In Situ TEM Concurrent and Successive Au Self-Ion Irradiation and He Implantation
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nuclear (including radiation effects), defects, me↗
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Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Enabling communication concurrency through flexible MPI endpoints
MPI defines a one-to-one relationship between MPI processes and ranks. This model captures many use cases effectively; however, it also limits communication concurrency and interoperability between MPI and programming models that utilize threads. This paper describes the MPI endpoints extension, which relaxes the longstanding one-to-one relationship between MPI processes and ranks. Using endpoints, an MPI implementation can map separate communication contexts to threads, allowing them to drive communication independently. Endpoints also enable threads to be addressable in MPI operations, enhancing interoperability between MPI and other programming models. These characteristics are illustrated through several examples and an empirical study that contrasts current multithreaded communication performance with the need for high degrees of communication concurrency to achieve peak communication performance.
Communication↗
Offline multiple adaptive planning strategy for concurrent irradiation of the prostate and pelvic lymph nodes
Purpose: Concurrent irradiation of the prostate and pelvic lymph nodes (PLNs) can be challenging due to the independent motion of the two target volumes. To address this challenge, the authors have proposed a strategy referred to as Multiple Adaptive Planning (MAP). To minimize the number of MAP plans, the authors’ previous work only considered the prostate motion in one major direction. After analyzing the pattern of the prostate motion, the authors investigated a practical number of intensity-modulated radiotherapy (IMRT) plans needed to accommodate the prostate motion in two major directions simultaneously. Methods: Six patients, who received concurrent irradiation of the prostate and PLNs, were selected for this study. Nine MAP-IMRT plans were created for each patient with nine prostate contours that represented the prostate at nine locations with respect to the PLNs, including the original prostate contour and eight contours shifted either 5 mm in a single anterior-posterior (A-P), or superior-inferior (S-I) direction, or 5 mm in both A-P and S-I directions simultaneously. From archived megavoltage cone beam CT (MV-CBCT) and a dual imaging registration, 17 MV-CBCTs from 33 available MV-CBCT from these patients showed large prostate displacements (>3 mm in any direction) with respect to the pelvic bones. For each of these 17 fractions, one of nine MAP-IMRT plans was retrospectively selected and applied to the MV-CBCT for dose calculation. For comparison, a simulated isocenter-shifting plan and a reoptimized plan were also created for each of these 17 fractions. The doses to 95% (D95) of the prostate and PLNs, and the doses to 5% (D5) of the rectum and bladder were calculated and analyzed. Results: For the prostate, D95 > 97% of the prescription dose was observed in 16, 16, and 17 of 17 fractions for the MAP, isocenter-shifted, and reoptimized plans, respectively. For PLNs, D95 > 97% of the prescription doses was observed in 10, 3, and 17 of 17 fractions for the three types of verification plans, respectively. The D5 (mean ± SD) of the rectum was 45.78 ± 5.75, 45.44 ± 4.64, and 44.64 ± 2.71 Gy, and the D5 (mean ± SD) of the bladder was 45.18 ± 2.70, 46.91 ± 3.04, and 45.67 ± 3.61 Gy for three types of verification plans, respectively. Conclusions: The MAP strategy with nine IMRT plans to accommodate the prostate motions in two major directions achieved good dose coverage to the prostate and PLNs. The MAP approach can be immediately used in clinical practice without requiring extra hardware and software.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius
Abstract Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grew while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.
59 BASIC BIOLOGICAL SCIENCES↗
DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models
Not provided.
