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At least 865 records · Page 48

Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine

Label-free quantitative MS based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a straightforward and robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we present Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates NSAF values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution accurate-mass instruments. NSAF has distinct advantages over other MS-based quantification methods, including a higher dynamic range as compared to isobaric tags, no requirement to align and re-extract MS1 peaks, and increased speed. MSpC features an easy to use graphic user interface that additionally calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. MSpC determinations of protein concentration were linear over several orders of magnitude based on the analysis of several high-mass accuracy datasets either obtained from PRIDE or generated with total cell extracts spiked with purified Arabidopsis 20S proteasomes. Lastly, the MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.

59 BASIC BIOLOGICAL SCIENCES↗

Consequences of Ca multisite occupation for the conducting properties of BaTiO{sub 3}

In combination with the dielectric modulus formalism and theoretical calculations, a newly developed defect incorporation mode, which is a combination of the standard A- and B-site doping mechanisms, is used to explain the conducting properties in 5 mol% Ca-doped BaTiO{sub 3}. Simulation results for Ca solution energies in the BaTiO{sub 3} lattice show that the new oxygen vacancy inducing mixed mode exhibits low defect energies. A reduction in dc conductivity compared with undoped BaTiO{sub 3} is witnessed for the incorporation of Ca. The conducting properties of 5 mol% Ca-doped BaTiO{sub 3} are analyzed using molecular dynamics and impedance spectroscopy. The ionic conductivity activation energies for each incorporation mode are calculated and good agreement with experimental data for oxygen migration is observed. The likely existence of the proposed defect configuration is also analyzed on the basis of these methods. - Graphical abstract: Oxygen vacancy formation as a result of self-compensation in Ca-doped BaTiO{sub 3}.

36 MATERIALS SCIENCE↗

Real-Time Interactive 4D-STEM Phase-Contrast Imaging From Electron Event Representation Data: Less computation with the right representation

The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning transmission electron microscopy has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four dimensional-scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed commonly available computing infrastructure. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis. The 4D Camera, a DED with 87 kHz frame-rate developed at Lawrence Berkeley National Laboratory, reduces the raw data to a linear-index encoded electron event representation (EER). Here we show with experimental data from the 4D Camera that linear-index encoded EER and its direct use in 4D-STEM phase contrast imaging methods enables real-time, interactive phase-contrast from large-area 4D-STEM datasets. Furthermore, we detail the computational complexity advantages of the EER and the necessary computational steps to achieve real-time interactive ptychography and center-of-mass differential phase contrast using commonly available hardware accelerators.

4D-STEM↗

Graphical methods for the sensitivity analysis in discriminant analysis

Similar to regression, many measures to detect influential data points in discriminant analysis have been developed. Many follow similar principles as the diagnostic measures used in linear regression in the context of discriminant analysis. Here we focus on the impact on the predicted classification posterior probability when a data point is omitted. The new method is intuitive and easily interpretative compared to existing methods. We also propose a graphical display to show the individual movement of the posterior probability of other data points when a specific data point is omitted. This enables the summaries to capture the overall pattern of the change.

97 MATHEMATICS AND COMPUTING↗

GPGPU Enabled Adaptive Volume Visualization Using Commodity Game Engines

The amount of data produced by researchers in fields like nuclear engineering, materials science, and medicine has dramatically increased in recent years. There is a growing need to analyze and visualize this data in order to derive new insights. However, creating a visualization of data that is many gigabytes in size in real time is a difficult task since most graphics processing units (GPUs) are unable to hold this much data at one time. In order to alleviate this issue, an adaptive volume visualizer has been developed that is capable of rendering large scale datasets with high levels of detail at interactive framerates.

