Molecular Graphics: Bridging Structural Biologists and Computer Scientists
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “Computer Graphics”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Computationally efficient Bayesian estimation of graphical networks for omics data
Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.
EM algorithm↗
Adiabatic Quantum Computation Applied to Deep Learning Networks
Training deep learning networks is a difficult task due to computational complexity, and this is traditionally handled by simplifying network topology to enable parallel computation on graphical processing units (GPUs). However, the emergence of quantum devices allows reconsideration of complex topologies. We illustrate a particular network topology that can be trained to classify MNIST data (an image dataset of handwritten digits) and neutrino detection data using a restricted form of adiabatic quantum computation known as quantum annealing performed by a D-Wave processor. We provide a brief description of the hardware and how it solves Ising models, how we translate our data into the corresponding Ising models, and how we use available expanded topology options to explore potential performance improvements. Although we focus on the application of quantum annealing in this article, the work discussed here is just one of three approaches we explored as part of a larger project that considers alternative means for training deep learning networks. The other approaches involve using a high performance computing (HPC) environment to automatically find network topologies with good performance and using neuromorphic computing to find a low-power solution for training deep learning networks. Our results show that our quantum approach can find good network parameters in a reasonable time despite increased network topology complexity; that HPC can find good parameters for traditional, simplified network topologies; and that neuromorphic computers can use low power memristive hardware to represent complex topologies and parameters derived from other architecture choices.
97 MATHEMATICS AND COMPUTING↗
HELIOS-K: An ultrafast, open-source opacity calculator for radiative transfer
We present an ultrafast opacity calculator that we name HELIOS-K. It takes a line list as an input, computes the shape of each spectral line, and provides an option for grouping an enormous number of lines into a manageable number of bins. We implement a combination of Algorithm 916 and Gauss–Hermite quadrature to compute the Voigt profile, write the code in CUDA, and optimize the computation for graphics processing units (GPUs). We restate the theory of the k-distribution method and use it to reduce ∼10{sup 5}–10{sup 8} lines to ∼10–10{sup 4} wavenumber bins, which may then be used for radiative transfer, atmospheric retrieval and general circulation models. The choice of line-wing cutoff for the Voigt profile is a significant source of error and affects the value of the computed flux by ∼10%. This is an outstanding physical (rather than computational) problem, due to our incomplete knowledge of pressure broadening of spectral lines in the far line wings. We emphasize that this problem remains regardless of whether one performs line-by-line calculations or uses the k-distribution method and affects all calculations of exoplanetary atmospheres requiring the use of wavelength-dependent opacities. We elucidate the correlated-k approximation and demonstrate that it applies equally to inhomogeneous atmospheres with a single atomic/molecular species or homogeneous atmospheres with multiple species. Using a NVIDIA K20 GPU, HELIOS-K is capable of computing an opacity function with ∼10{sup 5} spectral lines in ∼1 s and is publicly available as part of the Exoclimes Simulation Platform (www.exoclime.org).
79 ASTRONOMY AND ASTROPHYSICS↗
Experiences in autotuning matrix multiplication for energy minimization on GPUs
In this study, we report extensive results and analysis of autotuning the computationally intensive graphics processing units kernel for dense matrix–matrix multiplication in double precision. In contrast to traditional autotuning and/or optimization for runtime performance only, we also take the energy efficiency into account. For kernels achieving equal performance, we show significant differences in their energy balance. We also identify the memory throughput as the most influential metric that trades off performance and energy efficiency. Finally, as a result, the performance optimal case ends up not being the most efficient kernel in overall resource use.
97 MATHEMATICS AND COMPUTING↗
Converting DYNAMO simulations to Powersim Studio simulations
DYNAMO is a computer program for building and running 'continuous' simulation models. It was developed by the Industrial Dynamics Group at the Massachusetts Institute of Technology for simulating dynamic feedback models of business, economic, and social systems. The history of the system dynamics method since 1957 includes many classic models built in DYANMO. It was not until the late 1980s that software was built to take advantage of the rise of personal computers and graphical user interfaces that DYNAMO was supplanted. There is much learning and insight to be gained from examining the DYANMO models and their accompanying research papers. We believe that it is a worthwhile exercise to convert DYNAMO models to more recent software packages. We have made an attempt to make it easier to turn these models into a more current system dynamics software language, Powersim © Studio produced by Powersim AS 2 of Bergen, Norway. This guide shows how to convert DYNAMO syntax into Studio syntax.
97 MATHEMATICS AND COMPUTING↗
A Module for Graphical Display of Model Results with the CBP Toolbox
This report describes work performed by the Savannah River National Laboratory (SRNL) in fiscal year 2014 to add enhanced graphical capabilities to display model results in the Cementitious Barriers Project (CBP) Toolbox. Because Version 2.0 of the CBP Toolbox has just been released, the graphing enhancements described in this report have not yet been integrated into a new version of the Toolbox. Instead they have been tested using a standalone GoldSim model and, while they are substantially complete, may undergo further refinement before full implementation. Nevertheless, this report is issued to document the FY14 development efforts which will provide a basis for further development of the CBP Toolbox.
