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At least 865 records · Page 48

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DOE OSTI2017

A Method to Alleviate the Long History Problem Encountered in Monte Carlo Simulations via Weight Window Variance Reduction

When the weight window is implemented in large and complex models, streaming path and deep penetration could lead to a long history problem that takes a disproportionate amount of time for the accomplishment of Monte Carlo simulations and exerts a detrimental effect on the efficiency of parallel computing. An approach set the limitation of weight window splitting was proposed for the alleviation of long history problem. Tests were conducted on a streaming dog-leg geometry model and a 3D model of the Chinese Fusion Engineering Testing Reactor. The results show that a suitable parameter in the alleviation method could optimize both the performance of variance reduction and the efficiency of parallel calculation, which makes long history problem tractable.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

An active learning high-throughput microstructure calibration framework for solving inverse structure–process problems in materials informatics

Determining a process–structure–property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process–property linkage by bypassing the materials structure, or in the context of structure–property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process–structure linkage, which has a great implication in reverse engineering. In this paper, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization to exploit high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A microfluidic spore chamber for long-term imaging of single-spore hyphal development.

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, and stress-associated phenomena such as microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research.

Antifungal screening↗

DOE OSTI2017

A fast platform for simulating semi-flexible fiber suspensions applied to cell mechanics

We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid–structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler–Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber–fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a cloud of semi-flexible fibers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Nitrogen-seeded divertor detachment in TCV L-mode plasmas

Most of the detachment experiments done to date on the tokamak à configuration variable (TCV), both in standard and alternative divertor geometries, focused on L-mode integrated core density ramps. In view of extending these studies to high-power, high-confinement regimes, where impurity seeding will be necessary for detachment, the properties of nitrogen seeded L-mode detachment in TCV are assessed here with the extensive set of edge and divertor diagnostics and similarities and differences with integrated core density ($\langle n_e \rangle$) ramp detachment experiments are elucidated. It is found that in high current, reversed field plasmas, detachment at the outer target is achieved with N 2 -seeding and density ramps, with target heat flux reductions of up to 90%, while the inner target only detaches with seeding. The Scrape-Off Layer radiation fraction reaches values of 60%–80% and in all situations, a stable radiator can form around the X-point. In this work, the most striking difference between seeding and density ramp is the behavior of the upstream quantities. During the $\langle n_e \rangle$-ramp, a broadening of the upstream density profile (density ‘shoulder’) occurs, concurrent with the outer target ion flux roll-over, while no such behavior occurs during nitrogen seeded detachment. Separatrix density, electron temperature and pressure also evolve strongly with increasing density, and are largely unaffected by the injection of nitrogen. Comparison of upstream and target pressures reveals that, in all cases, the outer target ion flux reduction coincides with the development of a parallel gradient of the total pressure. Common to all cases is also a reduction of energy confinement time with detachment, although this effect is weak for seeding at relatively high density. Studying the impact of the ∇B-drift direction in both nitrogen seeding and core density ramps reveals that drifts mainly affect the behavior at the inner strike point, highlighting the need to include them in edge transport simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Linac Coherent Light Source data analysis using psana

Psana ( Photon Science Analysis ) is a software package that is used to analyze data produced by the Linac Coherent Light Source X-ray free-electron laser at the SLAC National Accelerator Laboratory. The project began in 2011, is written primarily in C++ with some Python, and provides user interfaces in both C++ and Python. Most users use the Python interface. The same code can be run in real time while data are being taken as well as offline, executing on many nodes/cores using MPI for parallelization. It is publicly available and installable on the RHEL5/6/7 operating systems.

Damiani, D.↗

DOE OSTI2019

Fast and Scalable Implementations of Influence Maximization Algorithms

The Influence Maximization problem has been extensively studied in the past decade because of its practical applications in finding the key influencers in social networks. Due to the hardness of the underlying problem, existing algorithms have tried to trade off practical efficiency with approximation guarantees. However, even such approximate solutions take several hours of compute time on modest sized real world inputs. On the other hand, there is a lack of effective parallel and distributed algorithms to solve this problem. In this paper, we present efficient parallel algorithms for multithreaded and distributed systems to solve the influence maximization with approximation guarantee. Our algorithms extend state-of-the-art sequential approach based on computing reverse reachability sets. We present a detailed experimental evaluation, and analyze their performance and their sensitivity to input parameters, using real world inputs. Our experimental results demonstrate significant speedup on parallel architectures. We further show a speedup of up to 586X relative to the state-of-the-art sequential baseline using 1024 nodes of a supercomputer at far greater accuracy and twice the seed set size. To the best of our knowledge, this is the first effort in parallelizing the influence maximization operation at scale.

