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At least 793 records · Page 44

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementation of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integrated plasma facing component calorimetry for measurement of shot integrated deposited energy in the NSTX-U

Here, the upgrade to the National Spherical Torus eXperiment (NSTX-U) increases the injected neutral beam power up to 12 MW and the plasma current up to I p = 2 MA for plasma durations up to 5 s. The graphite plasma facing components have been re-designed to handle greater heat and energy fluxes than were seen in NSTX using a castellated design. We present the experimental testing and validation of a castellated graphite target, similar to the prototype tile design, instrumented with thermocouples at various depths in the castellation. During testing, incident heat flux is provided by a programmed electron beam system and surface temperatures are measured via infrared thermography directly viewing the target surface. It was found that the thermocouple response scaled linearly with the measured surface temperature rise regardless of thermocouple depth in the castellation. A sensitivity of 14.3 °C/kJ of deposited energy was found when treating individual castellations as a semi-infinite solid.

47 OTHER INSTRUMENTATION↗

A high performance cost-effective digital complex correlator for an X-band polarimetry survey

The detailed knowledge of the Milky Way radio emission is important to characterize galactic foregrounds masking extragalactic and cosmological signals. The update of the global sky models describing radio emissions over a very large spectral band requires high sensitivity experiments capable of observing large sky areas with long integration times. Here, we present the design of a new 10 GHz (X-band) polarimeter digital backend to map the polarization components of the galactic synchrotron radiation field of the Northern Hemisphere sky. The design follows the digital processing trends in radio astronomy and implements a large bandwidth (1 GHz) digital complex cross-correlator to extract the Stokes parameters of the incoming synchrotron radiation field. The hardware constraints cover the implemented VLSI hardware description language code and the preliminary results. The implementation is based on the simultaneous digitized acquisition of the Cartesian components of the two linear receiver polarization channels. The design strategy involves a double data rate acquisition of the ADC interleaved parallel bus, and field programmable gate array device programming at the register transfer mode. The digital core of the back-end is capable of processing 32 Gbps and is built around an Altera field programmable gate array clocked at 250 MHz, 1 GSps analog to digital converters and a clock generator. The control of the field programmable gate array internal signal delays and a convenient use of its phase locked loops provide the timing requirements to achieve the target bandwidths and sensitivity. This solution is convenient for radio astronomy experiments requiring large bandwidth, high functionality, high volume availability and low cost. Of particular interest, this correlator was developed for the Galactic Emission Mapping project and is suitable for large sky area polarization continuum surveys. The solutions may also be adapted to be used at signal processing subsystem levels for large projects like the square kilometer array testbeds.

79 ASTRONOMY AND ASTROPHYSICS↗

ASCR Workshop on Quantum Computing for Science

This report details the findings of the DOE ASCR Workshop on Quantum Computing for Science that was organized to assess the viability of quantum computing technologies to meet the computational requirements of the DOE’s science and energy mission, and to identify the potential impact of quantum technologies. The workshop was held on February 17-18, 2015, in Bethesda, MD, to solicit input from members of the quantum computing community. The workshop considered models of quantum computation and programming environments, physical science applications relevant to DOE's science mission as well as quantum simulation, and applied mathematics topics including potential quantum algorithms for linear algebra, graph theory, and machine learning. This report summarizes these perspectives into an outlook on the opportunities for quantum computing to impact problems relevant to the DOE’s mission as well as the additional research required to bring quantum computing to the point where it can have such impact.

97 MATHEMATICS AND COMPUTING↗

Modeling and Integration of Flexible Demand in Heat and Electricity Integrated Energy System