Computer Science↗
Impact of Concurrent Solubilization and Fines Migration on Fracture Aperture Growth in Shales during Acidized Brine Injection
Acidic hydraulic fracturing fluid chemically and physically alters shale rock fabric during injection and shut-in, creating a “reaction-altered zone” along the fracture faces. To better characterize the variable thickness and composition of this reaction-altered zone under advective flow, we take a coupled experimental and modeling approach. A fluidic cell, with six fiducial markers, is first fabricated to keep the rock sample in place during the core floods and to allow image alignment of acquired images. Then, we conduct a series of reactive core floods in a clay-rich siliceous Wolfcamp shale sample with 10 wt % carbonate, using a synthetic fracturing fluid under no confining stress and at room temperature. High-resolution computed tomography (CT) scans are periodically conducted to observe the spatial alteration of the fracture network. We then perform scanning electron microscopy (SEM-EDS) on the two orthogonal surfaces (fracture surface and freshly cut profile face) to generate high-resolution elemental maps that show the change in mineralogy, both with distance along a given flow path along a fracture surface and with depth from the fracture surface into the shale matrix. These results are contrasted against a two-dimensional (2D) advection-diffusion reaction model developed previously for batch reactions between shale and synthetic fracturing fluids. The model simulates the geochemical interaction occurring at the fracture/matrix interface and penetrating into the shale matrix during the reactive core flood. Both model and experimental results show that the acidic brine is neutralized during the core flood, corresponding to an increase in fracture aperture as a function of fluid volume injected with the greatest change near the inlet. SEM-EDS scans reveal significant dissolution of carbonates on the fracture surface without pyrite oxidation. The reactive transport model indicates that carbonate depletion into the shale interior should be observable, yet SEM-EDS shows no discernible loss of carbonate in the orthogonal profile face. The combination of these observations suggests an additional fracture evolution mechanism in the reactive system, i.e., fines migration. We show that fines migration enhances the access of fracturing fluid to the matrix resulting in a more pronounced fracture widening. Finally, we conclude that coupled mineral dissolution and fines migration govern fracture aperture growth during acidized brine injection. In this work, we effectively show the underlying risk of relying solely on models that do not include an important (transport) process that can alter the system significantly and propose a combined chemomechanical mechanism for fracture evolution appropriate for this shale mineralogy.
58 GEOSCIENCES↗
Predicting Cycle-to-Cycle Variation With Concurrent Cycles in a Gasoline Direct Injected Engine With Large Eddy Simulations
High cycle-to-cycle variation (CCV) is detrimental to engine performance, as it leads to poor combustion and high noise and vibration. In this work, CCV in a gasoline engine is studied using large eddy simulation (LES). The engine chosen as the basis of this work is a single-cylinder gasoline direct injection (GDI) research engine. Two stoichiometric part-load engine operating points (6 BMEP, 2000 RPM) were evaluated: a non-dilute (0% EGR) case and a dilute (18% EGR) case. The experimental data for both operating conditions had 500 cycles. The measured CCV in IMEP was 1.40% for the non-dilute case and 7.78% for the dilute case. To estimate CCV from simulation, perturbed concurrent cycles of engine simulations were compared to consecutively obtained engine cycles. The motivation behind this is that running consecutive cycles to estimate CCV is quite time-consuming. For example, running 100 consecutive cycles requires 2–3 months (on a typical cluster), however, by running concurrently one can potentially run all 100 cycles at the same time and reduce the overall turnaround time for 100 cycles to the time taken for a single cycle (2 days). The goal of this paper is to statistically determine if concurrent cycles, with a perturbation applied to each individual cycle at the start, can be representative of consecutively obtained cycles and accurately estimate CCV. 100 cycles were run for each case to obtain statistically valid results. The concurrent cycles began at different timings before the combustion event, with the motivation to identify the closest time before spark to minimize the run time. Only a single combustion cycle was run for each concurrent case. The calculated standard deviation of peak pressure and coefficient of variance (COV) of indicated mean effective pressure (IMEP) were compared between the consecutive and concurrent methods to quantify CCV. It was found that the concurrent method could be used to predict CCV with either a velocity or numerical perturbation. Here, a large and small velocity perturbation were compared and both produced correct predictions, implying that the type of perturbation is not important to yield a valid realization. Starting the simulation too close to the combustion event, at intake valve close (IVC) or at spark timing, under-predicted the CCV. When concurrent simulations were initiated during or before the intake even, at start of injection (SOI) or earlier, distinct and valid realizations were obtained to accurately predict CCV for both operating points. By simulating CCV with concurrent cycles, the required wall clock time can be reduced from 2–3 months to 1–2 days. Additionally, the required core-hours can be reduced up to 41%, since only a portion of each cycle needs to be simulated.
