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NASA NTRS1990

Implicit solution of three-dimensional internal turbulent flows

The scalar form of the approximate factorization method was used to develop a new code for the solution of three-dimensional internal laminar and turbulent compressible flows. The Navier-Stokes equations in their Reynolds-averaged form are iterated in time until a steady solution is reached. Evidence is given to the implicit and explicit artificial damping schemes that proved to be particularly efficient in speeding up convergence and enhancing the algorithm robustness. A conservative treatment of these terms at domain boundaries is proposed in order to avoid undesired mass and/or momentum artificial fluxes. Turbulence effects are accounted for by the zero-equation Baldwin-Lomax turbulence model and the q-omega two-equation model. For the first, an investigation on the model behavior in case of multiple boundaries is performed. The flow in a developing S-duct is then solved in the laminar regime at Reynolds number (Re) 790 and in the turbulent regime at Re=40,000 using the Baldwin-Lomax model . The Stanitz elbow is then solved using an inviscid version of the same code at M(sub inlet)=0.4. Grid dependence and convergence rate are investigated showing that for this solver the implicit damping scheme may play a critical role for convergence characteristics. The same flow at Re=2.5x10(exp 6) is solved with the Baldwin-Lomax and the q-omega models. Both approaches showed satisfactory agreement with experiments, although the q-omega model is slightly more accurate.

Michelassi, V.↗

NASA NTRS2023

Modeling and Simulation for Exercise Vibration Isolation and Stabilization System Design

The microgravity environment that crew members experience on orbit presents a well-known health challenge, particularly when it comes to loss of muscle and bone mass. To counteract these negative effects, exercise countermeasures play a critical role in the daily routine of the crew on the International Space Station (ISS). To help inform requirements for upcoming exploration missions such as the Gateway Program, a new device, called the European Enhanced Exploration Exercise Device (E4D), is being built by the European Space Agency through their contractor, the Danish Aerospace Company. The E4D is being demonstrated on the ISS and is unique from other current exercise devices in that it provides four separate modalities in a single device: resistive, cycle ergometry, seated aerobic rowing, and rope pulling. To support the integration of E4D on ISS, a passive Vibration Isolation and Stabilization (VIS) system was required by NASA, and this responsibility was given to the Johnson Space Center. This paper describes the end-to-end process of modeling, simulation, and analysis used to inform the mechanical design of the VIS system. The process begins with the collection of representative exerciser motion capture (MoCap) through ground-based testing with the developmental E4D in both the Prototype Immersive Technology (PIT) Laboratory and the Active Response Gravity Offload System (ARGOS) facility at the Johnson Space Center. These collected MoCap data are processed through human biomechanics modeling to create forcing functions as input to a multibody dynamics simulation of the combined E4D/VIS system, with numerous resulting outputs. These outputs include microgravity accelerations, overall system displacements, internal and transmitted loads, as well as collisions. Microgravity accelerations are compared for compliance against ISS requirements while displacements are used for sway space determinations on the design and volumetric constraints within the targeted module. Internal loads are supplied to the supporting stress analysis teams and external loads for structural loads and dynamics teams, both at NASA and ESA. Finally, contact and clearance analysis is performed using the simulation to eliminate potential design issues. To ensure that the elements of the multibody simulation were verified and validated, correlation against multiple VIS related ground hardware testbeds was performed and characterized. In addition to the isolation part of the VIS problem, stabilization is also key to the integrated performance and evaluation. Due to the difficulty in defining ISS requirements in this area, the stability of the exerciser was inspected via analysis. Loss of balance was defined analytically as occurring when the resultant force vector acting on the exerciser lies outside the base of support of the feet. Both the VIS and E4D teams have recently gone through their Critical Design Reviews (CDRs) and the iterative model-based approach has been integral to inform mechanical design, particularly in the case of the VIS. This same end-to-end approach is now being applied for the Gateway Program, where an Exploration Exercise Device (EED) derived from the E4D and notional VIS for the device are under concept development.

Countermeasures↗

NASA NTRS2014

Deducing Electronic Unit Internal Response During a Vibration Test Using a Lumped Parameter Modeling Approach

During random vibration testing of electronic boxes there is often a desire to know the dynamic response of certain internal printed wiring boards (PWBs) for the purpose of monitoring the response of sensitive hardware or for post-test forensic analysis in support of anomaly investigation. Due to restrictions on internally mounted accelerometers for most flight hardware there is usually no means to empirically observe the internal dynamics of the unit, so one must resort to crude and highly uncertain approximations. One common practice is to apply Miles Equation, which does not account for the coupled response of the board in the chassis, resulting in significant over- or under-prediction. This paper explores the application of simple multiple-degree-of-freedom lumped parameter modeling to predict the coupled random vibration response of the PWBs in their fundamental modes of vibration. A simple tool using this approach could be used during or following a random vibration test to interpret vibration test data from a single external chassis measurement to deduce internal board dynamics by means of a rapid correlation analysis. Such a tool might also be useful in early design stages as a supplemental analysis to a more detailed finite element analysis to quickly prototype and analyze the dynamics of various design iterations. After developing the theoretical basis, a lumped parameter modeling approach is applied to an electronic unit for which both external and internal test vibration response measurements are available for direct comparison. Reasonable correlation of the results demonstrates the potential viability of such an approach. Further development of the preliminary approach presented in this paper will involve correlation with detailed finite element models and additional relevant test data.