97 MATHEMATICS AND COMPUTING↗

Conservation laws, bilinear forms and solitons for a fifth-order nonlinear Schrödinger equation for the attosecond pulses in an optical fiber

Under investigation in this paper is a fifth-order nonlinear Schrödinger equation, which describes the propagation of attosecond pulses in an optical fiber. Based on the Lax pair, infinitely-many conservation laws are derived. With the aid of auxiliary functions, bilinear forms, one-, two- and three-soliton solutions in analytic forms are generated via the Hirota method and symbolic computation. Soliton velocity varies linearly with the coefficients of the high-order terms. Head-on interaction between the bidirectional two solitons and overtaking interaction between the unidirectional two solitons as well as the bound state are depicted. For the interactions among the three solitons, two head-on and one overtaking interactions, three overtaking interactions, an interaction between a bound state and a single soliton and the bound state are displayed. Graphical analysis shows that the interactions between the two solitons are elastic, and interactions among the three solitons are pairwise elastic. Stability analysis yields the modulation instability condition for the soliton solutions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SU-F-T-540: Comprehensive Fluence Delivery Optimization with Multileaf Collimation

Purpose: Multileaf collimator (MLC) leaf sequencing is performed via commercial black-box implementations, on which a user has limited to no access. We have developed an explicit, generic MLC sequencing model to serve as a tool for future investigations of fluence map optimization, fluence delivery optimization, and rotational collimator delivery methods. Methods: We have developed a novel, comprehensive model to effectively account for a variety of transmission and penumbra effects previously treated on an ad hoc basis in the literature. As the model is capable of quantifying a variety of effects, we utilize the asymmetric leakage intensity across each leaf to deliver fluence maps with pixel size smaller than the narrowest leaf width. Developed using linear programming and mixed integer programming formulations, the model is implemented using state of the art open-source solvers. To demonstrate the versatility of the algorithm, a graphical user interface (GUI) was developed in MATLAB capable of accepting custom leaf specifications and transmission parameters. As a preliminary proof-ofconcept, we have sequenced the leaves of a Varian 120 Leaf Millennium MLC for five prostate cancer patient fields and one head and neck field. Predetermined fluence maps have been processed by data smoothing methods to obtain pixel sizes of 2.5 cm{sup 2}. The quality of output was analyzed using computer simulations. Results: For the prostate fields, an average root mean squared error (RMSE) of 0.82 and gamma (0.5mm/0.5%) of 91.4% were observed compared to RMSE and gamma (0.5mm/0.5%) values of 7.04 and 34.0% when the leakage considerations were omitted. Similar results were observed for the head and neck case. Conclusion: A model to sequence MLC leaves to optimality has been proposed. Future work will involve extensive testing and evaluation of the method on clinical MLCs and comparison with black-box leaf sequencing algorithms currently used by commercial treatment planning systems.

60 APPLIED LIFE SCIENCES↗

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-time and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Spatial core-edge coupling of the particle-in-cell gyrokinetic codes GEM and XGC

Two existing particle-in-cell gyrokinetic codes, GEM for the core region and XGC for the edge region, have been successfully coupled with a spatial coupling scheme at the interface in a toroidal geometry. Additionally, a mapping technique is developed for transferring data between GEM's structured and XGC's unstructured meshes. Two examples of coupled simulations are presented to demonstrate the coupling scheme. The optimization of GEM for graphics processing unit is also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ASCENDS: Advanced data SCiENce toolkit for Non-Data Scientists

Recently, advances in machine learning and artificial intelligence have been playing more and more critical roles in a wide range of areas. For the last several years, industries have shown that how learning from data, identifying patterns and making decisions with minimal human intervention can be extremely useful to their business (e.g., image classification, recommending a product to a customer, finding friends in a social network, predicting customers actions, etc.). These success stories have been motivating scientists who study physics, chemistry, materials, medicine, and many other subjects, to explore a new pathway of utilizing machine learning techniques like regression and classification for their scientific activities. However, most existing machine learning tools, systems, and methodologies have been developed for programming experts but not for scientists (or any users) who have no or little knowledge of programming. ASCENDS is a toolkit that is developed to assist scientists (or any persons) who want to use their data for machine learning tasks, more specifically, correlation analysis, regression, and classification. ASCENDS does not require programming skills. Instead, it provides a set of simple but powerful CLI (Command Line Interface) and GUI (Graphic User Interface) tools for non-data scientists to be able to intuitively perform advanced data analysis and machine learning techniques. ASCENDS has been implemented by wrapping around opensource software including Keras, TensorFlow, and scikit-learn.

