A Conservative Optimization-Based Semi-Lagrangian Spectral Element Method for Passive Tracer Transport.
Abstract not provided.
Bochev, Pavel B.↗
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A Conservative Optimization-based Semi-Lagrangian Spectral Element Method for Passive Tracer Transport.
Abstract not provided.
Bochev, Pavel B.↗
Noise minimization by bias-variance optimization in particle-based plasma simulation methods.
Abstract not provided.
Evstatiev, Evstati Georgiev↗
Optimization, Inference and Learning for Advanced Networks
This piece of software aims at providing an implementation of methods to perform efficient optimization, probabilistic inference and model selection and learning for various type of networked systems. The software contains a suite of methods and functions that: 1) perform probabilistic inference and random sampling on networked models 2) select or learn networked models from data 3) solve optimization tasks with a networked structure Network models that are supported by these features include, but are not limited to, factor graphs and Markov random fields such as Ising models, Potts models, p-spins models, Gaussian random fields and restricted Boltzmann machine.
Hijazi, Hassan↗
SU-E-T-806: Very Fast GPU-Based IMPT Dose Computation
Purpose: Designing particle therapy treatment plans is a dosimetrist-in-the-loop optimization wherein the conflicting constraints of achieving a desired tumor dose distribution must be balanced against the need to minimize the dose to nearby OARs. IMPT introduces an additional, inner, numerical optimization step in which the dosimetrist’s current set of constraints are used to determine the weighting of beam spots. Very fast dose calculations are needed to enable the dosimetrist to perform many iterations of the outer optimization in a commercially reasonable time. Methods: We have developed a GPU-based convolution-type dose computation algorithm that more accurately handles heterogeneities than earlier algorithms by redistributing energy from dose computed in a water volume. The depth dependence of the beam size is handled by pre-processing Bragg curves using a weighted superposition of Gaussian bases. Additionally, scattering, the orientation of treatment ports, and the non-parallel propagation of beams are handled by large, but sparse, energy-redistribution matrices that implement affine transforms. Results: We tested our algorithm using a brain tumor dataset with 1 mm voxels and a single treatment port from the patient’s anterior through the sinuses. The resulting dose volume is 100 × 100 × 230 mm with 66,200 beam spots on a 3 × 3 × 2 mm grid. The dose computation takes <1 msec on a GeForce GTX Titan GPU with the Gamma passing rate for 2mm/2% criterion of 99.1% compared to dose calculated by an alternative dose algorithm based on pencil beams. We will present comparisons to Monte Carlo dose calculations. Conclusion: Our high-speed dose computation method enables the IMPT spot weights to be optimized in <1 second, resulting in a nearly instantaneous response to user changes to dose constraints. This permits the creation of higher quality plans by allowing the dosimetrist to evaluate more alternatives in a short period of time.
60 APPLIED LIFE SCIENCES↗
HLA-Clus: HLA class I clustering based on 3D structure
In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria. The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained and transformed into clouds of labeled points. Second, similarities between alleles are determined using a newly defined structure distance metric that accounts for spatial and physicochemical similarities. Finally, alleles are clustered via hierarchical or nearest-neighbor approaches. We also interfaced HLA-Clus with the peptide:HLA affinity predictor MHCnuggets. By using the nearest neighbor clustering method to select optimal allele-specific deep learning models in MHCnuggets, the average accuracy of peptide binding prediction of rare alleles was improved. The HLA-Clus package offers a solution for characterizing the peptide binding specificities of a large number of HLA alleles. This method can be applied in HLA functional studies, such as the development of peptide affinity predictors, disease association studies, and HLA matching for grafting. HLA-Clus is freely available at our GitHub repository (https://github.com/yshen25/HLA-Clus).
