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At least 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method

Ion mobility-mass spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, native-like or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a “trajectory method” (TM) based CCS calculator, named “Collidoscope,” which utilizes parallel processing and optimized trajectory sampling, and implements both He and N{sub 2} as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared with those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using X-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Crosslinking and Gelation of Polymer Brushes and Free Polymer Chains in a Confined Space during Controlled Radical Polymerization-A Computer Simulation Study

The confinement effect on crosslinking and gelation during controlled/living copolymerization of a monovinyl and a divinyl monomer was studied by Monte Carlo computer simulation using the dynamic lattice liquid method. The simulated reactions took place in plane-parallel slits of various widths for various grafting densities (GDs) and various initial initiator/crosslinker ratios ([X] 0 /[Ini] 0 ). Monomers and crosslinkers were initially randomly distributed in the slit, but initiators were either anchored to one solid plane (polymer brushes) or randomly distributed (free chains). For brushes, the gel point (GP) depended on GD and [X] 0 /[Ini] 0 . The higher these parameters, the lower was the gel point. The gel point was also affected by the slit width. For free, nongrafted chains, the dependence of GP on slit width was negligible. For brushes, a nonuniform density of crosslinks was found, the highest density was close to the wall. This asymmetry was high at the gel point and decreased at higher conversions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Abstract While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer ( Pty chographic G PU(multipl e )-based r econstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Transport induced by ion cyclotron range of frequencies waves

The Vlasov equation, which includes the effect of the ion cyclotron range of frequencies (ICRF) waves, can be written as the Fokker-Planck equation which describes the quasilinear transport in phase space by using the Lie-transform method. The radial transport fluxes of particle, energy and parallel momentum driven by ICRF waves in the slab geometry have been derived. The results show that the ICRF-induced radial redistributions of particle, energy and parallel momentum are driven by the inhomogeneity in energy of the equilibrium distribution function, and related to the correlation between the excursion in the real space and the excursion in energy. For the case with strong asymmetry of k{sub y} spectrum, the ICRF-induced radial transport driven by the energy inhomogeneity dominates the ICRF-induced radial transport driven by the spatial inhomogeneity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Magnetometry of single ferromagnetic nanoparticles using magneto-optical indicator films with spatial amplification

We present a magneto-optical technique to spatially amplify and image fringe fields from single ferromagnetic nanorods. The fringe fields nucleate magnetic domains in a low-coercivity, perpendicularly magnetized indicator film, which are expanded by an applied out-of-plane field from the nanoscale to the microscale for measurement with polar Kerr microscopy. The nucleation location and therefore magnetic orientation of the sample nanorod are detected as spatially dependent field biases in locally measured hysteresis loops of the indicator film. We first discuss our method to fabricate the high-sensitivity indicator film with low energy argon ion irradiation. We then present a map of the amplified signal produced from a single nanorod as measured by the indicator film and compare it with a simultaneously obtained, unamplified fringe field map. The comparison demonstrates the advantage of the amplification mechanism and the capability of the technique to be performed with single-spot magneto-optical Kerr effect magnetometers. Our signal-to-noise ratio determines a minimum measureable particle diameter of tens of nanometers for typical transition metals. We finally use our method to obtain hysteresis loops from multiple nanorods in parallel. Our technique is unperturbed by applied in-plane fields for magnetic manipulation of nanoparticles, is robust against many common noise sources, and is applicable in a variety of test environments. We conclude with a discussion of the future optimization and application of our indicator film technique.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Complex-energy approach to sum rules within nuclear density functional theory

The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish an efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study

Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, we report the results were found to be sensitive to the particular choice of interatomic potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Vehicle track segmentation using higher order random fields

Here, we present an approach to segment vehicle tracks in coherent change detection images, a product of combining two synthetic aperture radar images taken at different times. The approach uses multiscale higher order random field models to capture track statistics, such as curvatures and their parallel nature, that are not currently utilized in existing methods. These statistics are encoded as 3-by-3 patterns at different scales. The model can complete disconnected tracks often caused by sensor noise and various environmental effects. Coupling the model with a simple classifier, our approach is effective at segmenting salient tracks. We improve the F-measure on a standard vehicle track data set to 0.963, up from 0.897 obtained by the current state-of-the-art method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Observation of super-resolution in digital breast tomosynthesis

