cut-off on CBCT. Finally, in Step3, the registrations were reviewed on our in-house developed software and the erroneous areas were corrected via a local registration using level-set motion algorithm. Results: After Step1, there were considerable amount of registration errors in soft tissues and unrealistic stretching in the posterior to the neck and near the shoulder due to body truncation. The brain was also found deformed to a measurable extent near the superior border of CBCT. Such errors could be effectively removed by using a structure VOI and rigidity penalty. The rest of the local soft tissue error could be corrected using the interactive software tool. The estimated interactive correction time was approximately 5 minutes. Conclusion: The DIR using only the image pixel intensity was vulnerable to noise and body truncation. A corrective action was inevitable to achieve good quality of registrations. We found the proposed three-step hybrid method efficient and practical for CT/CBCT registrations in H&N. My department receives grant support from Industrial partners: (a) Varian Medical Systems, Palo Alto, CA, and (b) Philips HealthCare, Best, Netherlands.

60 APPLIED LIFE SCIENCES↗

Component-wise reduced-order model design optimization such as for lattice design optimization

Systems and methods for optimizing a lattice structure design are disclosed herein. In some embodiments, a method for optimizing a lattice structure design can include (i) modeling the lattice structure with a component-wise reduced-order model (CWROM) and (ii) optimizing the CWROM based on a selected criterion using a topology optimization algorithm for lattice design. The selected criterion can include a boundary condition and a load applied to the lattice structure. By modeling the lattice structure as a CWROM, the optimization process can be very fast while still permitting the accurate computation of physical quantities of the lattice structure.

Choi, Youngsoo↗

Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