42 ENGINEERING↗
Implementing Arbitrary/Common Concurrent Writes of CRCW PRAM
The Parallel Random Access Machines (PRAM) abstraction is the simplest and most elegant algorithmic model for the design and analysis of parallel algorithms. It consists of different models categorized based on the underlying memory access mode used, the most powerful of which is the Concurrent Read Concurrent Write (CRCW) model. A PRAM algorithm describes a series of rounds, each of which consists of a collection of operations that can be executed concurrently within the same time step. However, the lack of support for concurrent memory accesses and the prevalence of asynchronous programming models led to the belief that implementing CRCW PRAM algorithms is unattainable and prompted many to avoid this model except for theoretical studies of optimal performance.In this work, we study the arbitrary and common concurrent writes in the CRCW PRAM model and explore implementation challenges on general-purpose systems. Moreover, we examine current practices for implementing common/arbitrary concurrent writes and propose a new efficient lightweight and thread-safe method to implement concurrent writes through leveraging atomic instructions. To demonstrate the efficacy of our method, we developed OpenMP kernels for classical CRCW PRAM algorithms and provide experimental results and comparisons based on run time performance measured over the x86 multicore architecture. Our results show a performance speedup compared to current practices up to 4.5x across all our benchmarks.
Ghanim, Fady↗
Implementing Concurrent Non-Event Transitionsin CMS
Available on CMS information serverCMS CR -2018/277The Compact Muon Solenoid ExperimentMailing address: CMS CERN, CH-1211 GENEVA 23, SwitzerlandConference Report15 October 2018 (v2, 21 November 2018)Implementing Concurrent Non-Event Transitionsin CMSChristopher Jones for the CMS CollaborationAbstractSince the beginning of the LHC Run 2 in 2016 the CMS data processing framework, CMSSW, hasbeen running with multiple threads during production of data and simulation via the use of IntelsThread Building Blocks (TBB) library. The TBB library utilizes tasks as concurrent units of work.CMS used these tasks to allow both concurrent processing of events as well as concurrent running ofmodules processing the same event. This design has served CMS well and has allowed jobs to utilizeless memory per core as well as reduce the number of jobs that must be tracked by CMSs worflowmanagement system. As CMS has begun to utilize greater number of threads in a job, the effect ofserialization points in the framework has decreased jobs CPU efficiency. One major serialization pointoccurs when the framework processes a non-Event transition. These transitions occur when a new Runor LuminosityBlock is to be processed. In this talk we will discuss how the different transitions definethe processing model for CMSSW and how we were able to successfully allow concurrent process-ing of those transitions using TBB via task queues. We will also show CPU efficiency comparisonsbetween the same work being done with and without the additional concurrency.
Jones, Christopher↗
A concurrent irradiation-mechanics multiscale coupling model
The vast majority of our current knowledge regarding the basic mechanisms controlling irradiation effect on mechanical properties is based almost entirely on the results of post-irradiation experiments or theoretical models. However, the concurrent effects of irradiation, mechanical stress, and thermal damage on the failure phenomena of materials and components remain largely unexplored due to its internal multiscale-multiphysics coupling nature. Here, we present here a concurrent irradiation-mechanics multiscale coupling model. The concurrent evolutions of nanoscale irradiation defect clusters, microscale dislocation configurations, and mechanical responses are well captured based on coupling cluster dynamics, discrete dislocation dynamics, and the finite element methods using an effective time marching scheme. Model predictions of defect densities and size are in general agreement with experimental observations. Irradiation hardening is shown to take place also in samples undergoing concurrent irradiation-mechanical loading, similar to samples tested post-irradiation. However, the occurrence of plastic flow localization and dislocation channel formation is not accompanied with apparent yield drop (softening) under concurrent irradiation-mechanical loading conditions, which is different from the post-irradiation case.
42 ENGINEERING↗
Concurrent Changes in Extreme Hydroclimate Events in the Colorado River Basin
Extreme events resulting in catastrophic damage have more than doubled in the last five years, costing hundreds of lives and thousands of homes, and heavily undermining regional economic stability. At present, most of these hydroclimatic extreme events are documented by the media as individual events; however, in scientific terms, many are better understood as concurrent events—concurrent extremes of both temperature and precipitation (e.g., drought, floods). This paper considers concurrent changes in hydroclimate extremes, including heatwaves, drought, flooding, and low flows, in six historical-to-future (1970–1999, 2070–2099) Earth System Model (ESM) climate scenarios for the Colorado River basin. Results indicate that temperature-driven Impacts (heatwaves, drought) have the strongest responses while precipitation-driven Impacts have weaker responses. All Impacts exhibit an increase in magnitude from synoptic to annual time scales, with heatwaves increasing in strength about three times at the annual time scale versus the synoptic, while low flows only increase slightly. Critical watersheds in the Colorado were identified, highlighting the Blue River basin, Uncompahgre, East Taylor, Salt/Verde watersheds, locations of important water infrastructures, water resources, and hydrological research. Our results indicate that concurrent extreme hydroclimate events are projected to increase in the future and intensify within critical regions of the Colorado River basin. Considering extreme hydroclimate events concurrently is an important step towards linking economic and social effects of these events and their associated instabilities on a regional scale.
