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At least 19 records

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↗

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↗

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↗

Vorinostat and Concurrent Stereotactic Radiosurgery for Non-Small Cell Lung Cancer Brain Metastases: A Phase 1 Dose Escalation Trial

Purpose: To determine the maximum tolerated dose (MTD) of vorinostat, a histone deacetylase inhibitor, given concurrently with stereotactic radiosurgery (SRS) to treat non-small cell lung cancer (NSCLC) brain metastases. Secondary objectives were to determine toxicity, local failure, distant intracranial failure, and overall survival rates. Materials and Methods: In this multicenter study, patients with 1 to 4 NSCLC brain metastases, each ≤2 cm, were enrolled in a phase 1, 3 + 3 dose escalation trial. Vorinostat dose levels were 200, 300, and 400 mg orally once daily for 14 days. Single-fraction SRS was delivered on day 3. A dose-limiting toxicity (DLT) was defined as any Common Terminology Criteria for Adverse Events version 3.0 grade 3 to 5 acute nonhematologic adverse event related to vorinostat or SRS occurring within 30 days. Results: From 2009 to 2014, 17 patients were enrolled and 12 patients completed study treatment. Because no DLTs were observed, the MTD was established as 400 mg. Acute adverse events were reported by 10 patients (59%). Five patients discontinued vorinostat early and withdrew from the study. The most common reasons for withdrawal were dyspnea (n=2), nausea (n=1), and fatigue (n=2). With a median follow-up of 12 months (range, 1-64 months), Kaplan-Meier overall survival was 13 months. There were no local failures. One patient (8%) at the 400-mg dose level with a 2.0-cm metastasis developed histologically confirmed grade 4 radiation necrosis 2 months after SRS. Conclusions: The MTD of vorinostat with concurrent SRS was established as 400 mg. Although no DLTs were observed, 5 patients withdrew before completing the treatment course, a result that emphasizes the need for supportive care during vorinostat administration. There were no local failures. A larger, randomized trial may evaluate both the tolerability and potential local control benefit of vorinostat concurrent with SRS for brain metastases.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Concurrent reaction-bonded joining and densification of additively manufactured silicon carbide by liquid silicon infiltration

Here, in this study, additive-manufactured silicon carbide preforms were joined and densified by reaction bonding via liquid silicon infiltration. The silicon carbide preforms were first printed by binder jetting additive manufacturing. To demonstrate concurrent joining and densification, two preforms with carbon or parchment papers at the interface were concurrently joined and infiltrated by liquid silicon. Results showed a robust interface with thicknesses ranging from 150 to 500 µm, depending on the paper type and the number of paper layers. High-energy synchrotron X-ray revealed that β-phase silicon carbide was formed inside the interface. Finally, two additively manufactured samples with complicated channel geometry were successfully joined. Energy dispersive spectroscopy of the interface of the channeled samples showed a consistent and robust joining. This concurrent approach of joining and densification enables efficiency improvement of fabricating silicon carbide parts with complicated geometries and widens geometry freedom for additive manufacturing of silicon carbide.

36 MATERIALS SCIENCE↗

Concurrent atomistic-continuum modeling of crystalline materials

In the work reported here, we present a concurrent atomistic-continuum (CAC) method for modeling and simulation of crystalline materials. The CAC formulation extends the Irving-Kirkwood procedure for deriving transport equations and fluxes for homogenized molecular systems to that for polyatomic crystalline materials by employing a concurrent two-level description of the structure and dynamics of crystals. A multiscale representation of conservation laws is formulated, as a direct consequence of Newton's second law, in terms of instantaneous expressions of unit cell-averaged quantities using the mathematical theory of distributions. Finite element (FE) solutions to the conservation equations, as well as fluxes and temperature in the FE representation, are introduced, followed by numerical examples of the atomic-scale structure of interfaces, dynamics of fracture and dislocations, and phonon thermal transport across grain boundaries. In addition to providing a methodology for concurrent multiscale simulation of transport processes under a single theoretical framework, the CAC formulation can also be used to compute fluxes (stress and heat flux) in atomistic and coarse-grained atomistic simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Concurrent conversation modeling and parallel simulation of the naming game in social networks

The Naming Game is an effective self-organization model to understand the emergence of linguistic consensus and to investigate the system dynamics in a variety of phenomena over social networks of autonomous agents. The Naming Game is an effective description for the evolution of consensus despite the absence of any central coordination or specialized initialization even in large-scale networks. While the classical game is effective in description, it was defined with inherently sequential evaluation semantics over the entire network. Here, we develop a new concurrent model as a relaxation of the classical formulation and express it in a discrete event style of evaluation. Further, with the uncovered concurrency that was absent in the classical algorithm, we map the concurrent model to parallel discrete event simulation. Using a prototype implementation, we present an initial parallel performance study on networks containing hundreds of thousands of individuals, with a decrease in simulation time in the best-observed case from 4800 seconds down to 1400 seconds.