This paper is focused on utilizing customers' flexible energy demand, including both heat demand and electricity demand, to provide balancing resources and relieve the difficulties of integrating variable wind power with the combined heat and power. The integration of heat and electricity energy systems providing customers with multiple options for fulfilling their energy demand is described. Customer aggregators are introduced to supply downstream demand in the most economical way. Controlling customers' energy consumption behaviors enables aggregators to adjust their energy demand in response to supply conditions. Incorporating aggregators' flexible energy demand into the centralized energy dispatch model, a two-level optimization problem (TLOP) is first formed where the system operatormaximizes social welfare subject to aggregators' strategies, which minimize the energy purchase cost. Furthermore, the subproblems are linearized based on several reasonable assumptions. Optimal conditions of the subproblems are then transformed as energy demands to be described as explicit piecewise-linear functions of electricity prices corresponding to the demand bid curves. In this way, the TLOP is transformed to a standard optimization problem, which requires aggregators to only submit a demand bid to run the centralized energy dispatch program. All the parameters pertaining to the aggregators' energy consumption models are internalized in the bid curves. The proposed technique is illustrated in a modified testing system.

combined heat and power (CHP)↗

The strangeness program at GlueX

The GlueX experiment located at Jefferson Lab studies the spectrum of hadrons using photoproduction on a LH2 target in a wide variety of final states. With its detector system capable of measuring neutral and charged final state particles over almost the full solid angle, and very good particle iden- tification capabilities, GlueX can measure many different hadrons containing strangeness. A linearly polarized photon beam allows the measurement of po- larization observables, which contain information about the production mecha- nisms involved in generating strange particles in photoproduction. In addition, GlueX can perform precise cross-section measurements, which help to study the spectrum of strange hadrons. In this presentation, the GlueX experiment is introduced, and recent progress of its strangeness program is discussed. We present recent results on ?0 beam asymmetries, ?(1520) spin-density matrix elements and ongoing studies of the ?(1405) lineshape. We also present our recent progress on measurements of ?? ? and ?(?) photoproduction. Also, future prospects for strangeness measurements at GlueX are discussed.

Pauli, Peter↗

SU-F-T-262: Commissioning Varian Portal Dosimetry for EPID-Based Patient Specific QA in a Non-Aria Environment

Purpose: Development of an in-house program facilitates a workflow that allows Electronic Portal Imaging Device (EPID) patient specific quality assurance (QA) measurements to be acquired and analyzed in the Portal Dosimetry Application (Varian Medical Systems, Palo Alto, CA) using a non-Aria Record and Verify (R&V) system (MOSAIQ, Elekta, Crawley, UK) to deliver beams in standard clinical treatment mode. Methods: Initial calibration of an in-house software tool includes characterization of EPID dosimetry parameters by importing DICOM images of varying delivered MUs to determine linear mapping factors in order to convert image pixel values to Varian-defined Calibrated Units (CU). Using this information, the Portal Dose Image Prediction (PDIP) algorithm was commissioned by converting images of various field sizes to output factors using the Eclipse Scripting Application Programming Interface (ESAPI) and converting a delivered configuration fluence to absolute dose units. To verify the algorithm configuration, an integrated image was acquired, exported directly from the R&V client, automatically converted to a compatible, calibrated dosimetric image, and compared to a PDIP calculated image using Varian’s Portal Dosimetry Application. Results: For two C-Series and one TrueBeam Varian linear accelerators, gamma comparisons (global 3% / 3mm) of PDIP algorithm predicted dosimetric images and images converted via the inhouse system demonstrated agreement for ≥99% of all pixels, exceeding vendor-recommended commissioning guidelines. Conclusion: Combinations of a programmatic image conversion tool and ESAPI allow for an efficient and accurate method of patient IMRT QA incorporating a 3rd party R&V system.

60 APPLIED LIFE SCIENCES↗

RPI LINAC refurbishment and upgrade project

The Electron Linear Accelerator at Rensselaer Polytechnic Institute (RPI) was constructed in the late 1950s and started operation in 1961 [1]. The facility was designed and used primarily for measurements of Nuclear Data (ND) with emphasis on the resonance energy region. As such it was designed to produce short pulses of neutrons (5-5000 ns) and equipped with detection stations at different neutron flight path distances from the source (15 m-250 m). When the LINAC started operation it was one of the most powerful accelerators in the world for high energy-resolution measurements in the resonance region. The original LINAC with some upgrades is still in operation but no longer provides world class capabilities for measurements with short pulses. In 2011 discussions between the RPI ND group, Naval Reactors, and the Nuclear Criticality Safety Program about the future of the LINAC concluded that maintaining the capability to perform world-class nuclear data measurements at RPI was desirable. To that end, it was decided to refurbish the facility and upgrade the accelerator capabilities to enable high accuracy measurement in the resonance region with narrow neutron pulse and high electron beam power. Located at a major US technical university, this project provides a needed US nuclear data capability for both research and education, and also includes external users and industrial applications.