random vibration response↗

DOE OSTI2020

Retrieval of energy spectra for all flavours of neutrinos from core-collapse supernova with multiple detectors

ABSTRACT We present a new method by which to retrieve energy spectrum for all falvours of neutrinos from core-collapse supernova (CCSN). In the retrieval process, we do not assume any analytic formulas to express the energy spectrum of neutrinos but rather take a direct way of spectrum reconstruction from the observed data; the singular value decomposition algorithm with a newly developed adaptive energy-gridding technique is adopted. We employ three independent reaction channels having different flavour sensitivity to neutrinos. Two reaction channels, inverse beta decay on proton and elastic scattering on electrons, from a water Cherenkov detector such as Super-Kamiokande (SK) and Hyper-Kamiokande (HK), and a charged current reaction channel with Argon from the Deep Underground Neutrino Experiment (DUNE) are adopted. Given neutrino oscillation models, we iteratively search the neutrino energy spectra at the CCSN source until they provide the consistent event counts in the three reaction channels. We test the capability of our method by demonstrating the spectrum retrieval to a theoretical neutrino data computed by our recent three-dimensional CCSN simulation. Although the energy spectrum with either electron-type or electron-type antineutrinos at the CCSN source has relatively large error compared to that of other species, the joint analysis with HK + DUNE or SK + DUNE will provide precise energy spectrum of all flavours of neutrinos at the source. Finally, we discuss perspectives for improvements of our method by using neutrino data of other detectors.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Weighted relaxation for multigrid reduction in time

Current trends in computer architectures now mean that faster computation speed must come primarily from increased concurrency, not faster clock speeds, which are stagnating. Thus, this situation creates bottlenecks for serial algorithms, including the well-known bottleneck for sequential time-integration, where each individual time-value (i.e., time-step) is computed sequentially. One approach to alleviate this and achieve parallelism in time is with multigrid. Here, in this work, we consider multigrid-reduction-in-time (MGRIT), a multilevel method applied to the time dimension that computes multiple time-steps in parallel. Like all multigrid methods, MGRIT relies on the complementary relationship between relaxation on a fine-grid and a correction from the coarse grid to solve the problem. All current MGRIT implementations are based on unweighted-Jacobi relaxation; here we introduce the concept of weighted relaxation to MGRIT. We derive new convergence bounds for weighted relaxation, and use this analysis to guide the selection of relaxation weights. Numerical results then demonstrate that by choosing appropriate non-unitary relaxation weights, one can achieve faster convergence rates and lower iteration counts for MGRIT when compared with unweighted relaxation. In most cases, weighted relaxation yields a 10%–20% saving in iterations, which is significant when using large high-performance computers. For A-stable integration schemes, results also illustrate that under-relaxation can restore convergence in some cases where unweighted relaxation is not convergent.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2015

Space Biotech: Hindsight, Insight, Foresight

Over the past forty years, microgravity has inspired and enabled applications in a wide range of sectors including medicine, materials, computers, communications, and national defense. Trends show that demand for high-tech solutions is increasing in these sectors, solutions that require higher resolution, greater precision, novel materials, innovative processes, and more sophisticated tools. These are areas where microgravity can offer unique capabilities for innovation. The Emerging Space Office (ESO) has engaged in multiple studies over the past year that have found that microgravity RD is one of the most promising technology areas for contributing to economic growth and to NASAs mission. The focus of these studies was on terrestrial markets rather than NASA applications, applied research rather than basic research, and commercial rather than academic investigators. There have been more success stories than are generally appreciated and there are significant areas of promising future potential. Many of the problems that have limited commercial microgravity development in the past are being solved. Microgravity research and development (RD) requires iteration and learning, as rapidly as possible. New technologies enable high throughput and rapid data collection in increasingly small payloads. The International Space Station is in orbit and provides a laboratory that is available 247 at least until 2024. Frequent flights by commercial space providers to and from the ISS now enable the fast learning cycles needed by high-tech industries. Launch costs are decreasing and the ability to return payloads to Earth is increasing. New commercial space laboratories, such as those being developed by SpaceX and Bigelow Aerospace, are in the final stages of development and testing. This ecosystem for microgravity RD has never been available before. These are game-changer conditions for attracting high-tech industries to space for terrestrial, as well as NASA, applications. However, few know that these capabilities are available or how to use them. In aggregate, the potential value for new applications from microgravity RD over the next ten years could add billions of dollars per year in terrestrial applications to the future economy, create new jobs, and generate a wide range of public benefits in medical advances, while broadening the customer base for the emerging space industry.