Perumalla, Kalyan↗

Positioning Accuracy in a Concurrent Robot-CNC Hybrid Manufacturing System

Abstract Additive manufacturing (AM) has gained notoriety for offering advantages over traditional manufacturing methods, such as increased design complexity and flexibility. However, it has not found widespread use beyond rapid prototyping. One hindrance to the acceptance of AM processes in industry is the time and cost of fabrication per component. While metal AM by itself can be inexpensive, extra manufacturing steps in the form of subtractive manufacturing (SM) may need to be performed to reach final part tolerances, leading to hybrid additive-subtractive manufacturing (HASM) of a part, which increases time and cost. A potential area to reduce cost is through increasing the efficiency of the HASM process by conducting additive and subtractive manufacturing simultaneously. Usually, HASM is performed in a process where AM is completed in one machine or cell and transferred to another machine or cell for SM in a sequential assembly line process. This efficiency decreases part cost, but high aspect ratio parts or parts with internal geometry that require interleaved additive deposition and machining cannot be produced. One unexplored solution to simultaneous HASM that allows for interleaved operations is to operate the deposition head and machining spindle concurrently within the same machine envelope, known as concurrent HASM (CHASM). In this type of process, both AM and SM occur simultaneously on a batch of small parts or a single large part, maintaining a high efficiency without sacrificing the full range of complex geometries that AM allows for. A potential approach to the single-machine method could be to combine a robot and mill within the same envelope. A challenge to this approach, however, is control of both systems. Most machine controllers have limited external communication or, if a robot has been integrated, only offer movement of either the robot or mill at any given time. As a result, systems must pause either the AM or SM process to switch between them rather than working simultaneously. The present work investigates the positional accuracy of such a CHASM system comprised of a robotic arm and a 3-axis mill. Open-loop tests with limited communication between machines are performed on the system to verify positional error during concurrent robot-mill movements. Under certain conditions, it is demonstrated that position error can stay within 2 mm for the duration of a single layer; however, these tests show that, generally, the open-loop positioning performance of the system is inadequate for CHASM without part-specific hand-tuning of parameters. Based on these results, a set of requirements for successful robot-CNC CHASM is proposed for future integrations.

Goodwin, Jesse↗

Developing strong concurrent multiphysics multiscale coupling to understand the impact of microstructural mechanisms on the structural scale

The heterogeneity in mechanical fields introduced by microstructure plays a critical role in the localization of deformation. To resolve this incipient stage of failure, it is therefore necessary to incorporate microstructure with sufficient resolution. On the other hand, computational limitations make it infeasible to represent the microstructure in the entire domain at the component scale. In this study, the authors demonstrate the use of concurrent multi- scale modeling to incorporate explicit, finely resolved microstructure in a critical region while resolving the smoother mechanical fields outside this region with a coarser discretization to limit computational cost. The microstructural physics is modeled with a high-fidelity model that incorporates anisotropic crystal elasticity and rate-dependent crystal plasticity to simulate the behavior of a stainless steel alloy. The component-scale material behavior is treated with a lower fidelity model incorporating isotropic linear elasticity and rate-independent J 2 plas- ticity. The microstructural and component scale subdomains are modeled concurrently, with coupling via the Schwarz alternating method, which solves boundary-value problems in each subdomain separately and transfers solution information between subdomains via Dirichlet boundary conditions. Beyond cases studies in concurrent multiscale, we explore progress in crystal plastic- ity through modular designs, solution methodologies, model verification, and extensions to Sierra/SM and manycore applications. Advances in conformal microstructures having both hexahedral and tetrahedral workflows in Sculpt and Cubit are highlighted. A structure-property case study in two-phase metallic composites applies the Materials Knowledge System to local metrics for void evolution. Discussion includes lessons learned, future work, and a summary of funded efforts and proposed work. Finally, an appendix illustrates the need for two-way coupling through a single degree of freedom.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