43 PARTICLE ACCELERATORS↗

Deconstructing supergravity: massive supermultiplets

Given the success of the deconstruction program in obtaining ghost-free massive gravity from 5-D Einstein gravity, we propose a modification of the deconstruction procedure that incorporates supersymmetry at the linear level. We discuss the relevant limits of a conjectured interacting theory of a massive spin 2 supermultiplet, and determine the linear theory to be the N=1 Zinoviev theory, a supersymmetric extension of Fierz-Pauli theory. We develop a family of 1-site deconstruction procedures for fermionic fields (yielding Dirac and Majorana mass terms). The deconstruction procedure appropriate for giving fermions a Dirac mass is found to preserve half of the supersymmetry of the 5-D theory. We explicitly check this by deconstructing 5-D N=2 super-Maxwell theory down to 4-D N=1 super-Proca theory, and deconstructing linear 5-D N=2 supergravity down to 4-D N=1 Zinoviev theory, and derive the full 4-D supersymmetry algebras and Stückelberg symmetries from the 5-D superalgebras and gauge symmetries, respectively. We conjecture that this procedure should admit a generalization to fully non-linear theories.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High-Performance Computing Based EMT Simulation: Power Grid with IBRs

Electromagnetic transient (EMT) simulation of power grids with high-fidelity models of inverter-based resources (IBRs) is time-consuming and difficult to scale. The necessity for high-fidelity models of IBRs that incorporate the dynamics of individual inverters within IBRs has been showcased in recent studies. These studies focused on events with partial power reduction in each IBR during a transmission line fault in the power grid. These types of events have been documented in multiple North American Electric Reliability Council (NERC) reports in the past decade. It is imperative then to find solutions to speed-up EMT simulations and scale the size of the region with IBRs studied in EMT simulations. In this paper, a combination of numerical simulation algorithms with high-performance computing techniques are employed in discretization and linear solvers employed in the proposed RE-INTEGRATE EMT simulation platform for power grid with IBRs. For ease of scalability, modular and object-oriented programming is used as these techniques are implemented. Additionally, automation software is developed to convert legacy software codes to the proposed RE-INTEGRATE EMT simulation platform. Thereafter, this platform is evaluated on multi-core central processing units (CPUs). Finally, scale-up tests are performed to showcase the scalability that is possible.

Marthi, Phani Ratna Vanamali [ORNL] (ORCID:0000000↗

Quantum Dynamics at Scale: Ultrafast Control of Emergent Functional Materials

Confluence of extreme-scale quantum dynamics simulations (i.e. quantum@scale) and cutting-edge x-ray free-electron laser experiments are revolutionizing materials science. An archetypal example is the exciting concept of using picosecond light pulses to control emergent material properties on demand in atomically-thin layered materials. This paper describes efforts to scale our quantum molecular dynamics engine toward the United States' first exaflop/s computer, under an Aurora Early Science Program project named "Metascalable layered material genome". Key algorithmic and computing techniques incorporated are: (1) globally-scalable and locally-fast solvers within a linear-scaling divide-conquer-recombine algorithmic framework; (2) algebraic `BLASification' of computational kernels; and (3) data alignment and loop restructuring, along with register and cache blocking, for enhanced vectorization and efficient memory access. The resulting weak-scaling parallel efficiency was 0.93 on 131,072 Intel Xeon Phi cores for a 56.6 million atom (or 169 million valence-electron) system, whereas the various code transformations achieved 5-fold speedup. The optimized simulation engine allowed us for the first time to establish a significant effect of substrate on the dynamics of layered material upon electronic excitation.