54 ENVIRONMENTAL SCIENCES↗
CilkSpec: Optimistic Concurrency for Cilk
Recursive parallel programming models such as Cilk strive to simplify the task of parallel programming by enabling a simple divide-and-conquer model of programming. This model is effective in re- cursively partitioning work into smaller parts and combining their results. However, recursive work partitioning can impose additional constraints on concurrency than is implied by the true dependences in a program. In this paper, we present a speculation-based approach to alleviate the concurrency constraints imposed by such recursive parallel programs. We design a runtime infrastructure that supports speculative execution and a predictor to accurately learn and identify opportunities to relax extraneous concurrency constraints. Experimental evaluation demonstrates that speculative relaxation of concurrency constraints can deliver gains of up to 1.6× on 30 cores over baseline Cilk.
cilk↗
Pulsed Radiation Therapy With Concurrent Cisplatin Results in Superior Tumor Growth Delay in a Head and Neck Squamous Cell Carcinoma Murine Model
Purpose: To assess the efficacy of 3-week schedules of low-dose pulsed radiation treatment (PRT) and standard radiation therapy (SRT), with concurrent cisplatin (CDDP) in a head and neck squamous cell carcinoma xenograft model. Methods and Materials: Subcutaneous UT-SCC-14 tumors were established in athymic NIH III HO female mice. A total of 30 Gy was administered as 2 Gy/d, 5 d/wk for 3 weeks, either by PRT (10 × 0.2 Gy/d, with a 3-minute break between each 0.2-Gy dose) or SRT (2 Gy/d, uninterrupted delivery) in combination with concurrent 2 mg/kg CDDP 3 times per week in the final 2 weeks of radiation therapy. Treatment-induced growth delays were defined from twice-weekly tumor volume measurements. Tumor hypoxia was assessed by {sup 18}F-fluoromisonidazole positron emission tomography imaging, and calculated maximum standardized uptake values compared with tumor histology. Tumor vessel density and hypoxia were measured by quantitative immunohistochemistry. Normal tissues effects were evaluated in gut and skin. Results: Untreated tumors grew to 1000 mm{sup 3} in 25.4 days (±1.2), compared with delays of 62.3 days (±3.5) for SRT + CDDP and 80.2 days (±5.0) for PRT + CDDP. Time to reach 2× pretreatment volume ranged from 8.2 days (±1.8) for untreated tumors to 67.1 days (±4.7) after PRT + CDDP. Significant differences in tumor growth delay were observed for SRT versus SRT + CDDP (P=.04), PRT versus PRT + CDDP (P=.035), and SRT + CDDP versus PRT + CDDP (P=.033), and for survival between PRT versus PRT + CDDP (P=.017) and SRT + CDDP versus PRT + CDDP (P=.008). Differences in tumor hypoxia were evident by {sup 18}F-fluoromisonidazole positron emission tomography imaging between SRT and PRT (P=.025), although not with concurrent CDDP. Tumor vessel density differed between SRT + CDDP and PRT + CDDP (P=.011). No differences in normal tissue parameters were seen. Conclusions: Concurrent CDDP was more effective in combination PRT than SRT at restricting tumor growth. Significant differences in tumor vascular density were evident between PRT and SRT, suggesting a preservation of vascular network with PRT.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Continuous Activity Monitoring During Concurrent Chemoradiotherapy
Purpose: To perform a prospective trial testing the feasibility and utility of acquiring activity data as a measure of health status during concurrent chemoradiotherapy. Methods and Materials: Ambulatory patients who were planned for treatment with concurrent chemoradiotherapy with curative intent for cancers of the head and neck, lung, or gastrointestinal tract were provided with activity monitors before treatment initiation. Patients were asked to wear the devices continuously throughout the radiation therapy course. Step count data were downloaded weekly during radiation therapy and 2 and 4 weeks after radiation therapy completion. The primary objective was to demonstrate feasibility, defined as collection of step counts for 80% of the days during study subjects' radiation therapy courses. Secondary objectives included establishing step count as a dynamic predictor of unplanned hospitalization risk. Results: Thirty-eight enrolled patients were treated with concurrent chemoradiotherapy. Primary diagnoses included head and neck cancer (n=11), lung cancer (n=13), and a variety of gastrointestinal cancers (n=14). Step data were collected for 1524 of 1613 days (94%) during patients' radiation therapy courses. Fourteen patients were hospitalized during radiation therapy or within 4 weeks of radiation therapy completion. Cox regression modeling demonstrated a significant association between recent step counts (3-day average) and hospitalization risk, with a 38% reduction in the risk of hospitalization for every 1000 steps taken each day (hazard ratio 0.62, 95% confidence interval 0.46-0.83, P=.002). Inferior quality of life scores and impaired performance status were not associated with increased hospitalization risk. Conclusion: Continuous activity monitoring during concurrent chemoradiotherapy is feasible and well-tolerated. Step counts may serve as powerful, objective, and dynamic indicators of hospitalization risk.