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I/O-aware bandwidth allocation for petascale computing systems
In the Big Data era, the gap between the storage performance and an appli- cation's I/O requirement is increasing. I/O congestion caused by concurrent storage accesses from multiple applications is inevitable and severely harms the performance. Conventional approaches either focus on optimizing an ap- plication's access pattern individually or handle I/O requests on a low-level storage layer without any knowledge from the upper-level applications. In this paper, we present a novel I/O-aware bandwidth allocation framework to coordinate ongoing I/O requests on petascale computing systems. The motivation behind this innovation is that the resource management system has a holistic view of both the system state and jobs' activities and can dy- namically control the jobs' status or allocate resource on the y during their execution. We treat a job's I/O requests as periodical subjobs within its lifecycle and transform the I/O congestion issue into a classical scheduling problem. Based on this model, we propose a bandwidth management mech- anism as an extension to the existing scheduling system. We design several bandwidth allocation policies with different optimization objectives either on user-oriented metrics or system performance. We conduct extensive trace- based simulations using real job traces and I/O traces from a production IBM Blue Gene/Q system at Argonne National Laboratory. Experimental results demonstrate that our new design can improve job performance by more than 30%, as well as increasing system performance.
Trace Uranium Partitioning in a Multiphase Nano-FeOOH System
The characterization of trace elements in nanomaterials using extended X-ray absorption fine structure (EXAFS) spectroscopy constitutes a first step toward understanding how impurities or dopants affect the properties of the host phase. However, limitations to EXAFS interpretation complicate the analysis of trace concentrations of impurities that are distributed across multiple phases in a heterogeneous system. Ab initio molecular dynamics (AIMD)-informed EXAFS analysis was employed to investigate the immobilization of trace uranium associated with nanophase iron (oxyhydr)oxides, a model system for the geochemical sequestration of radiotoxic contaminants. The reductive transformation of ferrihydrite (Fe(OH)3) to nano-particulate iron oxyhydroxide minerals in the presence of uranyl (UO2)2+(aq) resulted in the preferential incorporation of U into goethite (a-FeOOH) over lepidocrocite (g-FeOOH), even though reaction conditions favored the formation of excess lepidocrocite. This unexpected result is supported by atomically resolved transmission electron microscopy. Using this model system, we demonstrate how AIMD-informed EXAFS analysis lifts the strict statistical limitations of traditional shell-by-shell EXAFS modeling, enabling the detailed analysis of the local bonding environment, charge compensation mechanisms, and oxidation states of polyvalent impurities in complex multi-phase nano-systems.
CFD Simulation of the Dosing Behavior within the Atomic Layer Deposition Feeding System
The effective operation of atomic layer deposition (ALD) feeding system is the premise of realizing specific ALD processes. In the present work, a detailed computational fluid dynamics (CFD) model of the feeding system has been developed and validated, which accounts for the roles of ALD valves and manifolds. A numerical simulation of the compressible fluid flow and heat/mass transfer within the feeding system was conducted. The dosing amounts and the spatiotemporal distributions of the precursors can be accurately predicted using the CFD model, as validated by experimental results. Different precursors, operating conditions, and structures of the feeding system were simulated and analyzed to examine the operating flexibility of the feeding system. The simulation results can be adopted as the upstream boundary conditions for simulations of the ALD process in the reaction chamber. The substrate-scale simulation indicates that the effect of the feeding system on the film deposition is highly related to the surface kinetics of ALD. The present work can serve as a guide for the development and optimization of different ALD-based processes via proper operation and even the design of the feeding system.
Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. I. Full cumulant expansions and system-bath entanglement
We study the Förster resonant energy transfer rate, absorption and emission spectra in multichromophoric systems. The multichromophoric Förster theory (MCFT) is determined from an overlap integral of generalized matrices related to the donor’s emission and acceptor’s absorption spectra, which are obtained via a full 2nd-order cumulant expansion technique developed in this work. We calculate the spectra and MCFT rate for both localized and delocalized systems, and calibrate the analytical 2nd-order cumulant expansion with the exact stochastic path integral method. We present three essential findings: (i) The role of the initial entanglement between the donor and its bath is found to be crucial in both the emission spectrum and the MCFT rate. (ii) The absorption spectra obtained by the cumulant expansion method are nearly identical to the exact spectra for both localized and delocalized systems, even when the system-bath coupling is far from the perturbative regime. (iii) For the emission spectra, the cumulant expansion can give reliable results for localized systems, but fail to provide reliable spectra of the high-lying excited states of a delocalized system, when the system-bath coupling is large and the thermal energy is small. This paper also provides a simple golden-rule derivation of the MCFT, reviews existing methods, and motivates further developments in the subsequent papers.
PE5–PPE4–EspG 3 heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems
Mycobacterium tuberculosis has evolved numerous type VII secretion (ESX) systems to secrete multiple factors important for both growth and virulence across their cell envelope. ESX-1, ESX-3, and ESX-5 systems have been shown to each secrete a distinct set of substrates, including PE and PPE families of proteins, named for conserved Pro-Glu and Pro-Pro-Glu motifs in their N termini. Proper secretion of the PE–PPE proteins requires the presence of EspG, with each system encoding its own unique copy. There is no cross-talk between any of the ESX systems, and how each EspG recognizes its subset of PE–PPE proteins is currently unknown. The only current structural characterization of PE–PPE–EspG heterotrimers is from the ESX-5 system. Here we present the crystal structure of the PE5 mt –PPE4 mt –EspG 3mm heterotrimer from the ESX-3 system. Our heterotrimer reveals that EspG 3mm interacts exclusively with PPE4 mt in a similar manner to EspG 5 , shielding the hydrophobic tip of PPE4 mt from solvent. The C-terminal helical domain of EspG 3mm is dynamic, alternating between “open” and “closed” forms, and this movement is likely functionally relevant in the unloading of PE–PPE heterodimers at the secretion machinery. In contrast to the previously solved ESX-5 heterotrimers, the PE–PPE heterodimer of our ESX-3 heterotrimer is interacting with its chaperone at a drastically different angle and presents different faces of the PPE protein to the chaperone. We conclude that the PPE–EspG interface from each ESX system has a unique shape complementarity that allows each EspG to discriminate among noncognate PE–PPE pairs.
Battery Energy Storage System (BESS) and Battery Management System (BMS) for Grid-Scale Applications
The current electric grid is an inefficient system that wastes significant amounts of the electricity it produces because there is a disconnect between the amount of energy consumers require and the amount of energy produced from generation sources. Power plants typically produce more power than necessary to ensure adequate power quality. By taking advantage of energy storage within the grid, many of these inefficiencies can be removed. Advanced modeling is required when using battery energy storage systems (BESS) for grid storage in order to accurately monitor and control the storage system. Battery management systems (BMS) control how the storage system will be used and a BMS that utilizes advanced physics-based models will offer for much more robust operation of the storage system. The paper outlines the current state of the art for modeling in BMS and the advanced models required to fully utilize BMS for both lithium-ion batteries and vanadium redox-flow batteries. In addition, system architecture and how it can be useful in monitoring and control is discussed. A pathway for advancing BMS to better utilize BESS for grid-scale applications is outlined.
Impact of Spatial Variation in Flexibility on System Operations in Electric Power Systems
With the expansion of renewable energy resources in the electric power systems, having flexibility in the setup will allow to maintain the system's reliability and prevailing operations. Such flexibility can be extracted from utility operated and/or consumer owned devices, such as, storage devices, electric vehicles, etc. For the demand side, generally consumer preferences, incentives, etc. enact on the availability of the flexibility; besides, both the spatial and temporal dimension dictates the degree of the flexibility. Consequently, the optimal dispatch of the grid resources might appear intractable as the considerable amount of flexibility are obliquely stemming from the ungovernable consumer devices. Thus characterizing the consequences of diverged feasible flexibility in the system is crucial for operations. In this paper, a procedure is developed to quantify the degree of flexibility of power systems in terms of resource dispatch reconfiguration. Specifically, we develop optimization problems to attain equivalent resource configurations for the power systems to evaluate the spatial volatility of the network and asses the flexibility of the system. The developed process is then validated using numerical simulations for IEEE-30 bus test system.