Algebraic BLASification↗

Final report for project "Effects of Low-Dose Irradiation on NFkB Signaling Networks and Mitochondria"

Low dose ionizing radiation effects are difficult to study in human population because of the numerous confounding factors such as genetic and lifestyle differences. Research in mammalian model systems and in vitro is generally used in order to overcome this difficulty. In this program project three projects have joined together to investigate effects of low doses of ionizing radiation. These are doses at and below 10 cGy of low linear energy transfer ionizing radiation such as X-ray and gamma rays. This project was focused on cellular signaling associated with nuclear factor kappa B (NFkB) and mitochondria - subcellular organelles critical for cell aging and aging-like changes induced by ionizing radiation. In addition to cells in culture this project utilized animal tissues accumulated in a radiation biology tissue archive housed at Northwestern University (http://janus.northwestern.edu/janus2/index.php). Major trust of Project 1 was to gather all of the DoE sponsored irradiated animal (mouse, rat and dog) data and tissues under one roof and investigate mitochondrial DNA changes and micro RNA changes in these samples. Through comparison of different samples we were trying to delineate mitochondrial DNA quantity alterations and micro RNA expression differences associated with different doses and dose rates of radiation. Historic animal irradiation experiments sponsored by DoE were done in several national laboratories and universities between 1950’s and 1990’s; while these experiments were closed data and tissues were released to Project 1. Project 2 used cells in culture to investigate effects that low doses or radiation have on NFκB and its target genes manganese superoxide dismutase (MnSOD) and genes involved in cell cycle: Cyclins (B1 and D1) and cyclin dependent kinases (CDKs). Project 3 used cells in culture such as “normal” human cells (breast epithelial cell line MCF10A cells and skin keratinocyte cells HK18) and mouse embryo fibroblast (mef) cells to focus on role of NFkB protein and several other proteins such as survivin (BIRC5) in radiation dependent regulation of tumor necrosis factor alpha (TNFα) and its downstream signaling.

59 BASIC BIOLOGICAL SCIENCES↗

Autodifferentiable Spectrum Model for High-dispersion Characterization of Exoplanets and Brown Dwarfs

We present an autodifferentiable spectral modeling of exoplanets and brown dwarfs. This model enables a fully Bayesian inference of the high-dispersion data to fit the ab initio line-by-line spectral computation to the observed spectrum by combining it with the Hamiltonian Monte Carlo in recent probabilistic programming languages. An open-source code, ExoJAX, developed in this study, was written in Python using the GPU/TPU compatible package for automatic differentiation and accelerated linear algebra, JAX. We validated the model by comparing it with existing opacity calculators and a radiative transfer code and found reasonable agreements for the output. As a demonstration, we analyzed the high-dispersion spectrum of a nearby brown dwarf, Luhman 16 A, and found that a model including water, carbon monoxide, and H 2 /He collision-induced absorption was well fitted to the observed spectrum (R = 10 5 and 2.28-2.30 μm). As a result, we found that T0 = 1295$^{-32}_{+35}$ K at 1 bar and C/O = 0.62 ± 0.03, which is slightly higher than the solar value. This work demonstrates the potential of a full Bayesian analysis of brown dwarfs and exoplanets as observed by high-dispersion spectrographs and also directly imaged exoplanets as observed by high-dispersion coronagraphy.

79 ASTRONOMY AND ASTROPHYSICS↗

Mini Micropulse Lidar measurements in vertical and scanning modes

The Atmospheric Radiation Measurement (ARM) program operates ten Sigma Space (currently Droplet Measurement Technologies/DMT) micropulse lidar systems (MPL-4B-IDS/POL-FS series), which detect the backscattered light in two orthogonal linear polarization channels allowing to distinguish between spherical (e.g. water) and non-spherical (e.g. ice) scattering particles. The ARM MPLs have been providing valuable measurements to the aerosol and cloud research community for well over a decade. DMT’s Mini-Micropulse lidar (MiniMPL) is a compact version of the standard MPL. It reduces the power-aperture product to minimize cost, size, weight, power requirements and has all the electronics integrated with optics in a single box. Although as a result, it has a lower detection range than the MPL, limiting the measurements to the troposphere, its performance is promised to match that of the standard MPL within the troposphere. The MiniMPL weighs 13 kg, and the complete system, consisting of an optical transceiver and a laptop running the data acquisition and post-processing software, fits in a storm case, allowing its transport on domestic or international flights. This can be especially valuable for short field campaigns or Intensive Operational Periods, where time is of the essence when replacing a faulty instrument. In addition, the scanning polarization lidar capability (MiniMPL-SCAN option) could be of great interest for satisfying ARM measurement needs for certain research topics related to clouds and precipitation. To evaluate its full potential in comparison with co-located remote sensing instruments including the ARM MPL-4B-IDS/POL-FS at SGP, a miniMPL was hosted at the ARM Southern Great Plains (SGP) mega-site in 2020 for approximately 3 months. During this time the miniMPL was tested in both vertical sampling and scanning modes.