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
IL-1β directly inhibits milk lipid production in lactating mammary epithelial cells concurrently with enlargement of cytoplasmic lipid droplets
Highlights: • IL-1β inhibits milk lipid production concurrently with enlargement of lipid droplets. • IL-1β, IL-6, and TNF-α affect milk lipid production in different manners. • IL-1β rapidly induced activation of STAT3 concurrently with inactivation of STAT5. • IL-1β activates the mRNA expression of IL-6 and TNF-α in mammary epithelial cells. Mammary epithelial cells (MECs) in lactating mammary glands produce milk lipid, which provides a large percentage of calories and bioactive lipids for appropriate infant growth. However, secreted milk lipid is often reduced concurrently with increases in IL-1β, IL-6, and TNF-α in mammary glands with mastitis. In this study, we investigated whether those cytokines directly influenced lipid production and secretion. A lactating MEC culture model with high lipid production ability was prepared by culture with oleic acid. TNF-α, IL-1β, and IL-6 differentially affected lipid production and secretion in lactating MECs. In particular, IL-1β treatment significantly reduced amounts of secreted triglycerides by 97% compared with the control concurrently with enlargement of cytoplasmic lipid droplets in MECs. IL-1β also decreased mRNA expression of Fabp3 and Srebp1 and the amount of aquaporin 3, GLUT-1 and adipophilin in the milk lipid production pathway. Furthermore, IL-1β inactivated STAT5 and glucocorticoid signaling to induce milk production in MECs, whereas STAT3 and NFκB signaling was activated. IL-1β induced mRNA expression of IL-6 and TNF-α in MECs. Therefore, we suggest that IL-1β is a key inhibitor of lipid production and secretion in lactating MECs.
60 APPLIED LIFE SCIENCES↗
Multigrid methods with space–time concurrency
Here, we consider the comparison of multigrid methods for parabolic partial differential equations that allow space–time concurrency. With current trends in computer architectures leading towards systems with more, but not faster, processors, space–time concurrency is crucial for speeding up time-integration simulations. In contrast, traditional time-integration techniques impose serious limitations on parallel performance due to the sequential nature of the time-stepping approach, allowing spatial concurrency only. This paper considers the three basic options of multigrid algorithms on space–time grids that allow parallelism in space and time: coarsening in space and time, semicoarsening in the spatial dimensions, and semicoarsening in the temporal dimension. We develop parallel software and performance models to study the three methods at scales of up to 16K cores and introduce an extension of one of them for handling multistep time integration. We then discuss advantages and disadvantages of the different approaches and their benefit compared to traditional space-parallel algorithms with sequential time stepping on modern architectures.
97 MATHEMATICS AND COMPUTING↗
Fault Detection for Dynamical Systems using Differential Geometric and Concurrent Learning Approach
This paper presents a fault identification and estimation approach that brings together the differential geometric concept of observability codistribution with data driven concurrent learning. In order to identify faults in presence of unknown disturbances, we utilize the differential geometric approach to design a coordinate transformation, to find a subspace in which the effect of disturbances and system faults can be segregated. We then use concurrent learning to estimate magnitude of the constant fault. We illustrate the approach to fault isolation for a linear helicopter dynamics and a spherical pendulum dynamics. We use Lyapunov stability analysis to show that the fault estimate by concurrent learning converges to the actual fault value, and then illustrate the design of a recovery controller.
Fault detection and diagnosis↗