Electricity Distribution System Resilient Control System Metrics
In order to assess the resilience of a system, a set of measures must be defined. Varying control architecture while considering such a system of metrics targeted at resilience can determine the relative merit of the architectures with respect to the resilience of the system. Traditionally, electricity distribution is concerned with delivery of power from transmission or sub transmission to consumer loads with basic control of tap changing transformers and capacitor banks to regulate delivered voltage and provide reactive power support, respectively. In the near future, modern distribution systems architecture are anticipated to include substantially more controllable assets enabling more complicated control architectures to optimized based on reliability and economics. This paper reports on the definition of resilience metrics developed for modern distribution systems for delivery of electricity. Specifically, the metrics are focused on adaptive capacity related to the scale for which the system is able to resist, respond, recover and restore after disturbances in real or reactive power and time requirements to respond and restore the system to a complete normalcy.
Synchronized Wireless Measurement of High-Voltage Power System Frequency Using Mobile Embedded Systems
This paper focuses on synchronized wireless measurement of high-voltage (HV) power system frequency using mobile embedded systems (MESs) integrated with a wireless electric field sensor (WEFS). Unlike traditional synchronized frequency measurement devices, which rely on potential transformers and current transformers physically connected to system elements, a WEFS is used to realize wireless signal acquisition in the vicinity of any HV apparatus. The MES performs real-time frequency estimation using a recursive discrete Fourier transform based algorithm. Network time protocol (NTP) is used for time synchronization, increasing the system flexibility by eliminating global positioning system reliance. An NTP-based synchronized sampling control method is proposed and implemented in MES to compensate the sampling time error caused by local time drift and division residue. The proposed system has the advantages of portability and lower cost, making it highly accessible and useful for a wide array of synchronized frequency measurement applications. Experiment results verify the accuracy and effectiveness of the proposed system.
Study of microgrid resilience through co-simulation of power system dynamics and communication systems
The interdependence of power and communication systems in smart grid technologies is acknowledged, but difficult to quantify. Communication systems can be essential to maintaining stability in microgrids that are islanded due to extreme events. Though many power system studies assume the presence of communication networks, detailed modeling of power and communication systems for dynamic studies of microgrids is rare. The work presented in this paper develops a framework for power and communication system co-simulation to study the impact of communications system on microgrid stability. An operational use case is examined where a battery energy storage system operates to offset the loss of generation in an islanded microgrid. The framework is evaluated for different communication technologies, network structures, and communication media.
SU-E-CAMPUS-J-03: Commissioning of the On-Board Cone-Beam CT System Equipped On the Rotating Gantry of a Proton Therapy System
Purpose: Proton therapy requires highly-precise image guidance in patient setup to ensure accurate dose delivery. Cone-beam CT (CBCT) is expected to play an important role to reduce uncertainties in patient setup. Hokkaido University has developed a new proton therapy system dedicated to spot-scanning under a collaborative work with Hitachi Ltd. In our system, an orthogonal X-ray imaging system is mounted on a full-rotating gantry. On-board CBCT imaging is therefore available. We have conducted commissioning of the CBCT system for clinical use in proton therapy. Methods: The orthogonal X-ray imaging system, which consists of two sets of X-ray tubes and flat panel detectors (FPDs), are equipped on the rotating gantry. The FPDs are mounted on the proton beam nozzle and can be retracted when not in use. The distance between the X-ray source and the FPD is about 2.1 m. The maximum rotation speed of the gantry is 1 rpm, so CBCT images can be acquired in approximately 1 minute. The maximum reconstruction volume is nearly 40 cm in diameter and 20 cm in axial length. For commissioning of the CBCT system, mechanical accuracy of the rotating gantry first was evaluated. Imaging performance was examined via quantitative evaluation of image quality. Results: Through the mechanical test, the isocentricity of the gantry was confirmed to be less than 1 mm. Moreover, it was