97 MATHEMATICS AND COMPUTING↗

Dosimetric evaluation of total marrow irradiation using 2 different planning systems

This study compared 2 different treatment planning systems (TPSs) for quality and efficiency of total marrow irradiation (TMI) plans. The TPSs used in this study were VOxel-Less Optimization (VoLO) (Accuray Inc, Sunnyvale, CA) using helical dose delivery on a Tomotherapy Hi-Art treatment unit and Eclipse (Varian Medical Systems Inc, Palo Alto, CA) using volumetric modulated arc therapy (VMAT) dose delivery on a Varian iX treatment unit. A total dose of 1200 cGy was prescribed to cover 95% of the planning target volume (PTV). The plans were optimized and calculated based on a single CT data and structure set using the Alderson Rando phantom (The Phantom Laboratory, Salem, NY) and physician contoured target and organ at risk (OAR) volumes. The OARs were lungs, heart, liver, kidneys, brain, and small bowel. The plans were evaluated based on plan quality, time to optimize the plan and calculate the dose, and beam on time. The resulting mean and maximum doses to the PTV were 1268 and 1465 cGy for VoLO and 1284 and 1541 cGy for Eclipse, respectively. For 5 of 6 OAR structures the VoLO system achieved lower mean and D10 doses ranging from 22% to 52% and 3% to 44%, respectively. Total computational time including only optimization and dose calculation were 0.9 hours for VoLO and 3.8 hours for Eclipse. These times do not include user-dependent target delineation and field setup. Both planning systems are capable of creating high-quality plans for total marrow irradiation. The VoLO planning system was able to achieve more uniform dose distribution throughout the target volume and steeper dose fall off, resulting in superior OAR sparing. VoLO's graphics processing unit (GPU)–based optimization and dose calculation algorithm also allowed much faster creation of TMI plans.

61 RADIATION PROTECTION AND DOSIMETRY↗

SU-E-T-423: Fast Photon Convolution Calculation with a 3D-Ideal Kernel On the GPU

Purpose: The calculation time is a trade-off for improving the accuracy of convolution dose calculation with fine calculation spacing of the KERMA kernel. We investigated to accelerate the convolution calculation using an ideal kernel on the Graphic Processing Units (GPU). Methods: The calculation was performed on the AMD graphics hardware of Dual FirePro D700 and our algorithm was implemented using the Aparapi that convert Java bytecode to OpenCL. The process of dose calculation was separated with the TERMA and KERMA steps. The dose deposited at the coordinate (x, y, z) was determined in the process. In the dose calculation running on the central processing unit (CPU) of Intel Xeon E5, the calculation loops were performed for all calculation points. On the GPU computation, all of the calculation processes for the points were sent to the GPU and the multi-thread computation was done. In this study, the dose calculation was performed in a water equivalent homogeneous phantom with 150{sup 3} voxels (2 mm calculation grid) and the calculation speed on the GPU to that on the CPU and the accuracy of PDD were compared. Results: The calculation time for the GPU and the CPU were 3.3 sec and 4.4 hour, respectively. The calculation speed for the GPU was 4800 times faster than that for the CPU. The PDD curve for the GPU was perfectly matched to that for the CPU. Conclusion: The convolution calculation with the ideal kernel on the GPU was clinically acceptable for time and may be more accurate in an inhomogeneous region. Intensity modulated arc therapy needs dose calculations for different gantry angles at many control points. Thus, it would be more practical that the kernel uses a coarse spacing technique if the calculation is faster while keeping the similar accuracy to a current treatment planning system.

60 APPLIED LIFE SCIENCES↗

Experimentally Verified Alkane Adsorption Isotherms in Nanoporous Materials from Literature Meta-Analysis

Identification of independent experimental replicate measurements of well-defined physical properties provides a useful way to assess the reproducibility of literature reports of these properties. Prior meta-analysis of this kind for single-component adsorption of CO 2 and alcohols in nanoporous materials showed that ~20% of reported isotherms for these molecules were inconsistent with available replicate measurements. Here, we extend this analysis to the single-component adsorption of alkanes in nanoporous materials using a collection of 2998 experimental isotherms. Among these isotherms, 846 replicates were identified and analyzed. Many more replicates are available for CH 4 adsorption than for any other alkane. Our analysis finds that 15% of the replicate alkane isotherms are inconsistent with other replicate measurements. Furthermore, after discarding these outlier isotherms we report graphical and numerical consensus isotherms for 93 independent combinations of adsorbate, adsorbent, and temperature as well as an assessment of another 124 independent systems for which two replicate isotherms are available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.