Purpose: Digital breast tomosynthesis (DBT) is a 3D x-ray imaging modality in which tomographic sections of the breast are generated from a limited range of tube angles. Because oblique x-ray incidence shifts the image of an object in subpixel detector element increments with each increasing projection angle, it is demonstrated that DBT is capable of super-resolution (i.e., subpixel resolution). Methods: By convention, DBT reconstructions are performed on planes parallel to the breast support at various depths of the breast volume. In order for resolution in each reconstructed slice to be comparable to the detector, the pixel size should match that of the detector elements; hence, the highest frequency that can be resolved in the plane of reconstruction is the alias frequency of the detector. This study considers reconstruction grids with much smaller pixelation to visualize higher frequencies. For analytical proof of super-resolution, a theoretical framework is developed in which the reconstruction of a high frequency sinusoidal input is calculated using both simple backprojection (SBP) and filtered backprojection. To study the frequency spectrum of the reconstruction, its Fourier transform is also determined. The experimental feasibility of super-resolution was investigated by acquiring images of a bar pattern phantom with frequencies higher than the detector alias frequency. Results: Using analytical modeling, it is shown that the central projection cannot resolve frequencies exceeding the detector alias frequency. The Fourier transform of the central projection is maximized at a lower frequency than the input as evidence of aliasing. By contrast, SBP reconstruction can resolve the input, and its Fourier transform is correctly maximized at the input frequency. Incorporating filters into the reconstruction smoothens pixelation artifacts in the spatial domain and reduces spectral leakage in the Fourier domain. It is also demonstrated that the existence of super-resolution is dependent on position in the reconstruction and on the directionality of the input frequency. Consistent with the analytical results, experimental reconstructions of bar patterns showed visibility of frequencies greater than the detector alias frequency. Super-resolution was present at positions predicted from analytical modeling. Conclusions: This work demonstrates the existence of super-resolution in DBT. Super-resolution has the potential to impact the visualization of fine structural details in the breast, such as microcalcifications and other subtle signs of cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Spatial and rotational quality assurance of 6DOF patient tracking systems

Purpose: External tracking systems used for patient positioning and motion monitoring during radiotherapy are now capable of detecting both translations and rotations. In this work, the authors develop a novel technique to evaluate the 6 degree of freedom 6(DOF) (translations and rotations) performance of external motion tracking systems. The authors apply this methodology to an infrared marker tracking system and two 3D optical surface mapping systems in a common tumor 6DOF workspace. Methods: An in-house designed and built 6DOF parallel kinematics robotic motion phantom was used to perform motions with sub-millimeter and subdegree accuracy in a 6DOF workspace. An infrared marker tracking system was first used to validate a calibration algorithm which associates the motion phantom coordinate frame to the camera frame. The 6DOF positions of the mobile robotic system in this space were then tracked and recorded independently by an optical surface tracking system after a cranial phantom was rigidly fixed to the moveable platform of the robotic stage. The calibration methodology was first employed, followed by a comprehensive 6DOF trajectory evaluation, which spanned a full range of positions and orientations in a 20 × 20 × 16 mm and 5° × 5° × 5° workspace. The intended input motions were compared to the calibrated 6DOF measured points. Results: The technique found the accuracy of the infrared (IR) marker tracking system to have maximal root-mean square error (RMSE) values of 0.18, 0.25, 0.07 mm, 0.05°, 0.05°, and 0.09° in left–right (LR), superior–inferior (SI), anterior–posterior (AP), pitch, roll, and yaw, respectively, comparing the intended 6DOF position and the measured position by the IR camera. Similarly, the 6DOF RSME discrepancy for the HD optical surface tracker yielded maximal values of 0.46, 0.60, 0.54 mm, 0.06°, 0.11°, and 0.08° in LR, SI, AP, pitch, roll, and yaw, respectively, over the same 6DOF evaluative workspace. An earlier generation 3D optical surface tracking unit was observed to have worse tracking capabilities than both the IR camera unit and the newer 3D surface tracking system with maximal RMSE of 0.69, 0.74, 0.47 mm, 0.28°, 0.19°, and 0.18°, in LR, SI, AP, pitch, roll, and yaw, respectively, in the same 6DOF evaluation space. Conclusions: The proposed technique was found to be effective at evaluating the performance of 6DOF patient tracking systems. All observed optical tracking systems were found to exhibit tracking capabilities at the sub-millimeter and subdegree level within a 6DOF workspace.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-AB-202-11: Spatial and Rotational Quality Assurance of 6DOF Patient Tracking Systems