improved to 0.5 mm with an appropriate correction. The accurate rotation of the gantry contributes to the CBCT image quality. In the image quality test, objects with 7 line-pairs per cm, which corresponds to a line spacing of 0.071 cm, could be discerned. Spatial linearity and uniformity were also sufficient. Conclusion: Clinical commissioning of the on-board CBCT system for proton therapy was conducted, and CBCT images with sufficient quality were successfully obtained. This research was supported by the Cabinet Office, Government of Japan and the Japan Society for the Promotion of Science (JSPS) through the Funding Program for World-Leading Innovative R and D on Science and Technology (FIRST Program), initiated by the Council for Science and Technology Policy (CSTP)
SU-F-T-518: Development and Characterization of a Gated Treatment System Implemented with An In-House Optical Tracking System and the Elekta Response Interface
Purpose: To report the development and characterization of the first in-house gating system implemented with an optical tracking system (OTS) and the Elekta Response™ interface. Methods: The Response™ connects a patient tracking system with a linac, enabling the tracking system to control radiation delivery. The developed system uses an in-house OTS to monitor patient breathing. The OTS consists of two infrared-based cameras, tracking markers affixed on patient. It achieves gated or breath-held (BH) treatment by calling beam ON/OFF functions in the Response™ dynamic-link library (DLL). A 4D motion phantom was used to evaluate its dosimetric and time delay characteristics. Two FF- and two FFF-IMRT beams were delivered in non-gated, BH and gated mode. The sinusoidal gating signal had a 6 sec period and 15 mm amplitude. The duty cycle included 10%, 20%, 30% and 50%. The BH signal was adapted from the sinusoidal wave by inserting 15 sec BHs. Each delivery was measured with a 2D diode array (MapCHECK™) and compared with the non-gated delivery using gamma analysis (3%). The beam ON/OFF time was captured using the service graphing utility of the linac. Results: The gated treatments were successfully delivered except the 10% duty cycle. The BH delivery had perfect agreement (100%) with non-gated delivery; the agreement of gated delivery decreased from 99% to 88% as duty cycle reduced from 50% to 20%. The beam on/off delay was on average 0.25/0.06 sec. The delivery time for the 50%, 30% and 20% duty cycle increased by 29%, 71% and 139%, respectively. No dosimetric or time delay difference was noticed between FF- and FFF-IMRT beams. Conclusion: The in-house gating system was successfully developed with dosimetric and time delay characteristics in line with published results for commercial systems. It will be an important platform for further research and clinical development of gated treatment.
SU-F-T-640: Feasibility of Using a Commercially Available Surface Guided Radiotherapy System with An Open-Face SRS Immobilization System
Purpose: To evaluate the inherent accuracy of using a surface guided radiotherapy system (SGRT) in the setup and monitoring of patients receiving stereotactic radiosurgery with an open-face SRS immobilization system. Methods: An anthropomorphic head phantom was set up using the Qfix Encompass SRS Immobilization System on a Varian Edge with OSMS and Varian TrueBeam with AlignRT. The phantom was positioned at 0° gantry and couch. A reference image was acquired using the SGRT system and an ROI was created over the mask opening. The couch and gantry were rotated to different combinations focusing on clinically used SRS gantry/couch combinations and those blocking the SGRT cameras. Perceived surface deviation by the SGRT system from the reference image was recorded. A Winston-Lutz test was performed on couch angles tested and used to exclude couch walkout. The deviation magnitude was calculated using translational values and rotational raw values were recorded. Results: The maximum couch walkouts were: 0.4mm (Edge) and 0.5mm (TB). Solely rotating the gantry resulted in a median couch deviation of 0.2mm and range of 0.1–0.3mm for both linacs. Only rotating the couch (0° gantry) resulted in median deviations of 0.6mm and 0.5mm with ranges of 0.3–1.0mm and 0.3–0.7mm for the Edge and TB, respectively. Combining gantry and couch rotations, the median deviations were 0.7mm and 0.9mm with ranges of 0.3–1.1mm and 0.2–1.9mm for the Edge and TB, respectively. Including all combinations, rotation, roll, and pitch median deviations ranged from 0.1–0.3° with pitch demonstrating consistently higher values and a maximum deviation of 1.0° (both linacs). Conclusion: SGRT is a reliable monitoring tool, though taking into account system fluctuations, 1mm is too restrictive a site tolerance to use with the Qfix Encompass mask. Gantry rotation has little effect on system fluctuation even with camera blockage, whereas couch rotation has a larger effect.