97 MATHEMATICS AND COMPUTING↗
Nuclear Facility Accident (NFAC) Unit Test Report For HPAC Version 6.3
This is a unit test report for the Nuclear Facility Accident (NFAC) model for the Hazard Prediction and Assessment Capability (HPAC) version 6.3. NFAC’s responsibility as an HPAC component is three-fold. First, it must present an interactive graphical user interface (GUI) by which users can view and edit the definition of an NFAC incident. Second, for each incident defined, NFAC must interact with RTH to create activity table inputs and associate them with pseudo materials to be transported via SCIPUFF. Third, NFAC must create SCIPUFF releases with the associated pseudo materials for transport and dispersion. The goal of NFAC unit testing is to verify that the inputs it produces are correct for the source term or model definition as specified by the user via the GUI.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models
Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing (i) the KL divergence between prior and posterior and (ii) the Stein’s loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.
54 ENVIRONMENTAL SCIENCES↗
Development of Improved Graphical Displays for an Advanced Outage Control Center, Employing Human Factors Principles for Outage Schedule Management
The long-term viability of existing nuclear power plants in the United States (U.S.) is dependent upon a number of factors, including maintaining high capacity factors, maintaining nuclear safety, and reducing operating costs, particularly those associated with refueling outages. Refueling outages typically take 20-30 days, and for existing light water NPPs in the U.S., the reactor cannot be in operation during the outage. Furthermore, given that many NPPs generate between $1-1.5 million/day in revenue when in operation, there is considerable interest in shortening the length of refueling outages. Yet refueling outages are highly complex operations, involving multiple concurrent and dependent activities that are somewhat challenging to coordinate; therefore, finding ways to improve refueling outage performance, while maintaining nuclear safety has proven to be difficult. The Advanced Outage Control Center (AOCC) project is a research and development (R&D) demonstration activity under the LWRS Program. LWRS is an R&D program that works closely with industry R&D programs to establish technical foundations for the licensing and managing of long-term, safe, and economical operation of current fleet of NPPs. As such, the LWRS Advanced Outage Control Center project has the goal of improving the management of commercial NPP refueling outages. To accomplish this goal, INL is developing an advanced outage control center (OCC) that is specifically designed to maximize the usefulness of communication and collaboration technologies for outage coordination and problem resolution activities. The overall focus is on developing an AOCC with the following capabilities that enables plant and OCC staff to; Collaborate in real-time to address emergent issues; Effectively communicate outage status to all workers involved in the outage; Effectively communicate discovered conditions in the field to the OCC; Provide real-time work status; Provide automatic pending support notifications; Provide real-time requirements monitoring; Maximize their collective situational awareness to improve decision-making; and Leverage macro data to better support resource allocation. INL has partnered with several commercial NPP utilities to develop a number of advanced outage management technologies. These outage management technologies have focused on both collaborative technologies for control centers and developing mobile technologies for NPP field workers. This report describes recent efforts made in developing a suite of outage technologies to support more effective schedule management. Currently, a master outage schedule is created months in advance using the plant’s existing scheduling software (e.g., Primavera P6). Typically, during the outage, the latest version of the schedule is printed at the beginning of each shift. INL and its partners are developing technologies that will have capabilities such as Automatic Schedule Updating, Automatic Pending Support Notifications, and the ability to allocate and schedule outage support task resources on a sub-hour basis (e.g., outage Micro-Scheduling). The remaining sections of this report describe in more detail the scheduling challenges that occur during outages, how the outage scheduling technologies INL is developing helps address those challenges, and the latest developments on this task (e.g., work accomplished to date and the path forward)
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Implementation and Validation of a Generalized Actuator Disk Parameterization for Wind Turbine Simulations Within the FastEddy Model
ABSTRACT Fast and accurate large‐eddy simulation (LES) of the atmospheric boundary layer plays a crucial role in advancing wind energy research. Long‐duration wind farm studies at turbine‐resolving scales have become increasingly important to understand the intricate interactions between large wind farms and the atmospheric boundary layer. However, the prohibitive computational cost of these turbulence‐ and turbine‐resolving simulations has precluded such modeling to be exercised on a regular basis. To that end, we implement and validate the generalized actuator disk (GAD) model in the computationally efficient, graphics processing unit (GPU)–resident, LES model FastEddy. We perform single‐turbine simulations under three atmospheric stabilities (neutral, unstable, and stable) and compare them against observations from the Scaled Wind Farm Technology (SWiFT) facility and other LES codes from the recent Wakebench turbine wake model benchmark. Our idealized LES results agree well with observed wake velocity deficit and downstream recovery across stability regimes. Turbine response in terms of rotational speed, generated power, torque, and thrust coefficient are well predicted across stability regimes and are consistent with the LES results from the benchmark. The FastEddy simulations are found to be at least two orders of magnitude more efficient than the traditional CPU‐based LES models, opening the door for realistic LES simulations of full wind plants as a viable standard practice.