36 MATERIALS SCIENCE↗

Accelerated Climate Modeling For Energy

This is the final report on the work of the New York University team to the DOE Accelerated Climate Modeling For Energy (ACME) project. NYU was one of the original developers of the UV-CDAT tool for climate data analysis, which is being used in ACME. NYU primarily focused on the analysis package graphical user interface, workflow and provenance functionality. The most significant activities in the last year of the grant were the development of the new plotting system in UVCMetrics package and the package EzLinePlot for 1D plots which are described in detail.

54 ENVIRONMENTAL SCIENCES↗

Adaptive nonlocal means filtering based on local noise level for CT denoising

Purpose: To develop and evaluate an image-domain noise reduction method based on a modified nonlocal means (NLM) algorithm that is adaptive to local noise level of CT images and to implement this method in a time frame consistent with clinical workflow. Methods: A computationally efficient technique for local noise estimation directly from CT images was developed. A forward projection, based on a 2D fan-beam approximation, was used to generate the projection data, with a noise model incorporating the effects of the bowtie filter and automatic exposure control. The noise propagation from projection data to images was analytically derived. The analytical noise map was validated using repeated scans of a phantom. A 3D NLM denoising algorithm was modified to adapt its denoising strength locally based on this noise map. The performance of this adaptive NLM filter was evaluated in phantom studies in terms of in-plane and cross-plane high-contrast spatial resolution, noise power spectrum (NPS), subjective low-contrast spatial resolution using the American College of Radiology (ACR) accreditation phantom, and objective low-contrast spatial resolution using a channelized Hotelling model observer (CHO). Graphical processing units (GPU) implementation of this noise map calculation and the adaptive NLM filtering were developed to meet demands of clinical workflow. Adaptive NLM was piloted on lower dose scans in clinical practice. Results: The local noise level estimation matches the noise distribution determined from multiple repetitive scans of a phantom, demonstrated by small variations in the ratio map between the analytical noise map and the one calculated from repeated scans. The phantom studies demonstrated that the adaptive NLM filter can reduce noise substantially without degrading the high-contrast spatial resolution, as illustrated by modulation transfer function and slice sensitivity profile results. The NPS results show that adaptive NLM denoising preserves the shape and peak frequency of the noise power spectrum better than commercial smoothing kernels, and indicate that the spatial resolution at low contrast levels is not significantly degraded. Both the subjective evaluation using the ACR phantom and the objective evaluation on a low-contrast detection task using a CHO model observer demonstrate an improvement on low-contrast performance. The GPU implementation can process and transfer 300 slice images within 5 min. On patient data, the adaptive NLM algorithm provides more effective denoising of CT data throughout a volume than standard NLM, and may allow significant lowering of radiation dose. After a two week pilot study of lower dose CT urography and CT enterography exams, both GI and GU radiology groups elected to proceed with permanent implementation of adaptive NLM in their GI and GU CT practices. Conclusions: This work describes and validates a computationally efficient technique for noise map estimation directly from CT images, and an adaptive NLM filtering based on this noise map, on phantom and patient data. Both the noise map calculation and the adaptive NLM filtering can be performed in times that allow integration with clinical workflow. The adaptive NLM algorithm provides effective denoising of CT data throughout a volume, and may allow significant lowering of radiation dose.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