Purpose: External tracking systems used for patient positioning and motion monitoring during radiotherapy are now capable of detecting both translations and rotations (6DOF). In this work, we develop a novel technique to evaluate the 6DOF performance of external motion tracking systems. We apply this methodology to an infrared (IR) marker tracking system and two 3D optical surface mapping systems in a common tumor 6DOF workspace. Methods: An in-house designed and built 6DOF parallel kinematics robotic motion phantom was used to follow input trajectories with sub-millimeter and sub-degree accuracy. The 6DOF positions of the robotic system were then tracked and recorded independently by three optical camera systems. A calibration methodology which associates the motion phantom and camera coordinate frames was first employed, followed by a comprehensive 6DOF trajectory evaluation, which spanned a full range of positions and orientations in a 20×20×16 mm and 5×5×5 degree workspace. The intended input motions were compared to the calibrated 6DOF measured points. Results: The technique found the accuracy of the IR marker tracking system to have maximal root mean square error (RMSE) values of 0.25 mm translationally and 0.09 degrees rotationally, in any one axis, comparing intended 6DOF positions to positions measured by the IR camera. The 6DOF RSME discrepancy for the first 3D optical surface tracking unit yielded maximal values of 0.60 mm and 0.11 degrees over the same 6DOF volume. An earlier generation 3D optical surface tracker was observed to have worse tracking capabilities than both the IR camera unit and the newer 3D surface tracking system with maximal RMSE of 0.74 mm and 0.28 degrees within the same 6DOF evaluation space. Conclusion: The proposed technique was effective at evaluating the performance of 6DOF patient tracking systems. All systems examined exhibited tracking capabilities at the sub-millimeter and sub-degree level within a 6DOF workspace.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A New Class of AMG Interpolation Methods Based on Matrix-Matrix Multiplications

A new class of distance-two interpolation methods for algebraic multigrid (AMG) that can be formulated in terms of sparse matrix-matrix multiplications is presented and analyzed. Compared with similar distance-two prolongation operators, the proposed algorithms exhibit improved efficiency and portability to various computing platforms, since they allow one to easily exploit existing high-performance sparse matrix kernels. The new interpolation methods have been implemented in hypre, a widely used parallel multigrid solver library. With the proposed interpolations, the overall time of hypre's BoomerAMG setup can be considerably reduced, while sustaining equivalent, sometimes improved, convergence rates. Numerical results for a variety of test problems on parallel machines are presented that support the superiority of the proposed interpolation operators over the existing ones in hypre.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family of molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Exa-Graph/vite

MPI+OpenMP implementation of Louvain method for Graph Community Detection, with a number of parallel heuristics/approximate computing techniques Also called "CuVite"

Ghosh, Sayan↗
DOE OSTI2026

DIVA/DeviceEditor v6.1.2

DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.

Plahar, Hector [Lawrence Berkeley National Laborat↗
DOE OSTI2022

Scalable Second Order Optimization for Machine Learning

Many machine learning (ML) training tasks are essentially optimization processes that would at first glance appear eminently parallelizable and scalable. However, effective acceleration of these tasks with scalable parallel hardware has proven to be elusive. While standard methods for machine learning, e.g., stochastic gradient descent (SGD) for DNNs, tend to be resource efficient, they appear to be fundamentally sequential in nature.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Machine Committee Framework for Power Grid Disturbances Analysis Using Synchrophasors Data

Events detection is a key challenge in power grid frequency disturbances analysis. Accurate detection of events is crucial for situational awareness of the power system. In this paper, we study the problem of events detection in power grid frequency disturbance analysis using synchrophasors data streams. Current events detection approaches for power grid rely on individual detection algorithm. This study integrates some of the existing detection algorithms using the concept of machine committee to develop improved detection approaches for grid disturbance analysis. Specifically, we propose two algorithms—an Event Detection Machine Committee (EDMC) algorithm and a Change-Point Detection Machine Committee (CPDMC) algorithm. Both algorithms use parallel architecture to fuse detection knowledge of its individual methods to arrive at an overall output. The EDMC algorithm combines five individual event detection methods, while the CPDMC algorithm combines two change-point detection methods. Each method performs the detection task separately. The overall output of each algorithm is then computed using a voting strategy. The proposed algorithms are evaluated using three case studies of actual power grid disturbances. Compared with the individual results of the various detection methods, we found that the EDMC algorithm is a better fit for analyzing synchrophasors data; it improves the detection accuracy; and it is suitable for practical scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Fast and sensitive measurements of sub-3 nm particles using Condensation Particle Counters For Atmospheric Rapid Measurements (CPC FARM)

New particle formation (NPF) is the atmospheric process whereby gas molecules react and nucleate to form detectable particles. NPF has a strong impact on Earth's radiative balance as it produces roughly half of global cloud condensation nuclei. However, the time resolution and sensitivity of current instrumentation are inadequate in measuring the size distribution of sub-3 nm particles, the particles critical for understanding NPF. Here we present the Condensation Particle Counters For Atmospheric Rapid Measurements (CPC FARM), a method to measure the concentrations of freshly nucleated particles. The CPC FARM consists of five CPCs operating in parallel, each configured to operate at different detectable particle sizes between 1–3 nm. This study explores two methods to calculate the size distribution from the differential measurements across the CPC channels. The performance of both inversion methods was tested against the size distribution measured by a pair of stepping particle mobility sizers (SMPSs) during an ambient air sampling study in Pittsburgh, PA. Observational results indicate that the CPC FARM is more accurate with higher time resolution and sensitivity in the sub-3 nm range compared to the SMPS.

Cheng, Darren [Carnegie Mellon Univ., Pittsburgh, ↗