59 BASIC BIOLOGICAL SCIENCES↗
Low-dose-rate Brachytherapy for Prostate Cancer in Low-resource Settings
Purpose: In areas with limited health care, it is important to identify and implement effective treatment methods and to optimize available resources. We investigated the implementation of a low-dose-rate (LDR) brachytherapy program for the treatment of prostate cancer (PCa) in a low-resource setting such as Puerto Rico (PR), where PCa is the main cause of cancer-associated death. Methods and Materials: After institutional approval, the medical records of patients with nonmetastatic PCa undergoing LDR brachytherapy from 2008 to 2013 were reviewed from PR. The factors analyzed included adequate D{sub 90} (radiation dose delivered to 90% of the target volume) coverage (≥140 Gy), early and late toxicity (Common Terminology Criteria for Adverse Events grade >2), and prostate-specific antigen failure. Freedom from biochemical failure was evaluated using Kaplan-Meier analysis. Results: The barriers to implementation of LDR brachytherapy in a country with limited resources were identified. These included lack of access to funding for startup costs, specific referral patterns, lack of trained support staff, such as dosimetrists and physicists, and initial opposition from insurance companies for reimbursement. The initial results from 191 patients were included in the present study with a median follow-up period of 26 months. Prostate-specific antigen failure occurred in 6 patients (3%). No early or late gastrointestinal toxicity (grade >2) developed. Only 3 (2%) and 2 (1%) patients experienced early and late genitourinary toxicity (grade >2), respectively. The 2- and 3-year freedom from biochemical failure in this population was 97% and 95.9%, respectively. Conclusions: At present, limited data are available delineating the barriers faced by low-resource settings in the implementation of LDR brachytherapy. Our data highlight the issues unique to this environment and support the use of LDR brachytherapy as a reliable and effective treatment modality for patients with PCa in low-resource settings.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Magnetic Transition in Nonmetal N- and F-Doping g-ZnO Monolayer with Different Concentrations
In this paper, the geometrical, electronic, and magnetic properties of nonmetal (N, F) atom doping g-ZnO monolayer supercell forming 6.25, 12.5, and 25% concentrations have been investigated comprehensively using the first-principles method. The structural optimization implies that N or F atom doping g-ZnO monolayer causes the structural distortion around the doping atoms. Doping g-ZnO monolayer with one N atom is FM semiconductor, and the total magnetic moment is 0.651 μ{sub B}. The N–N-pair or two N–N-pair doping g-ZnO is AFM states. The total magnetic moments mainly originate from the spin polarization of the doping atom N, and the rest comes from the nearest Zn and O atoms. Doping g-ZnO with F atoms with the concentrations of 6.25, 12.5, and 25% all are nonmagnetic semiconductor. The F-doping can adjust energy band gap, which increases with the increase of F concentration.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Atmospheric retrieval analysis of the directly imaged exoplanet HR 8799b
Directly imaged exoplanets are unexplored laboratories for the application of the spectral and temperature retrieval method, where the chemistry and composition of their atmospheres are inferred from inverse modeling of the available data. As a pilot study, we focus on the extrasolar gas giant HR 8799b, for which more than 50 data points are available. We upgrade our non-linear optimal estimation retrieval method to include a phenomenological model of clouds that requires the cloud optical depth and monodisperse particle size to be specified. Previous studies have focused on forward models with assumed values of the exoplanetary properties; there is no consensus on the best-fit values of the radius, mass, surface gravity, and effective temperature of HR 8799b. We show that cloud-free models produce reasonable fits to the data if the atmosphere is of super-solar metallicity and non-solar elemental abundances. Intermediate cloudy models with moderate values of the cloud optical depth and micron-sized particles provide an equally reasonable fit to the data and require a lower mean molecular weight. We report our best-fit values for the radius, mass, surface gravity, and effective temperature of HR 8799b. The mean molecular weight is about 3.8, while the carbon-to-oxygen ratio is about unity due to the prevalence of carbon monoxide. Our study emphasizes the need for robust claims about the nature of an exoplanetary atmosphere to be based on analyses involving both photometry and spectroscopy and inferred from beyond a few photometric data points, such as are typically reported for hot Jupiters.
