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At least 1,189 records · Page 66

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗

Adiabatic state preparation study of methylene

Quantum computers attract much attention as they promise to outperform their classical counterparts in solving certain type of problems. One of them with practical applications in quantum chemistry is simulation of complex quantum systems. An essential ingredient of efficient quantum simulation algorithms are initial guesses of the exact wave functions with high enough fidelity. As was proposed in Aspuru-Guzik et al. [Science 309, 1704 (2005)], the exact ground states can in principle be prepared by the adiabatic state preparation method. Here, we apply this approach to preparation of the lowest lying multireference singlet electronic state of methylene and numerically investigate preparation of this state at different molecular geometries. We then propose modifications that lead to speeding up the preparation process. Finally, we decompose the minimal adiabatic state preparation employing the direct mapping in terms of two-qubit interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determining the impact of a severe dry to wet transition on watershed hydrodynamics in California, USA with an integrated hydrologic model

With the onset of climate change, regions relied upon for water supply are increasingly subject to end-member fluctuations between periods of severe drought followed by extreme precipitation. The impacts of these extreme conditions on watershed hydrodynamics in water-resource sensitive regions such as California are unknown despite their great importance for resilience and water management purposes. Understanding these impacts requires high-resolution physically based models to capture sharp variations of topography, land use, wetting fronts, etc. Here, an integrated hydrologic model was used in a high-performance computing framework to study the complex nonlinear dynamics occurring at a representative Californian watershed. The Cosumnes Watershed, one of the last major rivers in California without a dam, offers a rare opportunity to isolate the effects of water management from climate extremes. Here, we show model validation with comparisons between model outputs and local measurements in addition to various satellite-based products including (1) Snow Water Equivalent (SWE) with Snow Data Assimilation System (SNODAS) and a reconstruction method by Bair and co-authors, (2) soil moisture with Soil Moisture Active Passive (SMAP), and (3) evapotranspiration (ET) with Mapping Evapotranspiration at high Resolution with Internalized Calibration (METRIC). To assess changes in hydrodynamic behavior during climate extremes and their transitions, a simulation spanning a recent drought followed by the highest precipitation year on record (2015–2017) is discussed. From these simulations, we are able to highlight regions that are the most sensitive to climate extremes, which depend on many factors including hydrologic connectivity, geology and topography. These analyses provide a better understanding of the physical phenomena occurring in the watershed, strengthening our knowledge of how the system may respond to extreme conditions which might become the “new normal.”

54 ENVIRONMENTAL SCIENCES↗

Material Science Image Analysis using Quant-CT in ImageJ

We introduce a computational analysis workflow to access properties of solid objects using nondestructive imaging techniques that rely on X-ray imaging. The goal is to process and quantify structures from material science sample cross sections. The algorithms can differentiate the porous media (high density material) from the void (background, low density media) using a Boolean classifier, so that we can extract features, such as volume, surface area, granularity spectrum, porosity, among others. Our workflow, Quant-CT, leverages several algorithms from ImageJ, such as statistical region merging and 3D object counter. It also includes schemes for bilateral filtering that use a 3D kernel, for parallel processing of sub-stacks, and for handling over-segmentation using histogram similarities. The Quant-CT supports fast user interaction, providing the ability for the user to train the algorithm via subsamples to feed its core algorithms with automated parameterization. Quant-CT plugin is currently available for testing by personnel at the Advanced Light Source and Earth Sciences Divisions and Energy Frontier Research Center (EFRC), LBNL, as part of their research on porous materials. The goal is to understand the processes in fluid-rock systems for the geologic sequestration of CO2, and to develop technology for the safe storage of CO2 in deep subsurface rock formations. We describe our implementation, and demonstrate our plugin on porous material images. This paper targets end-users, with relevant information for developers to extend its current capabilities.

