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DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗

DOE OSTI2019

Evaluation of Acoustic Channel Capacity for Complex Piping Topology

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

Final Report for Transmission of Information by Acoustic Communication along Metal Pathways in Nuclear Facilities

Transmission of information using elastic waves on existing metallic pipes provides an alternative communication option for a nuclear facility. The advantages of this approach consist of transmitting information through barriers, such as the containment building wall. A viable candidate for acoustic communication channel is a chemical volume control system (CVCS) stainless steel pipe, which penetrates through the containment building wall. A laboratory bench-scale system consisting of a nuclear grade CVCS-like pipe and ultrasonic transducers was assembled for a preliminary communication system analysis. Because of low bandwidth and spectral dispersion of ultrasonic transducers, on off keying (OOK) protocol was chosen for data communication. Operation of the acoustic communication during normal and post-accident conditions involves data transmission on the CVCS pipe, which according to literature guidelines, will be at 50°C and 150°C, respectively. Preliminary communication system development was performed using paintbrush PZT transducers capable of continuous operation at temperatures up to 80°C. Next, high-temperature LiNbO 3 acoustic transducers, originally developed for flow metering applications of EBRII reactor at Argonne, were utilized to develop a high-temperature acoustic communication system. A Gaussian pulse shape filter was introduced to suppress ringing and thus reduce inter-symbol interference. This resulted in enhancement of data transmission bitrate. Heating tapes, temperature controllers, and thermal insulation were installed on the laboratory pipe to study acoustic communication at elevated temperature. This included development of custom insertion heating elements for controlling temperature at pipe ends. Demonstrations of communication at high temperature included transmission of images and text files. Main achievements thus far include demonstration of transmission of 90KB image at the bitrate of 10Kbps with bit error rate smaller than 10 -3 across the pipe heated to 50°C and 150°C. Final phase of project development involved investigating strategies for deployment of the ultrasonic communication system in a representative environment. Mechanisms Engineering Test Loop (METL) facility at ANL was chosen as a viable candidate for communication system demonstration. Analysis of piping manifolds at METL has shown that in a typical scenario, ultrasonic signals have to be transmitted over straight and bent piping sections. This report describes preliminary studies on transmission of information with ultrasonic shear waves across bent piping sections. A test article consisting of a stainless steel pipe bent at 90° was developed for laboratory analysis of ultrasonic signal transmission. The bent piping test article developed by welding two straight pipes to an elbow. For consistency, the diameter and wall thickness of the bent pipe is the same as that of the straight pipe utilized in prior studies. COMSOL computer simulations were performed to study ultrasonic refracted shear wave coupling and transmission across bent piping. Preliminary evaluations of ultrasonic shear wave transmission were conducted with piezoelectric (PZT) and LiNbO 3 transducers, with the signals recorded with previously developed LabView interface. Preliminary results have shown significant dispersion of transmitted signals, most likely due to reflections and scattering by piping welds. Signal distortion compensation algorithm based on time reversal modulation (TRM) was initially investigated for transmission through solids, and demonstrated for signals transmitted over the bent pipe. Using TRM, it was shown that communication bitrates of 100Kbps were achievable, in principle.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface and command-line tool for high-dimensional mass spectrometry data analysis workflows, offering ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation: algorithm implementations utilize all dimensions simultaneously to (i) offer greater separation between features, improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS data, demonstrating the advantages of a multidimensional approach in each data processing step.

Colby, Sean M↗

NASA NTRS1973

Integrated Digital Flight Control System for the Space Shuttle Orbiter

The objectives of the integrated digital flight control system (DFCS) is to provide rotational and translational control of the space shuttle orbiter in all phases of flight: from launch ascent through orbit to entry and touchdown, and during powered horizontal flights. The program provides a versatile control system structure while maintaining uniform communications with other programs, sensors, and control effectors by using an executive routine/functional subroutine format. The program reads all external variables at a single point, copies them into its dedicated storage, and then calls the required subroutines in the proper sequence. As a result, the flight control program is largely independent of other programs in the computer complex and is equally insensitive to characteristics of the processor configuration. The integrated structure is described of the control system and the DFCS executive routine which embodies that structure. The input and output, including jet selection are included. Specific estimation and control algorithm are shown for the various mission phases: cruise (including horizontal powered flight), entry, on-orbit, and boost. Attitude maneuver routines that interface with the DFCS are included.