SCALE Code System

The SCALE Code System is a widely-used modeling and simulation suite for nuclear safety analysis and design that is developed, maintained, tested, and managed by the Reactor and Nuclear Systems Division (RNSD) of Oak Ridge National Laboratory (ORNL). SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor and lattice physics, radiation shielding, spent fuel and radioactive source term characterization, and sensitivity and uncertainty analysis. Since 1980, regulators, licensees, and research institutions around the world have used SCALE for safety analysis and design. SCALE provides an integrated framework with dozens of computational modules including three deterministic and three Monte Carlo radiation transport solvers that are selected based on the desired solution strategy. SCALE includes current nuclear data libraries and problem-dependent processing tools for continuous-energy (CE) and multigroup (MG) neutronics and coupled neutron-gamma calculations, as well as activation, depletion, and decay calculations. SCALE includes unique capabilities for automated variance reduction for shielding calculations, as well as sensitivity and uncertainty analysis. SCALE’s graphical user interfaces assist with accurate system modeling, visualization of nuclear data, and convenient access to desired results.SCALE 6.2 provides many new capabilities and significant improvements of existing features.New capabilities include:• ENDF/B-VII.1 nuclear data libraries CE and MG with enhanced group structures,• Neutron covariance data based on ENDF/B-VII.1 and supplemented with ORNL data,• Covariance data for fission product yields and decay constants,• Stochastic uncertainty and correlation quantification for any SCALE sequence with Sampler,• Parallel calculations with KENO,• Problem-dependent temperature corrections for CE calculations,• CE shielding and criticality accident alarm system analysis with MAVRIC,• CE depletion with TRITON (T5-DEPL/T6-DEPL),• CE sensitivity/uncertainty analysis with TSUNAMI-3D,• Simplified and efficient LWR lattice physics with Polaris,• Large scale detailed spent fuel characterization with ORIGAMI and ORIGAMI Automator,• Advanced fission source convergence acceleration capabilities with Sourcerer,• Nuclear data library generation with AMPX, and• Integrated user interface with Fulcrum.Enhanced capabilities include:• Accurate and efficient CE Monte Carlo methods for eigenvalue and fixed source calculations,• Improved MG resonance self-shielding methodologies and data,• Resonance self-shielding with modernized and efficient XSProc integrated into most sequences,• Accelerated calculations with TRITON/NEWT (generally 4x faster than SCALE 6.1),• Spent fuel characterization with 1470 new reactor-specific libraries for ORIGEN,• Modernization of ORIGEN (Chebyshev Rational Approximation Method [CRAM] solver, API for high-performance depletion, new keyword input format)• Extension of the maximum mixture number to values well beyond the previous limit of 2147 to ~2 billion,• Nuclear data formats enabling the use of more than 999 energy groups,• Updated standard composition library to provide more accurate use of natural abundances, andvi• Numerous other enhancements for improved usability and stability.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

CRiSPPy: An advanced hydropower scheduling tool for the Colorado River Storage Project

The Western Area Power Administration (WAPA) plays a vital role in delivering reliable and cost-effective hydroelectric power to millions of customers across the western United States. The Colorado River Storage Project (CRSP) carries out WAPA’s mission in Arizona, Utah, Colorado, New Mexico, Nevada, Wyoming and Texas. Achieving this mission requires effective management of the Colorado River system, and depends on the use of advanced analytical tools and modeling methodologies. For many years, CRSP has relied on the Generation and Transmission Maximization Superlite (GTMax SL) model for its mid-term and long-term hydroscheduling needs. However, the evolving energy market, power system operations, environmental rules, and hydrology conditions, coupled with advancements in computational capabilities, have necessitated the development of a more modern and robust solution. This report introduces the Colorado River Storage Project Python-based (CRiSPPy) model, a new, advanced hydropower scheduling tool developed to address CRSP ever-evolving challenges. CRiSPPy represents a significant leap forward in our ability to model and optimize the operation of the Colorado River system. It incorporates state-of-the-art optimization algorithms, enhanced data management capabilities, and an advanced graphical user interface, providing WAPA CRSP personnel with unprecedented insights and decision-making support. This document details the development, capabilities, and implementation of CRiSPPy. It is intended to serve as a comprehensive resource for WAPA staff, stakeholders, and anyone interested in the future of hydropower scheduling in the Colorado River Basin. We are confident that CRiSPPy will enhance WAPA's mission while adapting to the challenges of a dynamic and increasingly complex environment. The version of CRiSPPy described in this report is the version 2.3. New versions of CRiSPPy will be developed as the tool keeps evolving to address CRSP challenges.

13 HYDRO ENERGY↗