54 ENVIRONMENTAL SCIENCES↗

The Beam Dynamics Updates of the Fermilab PIP-II 800 MeV Superconducting LINAC

The Proton Improvement Plan (PIP) -II is a high inten-sity proton facility being developed to support a neutrino program over the next two decades at Fermilab. At its core is the design and construction of a Continuous Wave (CW) compatible superconducting radio frequency (SRF) linear accelerator that would accelerate an average beam current of 2 mA up to 800 MeV. This paper presents recent updates in the beam dynamics leading to a reliable and robust linac design and simplifying the cryomodule assembly.

43 PARTICLE ACCELERATORS↗

Comparison of Approach-to-Critical Results in Current and Pulse Mode for Systems with High Starter Neutron Rates

Reactors and critical assemblies use a variety of detection systems to monitor the neutron population. The count rate is proportional to the neutron flux present at the location of the detector. When such systems are placed external to an assembly, it is often assumed that the relative leakage multiplication will be proportional to the detector count rate (assuming that the source term, system geometry, and detector placement have not changed). Such systems are often used in an approach-to-critical during reactor startup to ensure that the critical configuration is well predicted. Various types of detectors have been used during an approach-to-critical. These include 3 He, BF 3 , ion chambers, fission chambers, and fission foils. Any of these types of systems (or others) should work well when adequate counting statistics are available. These detector systems can be operated in either pulse or current mode. The National Criticality Experiments Research Center (NCERC) has two detection systems that are commonly used in critical assembly operations. The start-up (referred to as "SU" in this work) system is made up of 3 He proportional counters in pulse mode and the linear counter system (referred to as "LC" in this work) consists of compensated ion-chambers in current mode. Typically the SU system is used for approach-to-critical operations and the LC system is only used at/above delayed critical ( k eff = 1). This work investigates the use of the LC system for an approach-to-critical. It has been long hypothesized that such an approach would be feasible for systems with high starter neutron rates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

R-matrix Resolved Resonance Region Evaluation of 140,142 Ce

Oak Ridge National Laboratory completed the resolved resonance region (RRR) evaluation of the two most abundant cerium isotopes, 140 Ce (88.45%) and 142 Ce (11.11%), as requested by the US Nuclear Criticality Safety Program. These evaluations are based on recent high-resolution transmission and capture measurements performed on nat Ce and highly enriched 142 Ce samples at the JRC-Geel Linear Accelerator facility, as well as measured thermal constants available from the EXFOR database. Starting from the resonance parameters of the ENDF/B-VIII.0 library followed by a preliminary R-matrix analysis, an updated set of resonance parameters and corresponding covariance information were derived by fitting these measured data using the Reich–Moore approximation of the R -matrix theory, as implemented in the SAMMY code system. The 140 Ce RRR upper energy limit was kept at 200 keV, whereas the 142 Ce resonance region was extended from 13 to 26 keV. Updated statistical properties were obtained for the new evaluations and compared to those derived from the ENDF/B-VIII.0 nuclear data library. The new evaluation work improved some of the discrepancies found in previous work, such as the capture resonance integral and stellar Maxwellian-averaged cross sections. These integral quantities were mainly derived from the fit of the latest measured data, especially the neutron capture yield data for 142 Ce isotope.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Strategies for Constructing and Operating DNA Origami Linear Actuators

Abstract Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom‐up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one‐ and two‐pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single‐stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.

77 NANOSCIENCE AND NANOTECHNOLOGY↗