Source record↗

NASA NTRS1972

Correlation signatures of wet soils and snows

Interpretation, analysis, and development of algorithms have provided the necessary computational programming tools for soil data processing, data handling and analysis. Algorithms that have been developed thus far, are adequate and have been proven successful for several preliminary and fundamental applications such as software interfacing capabilities, probability distributions, grey level print plotting, contour plotting, isometric data displays, joint probability distributions, boundary mapping, channel registration and ground scene classification. A description of an Earth Resources Flight Data Processor, (ERFDP), which handles and processes earth resources data under a users control is provided.

Phillips, M. R.↗

NASA NTRS1985

Convection During Unidirectional Solidification

The fluid flow and solute segregation which occur during directional solidification, including effects of gravity and microgravity were studied. The nature of the fluid flow, its effects on the shape of the crystal-metal interface and the resulting distribution of solutes are examined. During solidification of a binary alloy at constant velocity vertically upwards, thermosolutal convection occurs if the solute rejection or preferential incorporation at the crystal-melt interface decreases the density of the melt. Numerical calculations of the solute, temperature, and flow fields are carried out by using previously developed algorithms for Schmidt numbers Sc = 1, 10, 81. The time periodic flow, which occurs over a narrow range of parameters, is investigated.

Coriell, S. R.↗

NASA NTRS1993

Stochastic damage evolution in textile laminates

A probabilistic model utilizing random material characteristics to predict damage evolution in textile laminates is presented. Model is based on a division of each ply into two sublaminas consisting of cells. The probability of cell failure is calculated using stochastic function theory and maximal strain failure criterion. Three modes of failure, i.e. fiber breakage, matrix failure in transverse direction, as well as matrix or interface shear cracking, are taken into account. Computed failure probabilities are utilized in reducing cell stiffness based on the mesovolume concept. A numerical algorithm is developed predicting the damage evolution and deformation history of textile laminates. Effect of scatter of fiber orientation on cell properties is discussed. Weave influence on damage accumulation is illustrated with the help of an example of a Kevlar/epoxy laminate.

Dzenis, Yuris A.↗

NASA NTRS2008

Virtual Shaker Testing: Simulation Technology Improves Vibration Test Performance

In the field of vibration testing, the interaction between the structure being tested and the instrumentation hardware used to perform the test is a critical issue. This is particularly true when testing massive structures (e.g. satellites), because due to physical design and manufacturing limits, the dynamics of the testing facility often couples with the test specimen one in the frequency range of interest. A further issue in this field is the standard use of a closed loop real-time vibration control scheme, which could potentially shift poles and change damping of the aforementioned coupled system. Virtual shaker testing is a novel approach to deal with these issues. It means performing a simulation which closely represents the real vibration test on the specific facility by taking into account all parameters which might impact the dynamic behavior of the specimen. In this paper, such a virtual shaker testing approach is developed. It consists of the following components: (1) Either a physical-based or an equation-based coupled electro-mechanical lumped parameter shaker model is created. The model parameters are obtained from manufacturer's specifications or by carrying out some dedicated experiments; (2) Existing real-time vibration control algorithm are ported to the virtual simulation environment; and (3) A structural model of the test object is created and after defining proper interface conditions structural modes are computed by means of the well-established Craig-Bampton CMS technique. At this stage, a virtual shaker test has been run, by coupling the three described models (shaker, control loop, structure) in a co-simulation routine. Numerical results have eventually been correlated with experimental ones in order to assess the robustness of the proposed methodology.