97 MATHEMATICS AND COMPUTING↗

Data acquisition and slow control interface for the Mu2e experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10000 over existing limits. The Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The data stream from the detector subsystems is read by a software filter algorithm that selects events which are combined with the data flux coming from a cosmic ray veto system. The Detector Control System (DCS) has been developed using the Experimental Physics and Industrial Control System (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS system has been integrated into otsdaq. A prototype of the TDAQ and the DCS systems has been built at Fermilab's Feynman Computing Center. In this study, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Fossil Energy Workshop on Quantum Information Science & Technology (Summary Report)

This report summarizes findings and discussion from the Fossil Energy Workshop on Quantum Information Science & Technology which took place on November 19-21, 2019. Quantum Information Science (QIS) is expected to profoundly change the practice of science and engineering in the coming decades. It is a rapidly progressing field, fueled by large investments from the private sector and governments. Its importance to the U.S. economy and national security is underscored by the National Quantum Initiative Act passed in December 2018. QIS includes quantum sensing, quantum communications, quantum simulation experiments, and quantum computation. QIS technology exploits quantum phenomena for performing tasks that are impossible to do today, such as finding prime factors of large numbers or elucidating reaction mechanisms in complex chemical systems. The opportunities for applying QIS to problems encountered in fossil energy technology development are not known today. This workshop brought together, for the first time, experts in these fields to exchange information and explore potential research opportunities for QIS to advance fossil energy. The goal of the workshop was to develop a set of priority research opportunities that can inform future research efforts in QIS and build a community of next-generation researchers at the intersection of QIS and fossil energy.

20 FOSSIL-FUELED POWER PLANTS↗

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗

Time-series learning of latent-space dynamics for reduced-order model closure

In this work, we study the performance of long short-term memory networks (LSTMs) and neural ordinary differential equations (NODEs) in learning latent-space representations of dynamical equations for an advection-dominated problem given by the viscous Burgers equation. Our formulation is devised in a nonintrusive manner with an equation-free evolution of dynamics in a reduced space with the latter being obtained through a proper orthogonal decomposition. In addition, we leverage the sequential nature of learning for both LSTMs and NODEs to demonstrate their capability for closure in systems that are not completely resolved in the reduced space. We assess our hypothesis for two advection-dominated problems given by the viscous Burgers equation. We observe that both LSTMs and NODEs are able to reproduce the effects of the absent scales for our test cases more effectively than does intrusive dynamics evolution through a Galerkin projection. This result empirically suggests that time-series learning techniques implicitly leverage a memory kernel for coarse-grained system closure as is suggested through the Mori–Zwanzig formalism.

97 MATHEMATICS AND COMPUTING↗

Confinement of magnetism in atomically thin La0.7Sr0.3CrO3/La0.7Sr0.3MnO3 heterostructures

Abstract At crystalline interfaces where a valence-mismatch exists, electronic, and structural interactions may occur to relieve the polar mismatch, leading to the stabilization of non-bulk-like phases. We show that spontaneous reconstructions at polar La 0.7 Sr 0.3 MnO 3 interfaces are correlated with suppressed ferromagnetism for film thicknesses on the order of a unit cell. We investigate the structural and magnetic properties of valence-matched La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 interfaces using a combination of high-resolution electron microscopy, first principles theory, synchrotron X-ray scattering and magnetic spectroscopy and temperature-dependent magnetometry. A combination of an antiferromagnetic coupling between the La 0.7 Sr 0.3 CrO 3 and La 0.7 Sr 0.3 MnO 3 layers and a suppression of interfacial polar distortions are found to result in robust long-range ferromagnetic ordering for ultrathin La 0.7 Sr 0.3 MnO 3 . These results underscore the critical importance of interfacial structural and magnetic interactions in the design of devices based on two-dimensional oxide magnetic systems.