79 ASTRONOMY AND ASTROPHYSICS↗
Structural modification of fentanyls for their retrospective identification by gas chromatographic analysis using chloroformate chemistry
Abstract The one-step breakdown and derivatization of a panel of nine fentanyls to yield uniquely tagged products that can be detected by Electron Ionization Gas Chromatography-Mass Spectrometry (EI-GC-MS) is presented. The method involves the treatment of the synthetic opioids with 2,2,2-trichloroethoxycarbonyl chloride (TrocCl) at 60 °C for 3 h in dichloromethane and furnishes two products from one fentanyl molecule that can be used to retrospectively identify the original opioid. Parameters that were studied and fully optimized for the method included temperature, solvent, nature of scavenging base and reaction time. One of the two resulting products from the reaction bears the trichloroethoxycarbonyl (Troc) tag attached to the norfentanyl portion of the original opioid and greatly aids in the opioid detection and identification process. The methodology has been applied to the chemical modification of a panel of nine fentanyls and in all cases the molecular ion peak for the Troc-norfentanyl product bearing the distinctive trichloroethyl isotopic signature can be clearly observed. The method’s LLOD was determined to be 10 ng/mL while its LLOQ was found to be 20 ng/mL. This methodology represents the first application of chloroformates in the chemical modification of this class of synthetic opioids that are notoriously inert to common derivatization strategies available for GC–MS analysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Novel Approach to Quantum Circuit Partitioning
Quantum synthesis presents an effective method of circuit optimization, but scales exponentially with the number of qubits in the circuit. This problem can be addressed by partitioning the circuit into blocks with a limited number of qubits. Existing partitioning algorithms make large trade-offs to achieve either high speed or quality. We propose a method of circuit partitioning which is competitive with existing algorithms for both metrics. The proposed method is compared with two existing methods across common circuit architectures, matching an exhaustive solution in performance and a fast solution on time.
Clark, Joseph↗
Improved crystal orientation and physical properties from single-shot XFEL stills
X-ray free-electron laser crystallography relies on the collection of still-shot diffraction patterns. New methods are developed for optimal modeling of the crystals’ orientations and mosaic block properties. X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model the diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg’s law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographic R factors and sharpening anomalous differences that are near the level of the noise.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
SU-F-T-347: An Absolute Dose-Volume Constraint Based Deterministic Optimization Framework for Multi-Co60 Source Focused Radiotherapy
Purpose: Treatment plan optimization in multi-Co60 source focused radiotherapy with multiple isocenters is challenging, because dose distribution is normalized to maximum dose during optimization and evaluation. The objective functions are traditionally defined based on relative dosimetric distribution. This study presents an alternative absolute dose-volume constraint (ADC) based deterministic optimization framework (ADC-DOF). Methods: The initial isocenters are placed on the eroded target surface. Collimator size is chosen based on the area of 2D contour on corresponding axial slice. The isocenter spacing is determined by adjacent collimator sizes. The weights are optimized by minimizing the deviation from ADCs using the steepest descent technique. An iterative procedure is developed to reduce the number of isocenters, where the isocenter with lowest weight is removed without affecting plan quality. The ADC-DOF is compared with the genetic algorithm (GA) using the same arbitrary shaped target (254cc), with a 15mm margin ring structure representing normal tissues. Results: For ADC-DOF, the ADCs imposed on target and ring are (D100>10Gy, D50,10, 0<12Gy, 15Gy and 20Gy) and (D40<10Gy). The resulting D100, 50, 10, 0 and D40 are (9.9Gy, 12.0Gy, 14.1Gy and 16.2Gy) and (10.2Gy). The objectives of GA are to maximize 50% isodose target coverage (TC) while minimize the dose delivered to the ring structure, which results in 97% TC and 47.2% average dose in ring structure. For ADC-DOF (GA) techniques, 20 out of 38 (10 out of 12) initial isocenters are used in the final plan, and the computation time is 8.7s (412.2s) on an i5 computer. Conclusion: We have developed a new optimization technique using ADC and deterministic optimization. Compared with GA, ADC-DOF uses more isocenters but is faster and more robust, and achieves a better conformity. For future work, we will focus on developing a more effective mechanism for initial isocenter determination.