Ricci, Stefano↗

NASA NTRS2009

Thermal Transport Model for Heat Sink Design

A document discusses the development of a finite element model for describing thermal transport through microcalorimeter arrays in order to assist in heat-sinking design. A fabricated multi-absorber transition edge sensor (PoST) was designed in order to reduce device wiring density by a factor of four. The finite element model consists of breaking the microcalorimeter array into separate elements, including the transition edge sensor (TES) and the silicon substrate on which the sensor is deposited. Each element is then broken up into subelements, whose surface area subtends 10 10 microns. The heat capacity per unit temperature, thermal conductance, and thermal diffusivity of each subelement are the model inputs, as are the temperatures of each subelement. Numerical integration using the Finite in Time Centered in Space algorithm of the thermal diffusion equation is then performed in order to obtain a temporal evolution of the subelement temperature. Thermal transport across interfaces is modeled using a thermal boundary resistance obtained using the acoustic mismatch model. The document concludes with a discussion of the PoST fabrication. PoSTs are novel because they enable incident x-ray position sensitivity with good energy resolution and low wiring density.

Chervenak, James A.↗

NASA NTRS2010

SensorWeb 3G: Extending On-Orbit Sensor Capabilities to Enable Near Realtime User Configurability

This research effort prototypes an implementation of a standard interface, Web Coverage Processing Service (WCPS), which is an Open Geospatial Consortium(OGC) standard, to enable users to define, test, upload and execute algorithms for on-orbit sensor systems. The user is able to customize on-orbit data products that result from raw data streaming from an instrument. This extends the SensorWeb 2.0 concept that was developed under a previous Advanced Information System Technology (AIST) effort in which web services wrap sensors and a standardized Extensible Markup Language (XML) based scripting workflow language orchestrates processing steps across multiple domains. SensorWeb 3G extends the concept by providing the user controls into the flight software modules associated with on-orbit sensor and thus provides a degree of flexibility which does not presently exist. The successful demonstrations to date will be presented, which includes a realistic HyspIRI decadal mission testbed. Furthermore, benchmarks that were run will also be presented along with future demonstration and benchmark tests planned. Finally, we conclude with implications for the future and how this concept dovetails into efforts to develop "cloud computing" methods and standards.

Mandl, Daniel↗

NASA NTRS2010

Real-Time Feature Tracking Using Homography

This software finds feature point correspondences in sequences of images. It is designed for feature matching in aerial imagery. Feature matching is a fundamental step in a number of important image processing operations: calibrating the cameras in a camera array, stabilizing images in aerial movies, geo-registration of images, and generating high-fidelity surface maps from aerial movies. The method uses a Shi-Tomasi corner detector and normalized cross-correlation. This process is likely to result in the production of some mismatches. The feature set is cleaned up using the assumption that there is a large planar patch visible in both images. At high altitude, this assumption is often reasonable. A mathematical transformation, called an homography, is developed that allows us to predict the position in image 2 of any point on the plane in image 1. Any feature pair that is inconsistent with the homography is thrown out. The output of the process is a set of feature pairs, and the homography. The algorithms in this innovation are well known, but the new implementation improves the process in several ways. It runs in real-time at 2 Hz on 64-megapixel imagery. The new Shi-Tomasi corner detector tries to produce the requested number of features by automatically adjusting the minimum distance between found features. The homography-finding code now uses an implementation of the RANSAC algorithm that adjusts the number of iterations automatically to achieve a pre-set probability of missing a set of inliers. The new interface allows the caller to pass in a set of predetermined points in one of the images. This allows the ability to track the same set of points through multiple frames.

Clouse, Daniel S.↗

NASA NTRS2010

The Kepler Science Operations Center Pipeline Framework Extensions

The Kepler Science Operations Center (SOC) is responsible for several aspects of the Kepler Mission, including managing targets, generating on-board data compression tables, monitoring photometer health and status, processing the science data, and exporting the pipeline products to the mission archive. We describe how the generic pipeline framework software developed for Kepler is extended to achieve these goals, including pipeline configurations for processing science data and other support roles, and custom unit of work generators that control how the Kepler data are partitioned and distributed across the computing cluster. We describe the interface between the Java software that manages the retrieval and storage of the data for a given unit of work and the MATLAB algorithms that process these data. The data for each unit of work are packaged into a single file that contains everything needed by the science algorithms, allowing these files to be used to debug and evolve the algorithms offline.