36 MATERIALS SCIENCE↗

Survival analysis of localized prostate cancer with deep learning

In recent years, data-driven, deep-learning-based models have shown great promise in medical risk prediction. By utilizing the large-scale Electronic Health Record data found in the U.S. Department of Veterans Affairs, the largest integrated healthcare system in the United States, we have developed an automated, personalized risk prediction model to support the clinical decision-making process for localized prostate cancer patients. This method combines the representative power of deep learning and the analytical interpretability of parametric regression models and can implement both time-dependent and static input data. To collect a comprehensive evaluation of model performances, we calculate time-dependent C-statistics C td over 2-, 5-, and 10-year time horizons using either a composite outcome or prostate cancer mortality as the target event. The composite outcome combines the Prostate-Specific Antigen (PSA) test, metastasis, and prostate cancer mortality. Our longitudinal model Recurrent Deep Survival Machine (RDSM) achieved C td 0.85 (0.83), 0.80 (0.83), and 0.76 (0.81), while the cross-sectional model Deep Survival Machine (DSM) attained C td 0.85 (0.82), 0.80 (0.82), and 0.76 (0.79) for the 2-, 5-, and 10-year composite (mortality) outcomes, respectively. In addition to estimating the survival probability, our method can quantify the uncertainty associated with the prediction. The uncertainty scores show a consistent correlation with the prediction accuracy. We find PSA and prostate cancer stage information are the most important indicators in risk prediction. Our work demonstrates the utility of the data-driven machine learning model in prostate cancer risk prediction, which can play a critical role in the clinical decision system.

60 APPLIED LIFE SCIENCES↗

Magneto-optical absorption in semiconducting spherical quantum dots: Influence of the dot-size, confining potential, and magnetic field

Semiconducting quantum dots – more fancifully dubbed artificial atoms – are quasi-zero dimensional, tiny, man-made systems with charge carriers completely confined in all three dimensions. The scientific quest behind the synthesis of quantum dots is to create and control future electronic and optical nanostructures engineered through tailoring size, shape, and composition. The complete confinement – or the lack of any degree of freedom for the electrons (and/or holes) – in quantum dots limits the exploration of spatially localized elementary excitations such as plasmons to direct rather than reciprocal space. Here we embark on a thorough investigation of the magneto-optical absorption in semiconducting spherical quantum dots characterized by a confining harmonic potential and an applied magnetic field in the symmetric gauge. This is done within the framework of Bohm-Pines’ random-phase approximation that enables us to derive and discuss the full Dyson equation that takes proper account of the Coulomb interactions. As an application of our theoretical strategy, we compute various single-particle and many-particle phenomena such as the Fock-Darwin spectrum; Fermi energy; magneto-optical transitions; probability distribution; and the magneto-optical absorption in the quantum dots. It is observed that the role of an applied magnetic field on the absorption spectrum is comparable to that of a confining potential. Increasing (decreasing) the strength of the magnetic field or the confining potential is found to be analogous to shrinking (expanding) the size of the quantum dots: resulting into a blue (red) shift in the absorption spectrum. The Fermi energy diminishes with both increasing magnetic-field and dot-size; and exhibits saw-tooth-like oscillations at large values of field or dot-size. Unlike laterally confined quantum dots, both (upper and lower) magneto-optical transitions survive even in the extreme instances. However, the intra-Landau level transitions are seen to be forbidden. The spherical quantum dots have an edge over the strictly two-dimensional quantum dots in that the additional (magnetic) quantum number makes the physics richer (but complex). A deeper grasp of the Coulomb blockade, quantum coherence, and entanglement can lead to a better insight into promising applications involving lasers, detectors, storage devices, and quantum computing.

36 MATERIALS SCIENCE↗

A new UHV micro positioning system for high load

In this work we report the design and performance of a novel compact in-vacuum actuator, designed to be compatible with all the motions required for the scissor-type ESRF mirror bender. These mirror benders include several linear actuators, which drive the mirror bending torques, as well as the main alignment motions such as pitch and translation along the normal to the mirror surface. The motions are provided by compact linear actuators, which consist of motor, reduction, spindle and nut, encapsulated on a closed air volume to provide vacuum compatibility. The actuator includes a hydroformed bellows to transmit the force to the actuator tip, and an electrical feedthrough for the motor cables. The design boundaries for these actuators are quite tight, as they must be integrated in a narrow volume, must be UHV compatible and must provide high resolution, for a relatively high load. As a result, they have limited mechanical performance, and in some cases poor reliability. To overcome these problems, we designed and implemented a different concept. In the proposed concept, the motor rotation is converted onto a linear motion by means of a cam instead of a spindle and a nut. This allows for much shorter and stiffer transmission system, with similar dimensions. The vacuum compatibility is intrinsic for this solution, since the whole mechanism of the actuator is UHV compatible. All motions are preloaded and guided by vacuum compatible (hybrid metal-ceramics) ball bearings. This allows the system reaching a repeatability and backlash well within the micron. The absence of friction allows for a high reliability and releases the maintenance needs of the system. The transmission is intrinsically irreversible, and the system can hold a load of 250 N within a few nanometers without any holding current on the motors. This allows the system to move reliably also in micro-stepping mode, providing a resolution well below the half-step nominal resolution of 100 nm. Performances have been tested on a prototype. We report the results of the tests obtained in air and in vacuum after bake-out. Two units of the new actuator have been installed at the photoemission beamline of ALBA (CIRCE) and are routinely used to align the 3 µm spot on the field of view of the Photoemission Electron Microscope. The absence of any noticeable backlash, or any friction effect and the reliability of the micro-stepping motion has simplified very much the alignment of the photon beam, reducing the alignment process to few minutes. The excellent performances and relatively high load capacity of this new compact actuator make of it a versatile element to be integrated in other systems requiring reliable in-vacuum positioning.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Computing with a Chemical Reservoir