Minutoli, Marco↗

DOE OSTI2019

Extreme-Scale Stochastic Particle Tracing for Uncertain Unsteady Flow Visualization and Analysis

We present an efficient and scalable solution to estimate uncertain transport behaviors-stochastic flow maps (SFMs)-for visualizing and analyzing uncertain unsteady flows. Computing flow maps from uncertain flow fields is extremely expensive because it requires many Monte Carlo runs to trace densely seeded particles in the flow. We reduce the computational cost by decoupling the time dependencies in SFMs so that we can process shorter sub time intervals independently and then compose them together for longer time periods. Adaptive refinement is also used to reduce the number of runs for each location. We parallelize over tasks-packets of particles in our design-to achieve high efficiency in MPI/thread hybrid programming. Such a task model also enables CPU/GPU coprocessing. We show the scalability on two supercomputers, Mira (up to 256K Blue Gene/Q cores) and Titan (up to 128K Opteron cores and 8K GPUs), that can trace billions of particles in seconds.

CPU-GPU hybrid parallelism↗

DOE OSTI2018

A Study of the Crystal Structure of Co{sub 40}Fe{sub 40}B{sub 20} Epitaxial Films on a Bi{sub 2}Te{sub 3} Topological Insulator

Laser molecular-beam epitaxy has been used to form Co{sub 40}Fe{sub 40}B{sub 20} layers on Bi{sub 2}Te{sub 3} topological insulator substrates, and their growth conditions have been studied. The possibility of growing epitaxial ferromagnetic layers on the surface of a topological insulator is demonstrated for the first time. The CoFeB layers have a body-centered cubic crystal structure with the (111) crystal plane parallel to the (0001) plane of Bi{sub 2}Te{sub 3}. 3D mapping in the reciprocal space of high-energy electron-diffraction patterns made it possible to determine the epitaxial relationships between the film and the substrate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

miniWeather

The code “miniWeather” solves the 2-D Euler equations with a Finite-Volume method on a regular Cartesian grid with Runge-Kutta time stepping, 4th-order hypervisocisty, and 4th-order spatial accuracy. The code is primarily a parallel programming training mini application in Fortran, C, and C++ with MPI, OpenMP, OpenMP offload, OpenACC, and C++ portability approaches. It can also serve as a mini application for acceptance testing for new machines and compilers for both functionality and performance.

Norman, MatthewR↗

DOE OSTI2023

LCIO

Performance of file systems shift during their life cycles. Evaluating this performance change over time is not trivial. Complexity arises in the interplay between external (i.e. application I/O workloads) and internal (i.e. the filesystem state) factors. Many benchmarks can test how a filesystem performs at the current snapshot state, but to observe the change over time necessitates that the filesystem state mutate (age) between benchmark runs. For a large-scale HPC parallel filesystem, the sheer scale and amount of interacting components during I/O operations magnify these challenges. LCIO addresses the question - how will the filesystem perform at different stages of its life cycle? LCIO is a synthetic benchmark, which provides the file system aging process to increase the amount of information that existing benchmarks like IOR and MDTest yield, as well as provide additional points of data that will be useful to system architects and engineers.

Bachstein, Matthew↗

DOE OSTI2025

Dataset for "A Microfluidic Spore Chamber for Long-Term Imaging of Single-Spore Hyphal Development"

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device’s capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research. Videos of the observed phenomena are included in this data set.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Time-Lapse Integration at FWU: Fluids, Rock Physics, Numerical Model Integration, and Field Data Comparison

We present the current status of time-lapse seismic integration at the Farnsworth (FWU) CO2 WAG (water-alternating-gas) EOR (Enhanced Oil Recovery) project at Ochiltree County, northwest Texas. As a potential carbon sequestration mechanism, CO2 WAG projects will be subject to some degree of monitoring and verification, either as a regulatory requirement or to qualify for economic incentives. In order to evaluate the viability of time-lapse seismic as a monitoring method the Southwest Partnership (SWP) has conducted time-lapse seismic monitoring at FWU using the 3D Vertical Seismic Profiling (VSP) method. The efficacy of seismic time-lapse depends on a number of key factors, which vary widely from one application to another. Most important among these are the thermophysical properties of the original fluid in place and the displacing fluid, followed by the petrophysical properties of the rock matrix, which together determine the effective elastic properties of the rock fluid system. We present systematic analysis of fluid thermodynamics and resulting thermophysical properties, petrophysics and rock frame elastic properties, and elastic property modeling through fluid substitution using data collected at FWU. These analyses will be framed in realistic scenarios presented by the FWU CO2 WAG development. The resulting fluid/rock physics models will be applied to output from the calibrated FWU compositional reservoir simulation model to forward model the time-lapse seismic response. Modeled results are compared with field time-lapse seismic measurements and strategies for numerical model feedback/update are discussed. While mechanical effects are neglected in the work presented here, complementary parallel studies are underway in which laboratory measurements are introduced to introduce stress dependence of matrix elastic moduli.