Klaus, Todd C.↗

NASA NTRS2012

Linked-List-Based Multibody Dynamics (MBDyn) Engine

This new release of MBDyn is a software engine that calculates the dynamics states of kinematic, rigid, or flexible multibody systems. An MBDyn multibody system may consist of multiple groups of articulated chains, trees, or closed-loop topologies. Transient topologies are handled through conservation of energy and momentum. The solution for rigid-body systems is exact, and several configurable levels of nonlinear term fidelity are available for flexible dynamics systems. The algorithms have been optimized for efficiency and can be used for both non-real-time (NRT) and real-time (RT) simulations. Interfaces are currently compatible with NASA's Trick Simulation Environment. This new release represents a significant advance in capability and ease of use. The two most significant new additions are an application programming interface (API) that clarifies and simplifies use of MBDyn, and a link-list infrastructure that allows a single MBDyn instance to propagate an arbitrary number of interacting groups of multibody top ologies. MBDyn calculates state and state derivative vectors for integration using an external integration routine. A Trickcompatible interface is provided for initialization, data logging, integration, and input/output.

MacLean, John↗

DOE OSTI2025

Optimizing inference of segmentation on high-resolution images in MLExchange

MLExchange is a machine learning (ML) operations platform providing web user-interfaces (UIs) for data visualization and analysis pipelines at synchrotron facilities. Among these UIs is the segmentation app which helps synchrotron users utilize ML algorithms to automatically segment high-resolution scientific images with minimal manual annotation effort. In this work, we share code optimizations that significantly speed up the segmentation inference workflow of large data in short time. By optimizing the sequence of CPU-GPU data transfers and introducing CPU parallelization to key operations, we improve the per-device, per-image frame computational efficiency and observe close to 3×$$\times$$ speedup over the original segmentation inference workflow run time when utilizing a single GPU. Further adaptations enabling multi-GPU inference yield more than 40×$$\times$$ speedup with 100 GPUs compared to the optimized single GPU inference workflow. This acceleration of the segmentation inference workflow will provide MLExchange users with easy access to segmentation results with little wait time.

Lu, Shizhao↗

DOE OSTI2024

Hy-DAT: A Tool to Address Hydropower Modeling Gaps Using Interdependency, Efficiency Curves, and Unit Dispatch Models

As the power system continues to be flooded with intermittent resources, it becomes more important to accurately assess the role of hydro and its impact on the power grid. While hydropower generation has been studied for decades, dependency of power generation on water availability and constraints in hydro operation are not well represented in power system models used in the planning and operation of large-scale interconnection studies. There are still multiple modeling gaps that need to be addressed; if not, they can lead to inaccurate operation and planning reliability studies, and consequently to unintentional load shedding or even blackouts. As a result, it is very important thathydropower is represented correctly in both steady-state and dynamic power system studies. In this paper, we discuss the development and use of the Hydrological Dispatch and Analysis Tool (Hy-DAT) as an interactive graphical user interface (GUI), that uses a novel methodology to address the hydropower modeling gaps like water availability and inter-dependency using a database, and algorithms, to generate accurate representative models for power system simulation.

Wang, Dewei↗

DOE OSTI2021

FTK: A Simplicial Spacetime Meshing Framework for Robust and Scalable Feature Tracking

In this work, we present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

ACCERT

The main function of ACCERT (The Algorithm for the Capital Cost Estimation of Reactor Technologies) is to provide an item-by-item estimate of the cost of a facility, at present a nuclear reactor complex, primarily nuclear power stations. The core of ACCERT is the large number of algorithms that have been developed and will continue to be developed. ACCERT is also a general methodology for identifying and organizing the individual items that are estimated using the ACCERT algorithms. ACCERT also summarize status and results; to save results and pull information from previous analyses; and to provide an interactive dynamic graphical user interface for a wide range of functions and visualizations.

Zhou, Jia [Argonne National Laboratory (ANL), Argo↗