Contemporary computation is expensive, with large language models and artificial intelligence becoming more common in daily life. However, high-performance computing is reaching the limits in speed and energy expenditure, and domain science requires ever-increasing computational capacity, with simulations and data analysis pipelines ever-growing in complexity. As we progress towards post-exascale computation, with the associated high energy costs, new methods of energy-conscious computation are required. Novel analog and hybrid digital-analog systems can overcome these challenges, and chemical reactions offer a promising avenue. Computers based on chemistry can provide compact desktop devices with immense computational power. These devices are readily scalable by considering greater reaction systems or vessels, meeting the high-performance requirements for scientific workflows. In this article, we present ChemComp, a compilation pipeline for the conversion of ordinary differential equations into implementable chemical reactions. We then demonstrate the solving capabilities of ChemComp by emulating a potential chemical reservoir device. We leverage the multi-layer intermediate representation (MLIR) compiler framework to implement an expressive chemical reaction abstraction and propose a path for chemical reaction networks (CRNs) to represent mathematical problems effectively. Combined, we demonstrate a potential workflow that can harness chemistry’s computing power to create energy-efficient, high-performance computation systems for contemporary computing needs.

artificial intelligence↗

SU-F-J-110: MRI-Guided Single-Session Simulation, Online Adaptation, and Treatment

Purpose: To develop a combined simulation and treatment workflow for MRI-guided radiation therapy using the ViewRay treatment planning and delivery system. Methods: Several features of the ViewRay MRIdian planning and treatment workflows are used to simulate and treat patients that require emergent radiotherapy. A simple “pre-plan” is created on diagnostic imaging retrieved from radiology PACS, where conformal fields are created to target a volume defined by a physician based on review of the diagnostic images and chart notes. After initial consult in radiation oncology, the patient is brought to the treatment room, immobilized, and imaged in treatment position with a volumetric MR. While the patient rests on the table, the pre-plan is applied to the treatment planning MR and dose is calculated in the treatment geometry. After physician review, modification of the plan may include updating the target definition, redefining fields, or re-balancing beam weights. Once an acceptable treatment plan is finalized and approved, the patient is treated. Results: Careful preparation and judicious choices in the online planning process allow conformal treatment plans to be created and delivered in a single, thirty-minute session. Several advantages have been identified using this process as compared to conventional urgent CT simulation and delivery. Efficiency gains are notable, as physicians appreciate the predictable time commitment and patient waiting time for treatment is decreased. MR guidance in a treatment position offers both enhanced contrast for target delineation and reduction of setup uncertainties. The MRIdian system tools designed for adaptive radiotherapy are particularly useful, enabling plan changes to be made in minutes. Finally, the resulting plans, typically 6 conformal beams, are delivered as quickly as more conventional AP/PA beam arrangements with comparatively superior dose distributions. Conclusion: The ViewRay treatment planning software and delivery system can accommodate a fast simulation and treatment workflow.

60 APPLIED LIFE SCIENCES↗

A lightweight approach to performance portability with targetDP

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

Computer Science↗

A Method to Constrain Genome-Scale Models with 13 C Labeling Data

Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13 C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13 C labeling data. A comparison shows that the results of this new method are similar to those found through 13 C Metabolic Flux Analysis ( 13 C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.

59 BASIC BIOLOGICAL SCIENCES↗