60 APPLIED LIFE SCIENCES↗
Compositing "Stand Off" Ground Penetrating Radar Scans of Differing Frequencies.
Methods have been developed to combine signals of various frequencies in a manner to produce clearer images in the presence of noise. Ground Penetrating Radar (GPR) scans at various frequencies are no exception. Methods using an optimization problem solver, the Expectation-Maximization (EM) Algorithm, define weights used to perform the task of combining GPR scans. In this paper, we explore using the Gaussian Mixture Model (GMM) feature of the EM Algorithm on GPR scans taken at various heights above ground ("Stand Off' GPR). This method demonstrates the same measured improvement toward producing a cleaner image as GPR scans taken at ground level using the same EM Algorithm method.
97 MATHEMATICS AND COMPUTING↗
Multiphase Optimal and Non-Singular Power Flow by Successive Linear Approximations
We propose an optimal power flow method for multiphase power systems. The method works for both radial and meshed networks, and is able to accommodate different types of load/source connections such as wye, delta, and combination thereof. Moreover, the method generates a sequence of nonsingular points (i.e., associated with non-singular power-flow Jacobian) in the electrical state space and a corresponding sequence of power injections, which can be used in real-time control settings. Under certain conditions, the sequences attain the local minimum. The method has been tested using several typical networks, including the IEEE 37-bus and 123-bus test feeders.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Multiphase Optimal and Non-Singular Power Flow by Successive Linear Approximations: Preprint
We propose an optimal power flow method for multiphase power systems. The method works for both radial and meshed networks, and is able to accommodate different types of load/source connections such as wye, delta, etc. Moreover, the method generates a sequence of non-singular points in the electrical state space and a corresponding sequence of power injections, which can be used in real-time control settings. Under certain conditions, the sequences attain the local minimum. The method has been tested using several typical networks, including the IEEE 37-bus and 123-bus test feeders.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Algebraic Multigrid with Optimal Interpolation and Adaptive Smoothers (Final Report)
The project team continued with work on developing new bootstrap AMG techniques for solving symmetric and non-symmetric PDE systems. The focus of this work is to derive more reliable measures of the quality of the coarse space set than the convergence rate of the standard F-relaxation form of CR and a more robust form of interpolation than the so-called ideal form. We have successfully derived a sharp variant of CR that gives the precise convergence rate of the two-grid method using this optimal interpolation and, in addition, we derived a new Generalized Bootstrap AMG setup algorithm that uses as its main tool a multilevel eigensolver for the generalized eigenvalue problem involving the system matrix and the symmetrized smoother. In addition, the approach allows for general block smoothers with overlap. We have applied the method to scalar diffusion problems, linear elasticity, and Maxwell’s and the method shows marked improvements over existing AMG methods for these problems. In addition, the team worked with CASC members on new forms of ideal AMG interpolation.
97 MATHEMATICS AND COMPUTING↗
THE MASS OF THE MILKY WAY AND M31 USING THE METHOD OF LEAST ACTION
We constrain the most likely range of masses for the Milky Way (MW) and M31 using an application of the numerical action method (NAM) that optimizes the fit to observed parameters over a large ensemble of NAM-generated solutions. Our 95% confidence level mass ranges, 1.5-4.5 × 10{sup 12} M{sub ☉} for MW and 1.5-5.5 × 10{sup 12} M{sub ☉} for M31, are consistent with the upper range of estimates from other methods and suggests that a larger proportion of the total mass becomes detectable when the peculiar motions of many nearby satellites are taken into account in the dynamical analysis. We test the method against simulated Local Group catalogs extracted from the Millennium Run to confirm that mass predictions are consistent with actual galaxy halo masses.
79 ASTRONOMY AND ASTROPHYSICS↗