4D↗

DOE OSTI2018

NSTX-U advances in real-time deterministic PCIe-based internode communication

Distributing control mechanisms across modern commercial off the shelf (COTS) GNU/Linux systems often introduces difficult to mitigate non-deterministic behavior. Existing methods to address this problem involve non-real-time technologies such as Remote Direct Memory Access (RDMA) over Infiniband or custom Ethernet solutions, such as RDMA over Converged Ethernet (RoCE) or userspace Ethernet drivers, that trade determinism for ease of use or lower cost. The National Spherical Torus Experiment Upgrade (NSTX-U) is pursuing a new design that allows direct communication between heterogeneous systems with scalable, microsecond latency with 1 μs of jitter on that latency, outside of the constant transmission delay at the physical layer. The future design of the NSTX-U Real-time Communication System will utilize direct PCIe-to-PCIe communication with kernel support tuned for low overhead, allowing two (or more, through a switch) real-time (RT) systems to communicate and share resources as one larger entity. As a result, this greatly increases the processing capability of the primary Plasma Control System (PCS), turning previously insurmountable computational challenges into a more manageable divide and conquer parallel task.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

Deformation and failure in extreme regimes by high-energy pulsed lasers: A review

The use of high-power pulsed lasers to probe the response of materials at pressures of hundreds of GPa up to several TPa, time durations of nanoseconds, and strain rates of 10 6 –10 1° s -1 is revealing novel mechanisms of plastic deformation, phase transformations, and even amorphization. This unique experimental tool, aided by advanced diagnostics, analysis, and characterization, allows us to explore these new regimes that simulate those encountered in the interiors of planets. Fundamental Materials Science questions such as dislocation velocity regimes, the transition between thermally-activated and phonon drag regimes, the slip-twinning transition, the ultimate tensile strength of metals, the dislocation mechanisms of void growth are being answered through this powerful tool. In parallel with experiments, molecular dynamics simulations provide modeling and visualization at comparable strain rates (10 8 –10 10 s -1 ) and time durations (hundreds of picoseconds). Finally, this powerful synergy is illustrated in our past and current work, using representative face-centered cubic (fcc) copper, body-centered cubic (bcc) tantalum and diamond cubic silicon as model structures.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Photophysical Properties and Electronic Structure of Porphyrins Bearing Zero to Four meso -Phenyl Substituents: New Insights into Seemingly Well Understood Tetrapyrroles

Six free base porphyrins bearing 0–4 meso substituents have been examined by steady-state and time-resolved absorption and fluorescence spectroscopy in both toluene and N,N-dimethylformamide (DMF). The lifetime of the lowest singlet excited state (S 1 ) decreases with an increase in the number of meso-phenyl groups; the values in toluene are H 2 P-0 (15.5 ns) > H 2 P-1 (14.9 ns) > H 2 P-2c (14.4 ns) > H 2 P-2t (13.8 ns) ~ H 2 P-3 (13.8 ns) > H 2 P-4 (12.8 ns), where “H 2 P” refers to the core free base porphyrin, the numerical suffix indicates the number of meso-phenyl groups, and “c” and “t” refer to cis and trans, respectively. The opposite trend is found for the fluorescence quantum yield; the values in toluene are H 2 P-0 (0.049) < H 2 P-1 (0.063) ~ H 2 P-2c (0.063) < H 2 P-2t (0.071) < H 2 P-3 (0.073) < H 2 P-4 (0.090). Similar trends occur in DMF. All radiative and non-radiative (internal conversion and intersystem crossing) rate constants for S 1 decay increase with increasing number of meso-phenyl groups. The increase in the rate constant for fluorescence parallels an increase in oscillator strength of the S o → S 1 absorption manifold. Here, the trend is reproduced by time-dependent density functional theory calculations. The calculations within the context of the four-orbital model reveal that the enhanced S o → S 1 radiative probabilities derive from a preferential effect of the meso-phenyl groups to raise the energy of the highest occupied molecular orbital, which underpins a parallel bathochromic shift in the S o → S 1 absorption wavelength. Polarizations of the S 1 and S 2 excited states with respect to molecular structural features (e.g., the central proton axis) are analyzed in the context of historical conventions for porphyrins versus chlorins and bacteriochlorins, where some ambiguity exists, including for porphine, one of the simplest tetrapyrroles. Collectively, the study affords fundamental insights into the photophysical properties and electronic structure of meso-phenylporphyrins that should aid their continued widespread use as benchmarks for tetrapyrrole-based architectures in chemical, solar-energy and life-sciences research.

14 SOLAR ENERGY↗

DOE OSTI2020

GridOPTICS/GridPACK

GridPACK is a software framework consisting of a set of modules designed to simplify the development of programs that model the power grid and run on parallel, high performance computing platforms. It also contains several fully developed applications, including powerflow, dynamic simulation, state estimation, Kalman filter analysis (dynamic state estimation), contingency analysis and real time path rating. These applications can be used either standalone or as components in more complicated workflows that combine several different types of application together. The framework modules are available as a combination of libraries and software templates and consist of components for setting up and distributing power grid networks, support for modeling the behavior of individual buses and branches in the network, converting the network models to the corresponding algebraic equations, and parallel routines for manipulating and solving large algebraic systems. The framework also contains a module for distributing tasks evenly amongst computing resources, even if individual tasks vary widely in their execution times. Additional modules support input and output, basic statistical analysis of contingency based calculations, distributed data structures, as well as basic profiling and error management.

Palmer, Bruce↗