TH-A-207B-02: QIBA Ultrasound Elasticity Imaging System Biomarker Qualification and User Testing of Systems
Imaging of tissue elastic properties is a relatively new and powerful approach to one of the oldest and most important diagnostic tools. Imaging of shear wave speed with ultrasound is has been added to most high-end ultrasound systems. Understanding this exciting imaging mode aiding its most effective use in medicine can be a rewarding effort for medical physicists and other medical imaging and treatment professionals. Assuring consistent, quantitative measurements across the many ultrasound systems in a typical imaging department will constitute a major step toward realizing the great potential of this technique and other quantitative imaging. This session will target these two goals with two presentations. A. Basics and Current Implementations of Ultrasound Imaging of Shear Wave Speed and Elasticity - Shigao Chen, Ph.D. Learning objectives-To understand: Introduction: Importance of tissue elasticity measurement Strain vs. shear wave elastography (SWE), beneficial features of SWE The link between shear wave speed and material properties, influence of viscosity Generation of shear waves External vibration (Fibroscan) ultrasound radiation force Point push Supersonic push (Aixplorer) Comb push (GE Logiq E9) Detection of shear waves Motion detection from pulse-echo ultrasound Importance of frame rate for shear wave imaging Plane wave imaging detection How to achieve high effective frame rate using line-by-line scanners Shear wave speed calculation Time to peak Random sample consensus (RANSAC) Cross correlation Sources of bias and variation in SWE Tissue viscosity Transducer compression or internal pressure of organ Reflection of shear waves at boundaries B. Elasticity Imaging System Biomarker Qualification and User Testing of Systems – Brian Garra, M.D. Learning objectives-To understand: Goals Review the need for quantitative medical imaging Provide examples of quantitative imaging biomarkers Acquaint the participant with the purpose of the RSNA Quantitative Imaging Biomarker Alliance and the need for such an organization Review the QIBA process for creating a quantitative biomarker Summarize steps needed to verify adherence of site, operators, and imaging systems to a QIBA profile Underlying Premise and Assumptions Objective, quantifiable results are needed to enhance the value of diagnostic imaging in clinical practice Reasons for quantification Evidence based medicine requires objective, not subjective observer data Computerized decision support tools (eg CAD) generally require quantitative input. Quantitative, reproducible measures are more easily used to develop personalized molecular medical diagnostic and treatment systems What is quantitative imaging? Definition from Imaging Metrology Workshop The Quantitative Imaging Biomarker Alliance Formation 2008 Mission Structure Example Imaging Biomarkers Being Explored Biomarker Selection Groundwork Draft Protocol for imaging and data evaluation QIBA Profile Drafting Equipment and Site Validation Technical Clinical Site and Equipment QA and Compliance Checking Ultrasound Elasticity Estimation Biomarker US Elasticity Estimation Background Current Status and Problems Biomarker Selection-process and outcome US SWS for Liver Fibrosis Biomarker Work Groundwork Literature search and analysis results Phase I phantom testing-Elastic phantoms Phase II phantom testing-Viscoelastic phantoms Digital Simulated Data Protocol and Profile Drafting Protocol: based on UPICT and existing literature and standards bodies protocols Profile-Current claims, Manufacturer specific appendices What comes after the profile Profile Validation Technical validation Clinical validation QA and Compliance Possible approaches Site Operator testing Site protocol re-evaluation Imaging system Manufacturer testing and attestation User acceptance testing and periodic QA Phantom Tests Digital Phantom Based Testing Standard QA Testing Remediation Schemes Profile Evolution Towards additional applications Towards higher accuracy and precision Supported in part by NIH contract HHSN268201300071C from NIBIB. Collaboration with GE Global Research, no personal support.; S. Chen, Some technologies described in this presentation have been licensed. Mayo Clinic and Dr. Chen have financial interests these technologies.