17 WIND ENERGY↗
Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
Burley, Stephen K. (ORCID:0000000224879713)↗
Accelerating Machine Learning Inference with GPUs in ProtoDUNE Data Processing
Abstract We study the performance of a cloud-based GPU-accelerated inference server to speed up event reconstruction in neutrino data batch jobs. Using detector data from the ProtoDUNE experiment and employing the standard DUNE grid job submission tools, we attempt to reprocess the data by running several thousand concurrent grid jobs, a rate we expect to be typical of current and future neutrino physics experiments. We process most of the dataset with the GPU version of our processing algorithm and the remainder with the CPU version for timing comparisons. We find that a 100-GPU cloud-based server is able to easily meet the processing demand, and that using the GPU version of the event processing algorithm is two times faster than processing these data with the CPU version when comparing to the newest CPUs in our sample. The amount of data transferred to the inference server during the GPU runs can overwhelm even the highest-bandwidth network switches, however, unless care is taken to observe network facility limits or otherwise distribute the jobs to multiple sites. We discuss the lessons learned from this processing campaign and several avenues for future improvements.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
A split imaging spectrometer for temporally and spatially resolved titanium absorption spectroscopy
We present a temporally and a spatially resolved spectrometer for titanium x-ray absorption spectroscopy along 2 axial symmetric lines-of-sight. Each line-of-sight of the instrument uses an elliptical crystal to acquire both the 2p and 3p Ti absorption lines on a single, time gated channel of the instrument. The 2 axial symmetric lines-of-sight allow the 2p and 3p absorption features to be measured through the same point in space using both channels of the instrument. The spatially dependent material temperature can be inferred by observing the 2p and the 3p Ti absorption features. The data are recorded on a two strip framing camera with each strip collecting data from a single line-of-sight. The design is compatible for use at both the OMEGA laser and the National Ignition Facility. The spectrometer is intended to measure the material temperature behind a Marshak wave in a radiatively driven SiO{sub 2} foam with a Ti foam tracer. In this configuration, a broad band CsI backlighter will be used for a source and the Ti absorption spectrum measured.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Numerical simulation of the dynamics of a liquid crystal in the case of plane strain using GPUs
Parallel computational algorithm is worked out for numerical implementation of two-dimensional dynamic model of a liquid crystal, which takes into account the mutual influence of three physical effects – transfer of acoustic energy due to translational motion, viscoelastic rotation of the particles under the action of tangential stresses, anisotropic thermal expansion and compression. The algorithm is based on the Godunov gap decay method, the Ivanov scheme with controlled dissipation of energy and the splitting method with respect to spatial variables. The CUDA technology for computer systems with graphic accelerators is used. Results of computations demonstrating the efficiency of proposed method and algorithm are represented.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Study of self-generated fields in strongly-shocked, low-density systems using broadband proton radiography
Here we report results from experiments on the study of field generation at the shock front in low-density gas configured in quasi-planar geometry using broad-energy proton probing. Experiments were conducted using three long pulse laser beams with a total energy of 6.4 kJ in 2 ns for shock generation and an 850 J, 10 ps short pulse laser to produce broadband protons for radiography. Observations of the deflection pattern of probe protons show the existence of self-generated electric fields at the shock front with the electric potential on the order of 300 V. Finally, analytical and particle tracking methods support this conclusion.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
An electron Bernstein wave heating scheme for the Proto-MPEX linear device
Linear plasma devices, such as the Prototype Material Plasma Exposure eXperiment (Proto-MPEX), are an economic method to study plasma-material interactions under high heat and particle fluxes. The Proto-MPEX device at Oak Ridge National Laboratory is a high-density helicon plasma generator with additional resonant electron heating to study plasma-material interactions in ITER-like conditions. Here, we present modeling results of an electron Bernstein wave (EBW) heating scheme for this device using a microwave-based system. A 28 GHz injection system is available to provide power levels up to 100 kW injected into low electron temperature and high electron density plasmas. A modified version of the GENRAY ray-tracing code, GENRAY-C, has been used to determine the EBW and electron cyclotron heating wave accessibility for these overdense plasmas. Modeling has shown that greater than 80% of mode conversion from the ordinary mode to the EBW is possible for 28 GHz injection in Proto-MPEX. Calculations show that by utilizing the effects of Doppler-shifted resonance absorption, power deposition near the core is possible. Finally, significant collisional damping, leading to edge absorption, is expected to occur for neutral pressures >1.0 mTorr; however, experiments can be designed to minimize these effects.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