Dynamic System Simulation of Fissile Solution Systems
Dynamic System Simulation (DSS) utilizes state-variables described by differential or difference equations to model system evolution. DSS techniques have been applied to develop a family of models to examine the time-dependent operational behavior of fissile solution systems. The base, or generic model, predicts the behavior of an aqueous homogeneous reactor (AHR), configured with a single cooling loop, operating at atmospheric pressure. A model specific for SUPO (Super Power), a uranium solution fueled AHR that operated at Los Alamos National Laboratory from 1951 to 1974, tailored from the generic model demonstrated close correlation with experimental data for steady-state operation1. SUPO is considered the benchmark for steady-state AHR operation. Subsequently specific models were tailored from the generic model for a variety of historical reactors including KEWB (Kinetics Experiments Water Boiler) “A-2” and “B-5” cores and Silene, which is considered the benchmark for AHR pulse operations. These models demonstrated DSS techniques could reliably be extended to different core geometries (SUPO and KEWB “A-2” were spherical; KEWB “B-5” and Silene cylindrical)2. This family of models also shows close correlation with experimental data in all modes of fissile solution system operation including pulse, free evolution, and steady-state. System response due to rate and amplitude of reactivity insertion closely matches experimental data. This report describes additional extensions of this family of models to include a wider design space for fissile solution systems. Pressurized cores, cooling schemes involving multiple cooling loops of various geometries, and accelerator-driven sub-critical system concepts are modeled.
Active Storage with Analytics Capabilities and I/O Runtime System for Petascale Systems
Computational scientists must understand results from experimental, observational and computational simulation generated data to gain insights and perform knowledge discovery. As systems approach the petascale range, problems that were unimaginable a few years ago are within reach. With the increasing volume and complexity of data produced by ultra-scale simulations and high-throughput experiments, understanding the science is largely hampered by the lack of comprehensive I/O, storage, acceleration of data manipulation, analysis, and mining tools. Scientists require techniques, tools and infrastructure to facilitate better understanding of their data, in particular the ability to effectively perform complex data analysis, statistical analysis and knowledge discovery. The goal of this work is to enable more effective analysis of scientific datasets through the integration of enhancements in the I/O stack, from active storage support at the file system layer to MPI-IO and high-level I/O library layers. We propose to provide software components to accelerate data analytics, mining, I/O, and knowledge discovery for large-scale scientific applications, thereby increasing productivity of both scientists and the systems. Our approaches include 1) design the interfaces in high-level I/O libraries, such as parallel netCDF, for applications to activate data mining operations at the lower I/O layers; 2) Enhance MPI-IO runtime systems to incorporate the functionality developed as a part of the runtime system design; 3) Develop parallel data mining programs as part of runtime library for server-side file system in PVFS file system; and 4) Prototype an active storage cluster, which will utilize multicore CPUs, GPUs, and FPGAs to carry out the data mining workload.
Low-Cost Metal Hydride Thermal Energy Storage System for Concentrating Solar Power Systems
The objective of this research was to evaluate and demonstrate a metal hydride-based TES system for use with a CSP system. A unique approach has been applied to this project that combines our modeling experience with the extensive material knowledge and expertise at both SRNL and Curtin University (CU). Because of their high energy capacity and reasonable kinetics many metal hydride systems can be charged rapidly. Metal hydrides for vehicle applications have demonstrated charging rates in minutes and tens of minutes as opposed to hours. This coupled with high heat of reaction allows metal hydride TES systems to produce very high thermal power rates (approx. 1kW per 6-8 kg of material). A major objective of this work is to evaluate some of the new metal hydride materials that have recently become available. A problem with metal hydride TES systems in the past has been selecting a suitable high capacity low temperature metal hydride material to pair with the high temperature material. A unique aspect of metal hydride TES systems is that many of these systems can be located on or near dish/engine collectors due to their high thermal capacity and small size. The primary objective of this work is to develop a high enthalpy metal hydride that is capable of reversibly storing hydrogen at high temperatures (> 650 °C) and that can be paired with a suitable low enthalpy metal hydride with low cost materials. Furthermore, a demonstration of hydrogen cycling between the two hydride beds is desired.