biotech↗

DOE OSTI2022

A Modern Ethernet Data Acquisition Architecture for Fermilab Beam Instrumentation

The Fermilab Accelerator Division, Instrumentation Department is adopting an open-source framework to replace our embedded VME-based data acquisition systems. Utilizing an iterative methodology, we first moved to embedded Linux, removing the need for VxWorks. Next, we adopted Ethernet on each data acquisition module eliminating the need for the VME backplane in addition to communicating with a rack mount server. Development of DDCP (Distributed Data Communications Protocol), allowed for an abstraction between the firmware and software layers. Each data acquisition module was adapted to read out using 1 GbE and aggregated at a switch which up linked to a 10 GbE network. Current development includes scaling the system to aggregate more modules, to increase bandwidth to support multiple systems and to adopt MicroTCA as a crate technology. The architecture was utilized on various beamlines around the Fermilab complex including PIP2IT, FAST/IOTA and the Muon Delivery Ring. In summary, we were able to develop a data acquisition framework which incrementally replaces VxWorks & VME hardware as well as increases our total bandwidth to 10 Gbit/s using off the shelf Ethernet technology.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Shutdown dose rate analysis with the Shift Monte Carlo radiation transport code and modular verification workflow

Calculation of the shutdown dose rate is crucial for safe fusion reactor operations. The Rigorous-two-step (R2S) method is a method that requires connected neutron transport, activation, and gamma transport. Shift has integrated variance reduction with a deterministic solver Denovo, supports multiple geometry formats, and is scalable. These features make it an attractive transport solver choice for an R2S workflow. An R2S workflow for the Shift Monte Carlo code is developed and compared to the existing Oak Ridge National Laboratory Shutdown Dose Rate Code Suite (ORCS) workflow. Also, a Python framework for integrating two R2S workflows is developed to mix and match each step in the R2S workflow for improved collaboration and verification experience. In this study, results show that the Shift-Denovo R2S workflow and the ORCS workflow calculate the shutdown dose rate of the ITER Shutdown Dose Rate benchmark problem with an average relative error of 2.285%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2024

Automation of the ICME Workflow Incorporating Material Digital Twins at Different Length Scales Within a Robust Information Management System

Recent successes in Integrated Computational Materials Engineering (ICME) have demonstrated the potential in designing ‘fit-for-purpose’ materials for a given application in a cost and time efficient manner. However, the material design process must contain a level of judicious automation in the material decision process; that is implementing some optimization algorithms to truly enable the benefits of ICME, particularly when considering materials at multiple length and time scales. Furthermore, the ability to effectively store developed material models, experimental data used for validation, and link models at multiple length and time scales must be implemented to ensure traceability across the material design process, such that the data gathered can be leveraged towards efficient material design. To enable such an optimization scheme a robust framework must exist: (1) that can capture changes made at a given length scale, (2) automatically propagate changes upstream to the highest scale, and (3) evaluate the material’s performance at the structural level. In this work, a developed framework for tracking material changes, automatically running the necessary simulations to determine the properties at the next highest scale, and saving each iteration of the design process to maintain the application’s digital thread is presented for polymer matrix composites (PMCs). The Automated Information Management Across Organizations and Scales (AIMAOS) program offers users an interactive graphical user interface (GUI) for defining constituent materials, building lamina and laminates, and applying effective laminate properties to finite element and composite optimization third party software. At each length scale, the necessary input files are automatically written, and subsequent analysis tools are called to solve for effective properties at the next scale, which are then read by the AIMAOS tool and displayed to the user. As changes are made to the material at lower length scales, information is automatically propagated upstream to higher length scales, and changes made are automatically tracked and versioned to maintain traceability during the design process. The AIMAOS tools serves as the first step in enabling optimized design of composites from the nano to the macroscale for a given application.

Brandon L Hearley↗

DOE OSTI2022

Impact of cyber attacks on distributed compressive sensing based state estimation in power distribution grids

Modern power distribution grids suffer from multiple vulnerabilities due to the tight integration between the physical system and the cyber infrastructure. Sophisticated and malicious cyber attacks continue to adversely impact the grid operation leading to performance degradation, service interruption, and grid failure. State estimation plays an essential role in grid monitoring and advancing cyber-attack situational awareness. In this regard, this paper first proposes a distributed compressive sensing (CS) state estimation approach for an unobservable distribution grid. Further, the proposed distributed CS approach divides the distribution grid into sub-areas to perform local state estimation. Then an alternating direction method of multipliers (ADMM) based iterative information exchange among neighboring areas is employed to complete the estimation process. In this estimation process, the impact of loss of measurement data, false data injection (FDI), replay, and neighborhood cyber-attacks is analyzed. Extensive simulations are performed on the IEEE 37-bus and IEEE 123-bus standard networks to demonstrate the algorithm’s robustness to the aforementioned cyber-attacks. A quantitative analysis of computational complexity and simulation time of the distributed CS based approach is also presented.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

A Customizable Metric to Provide a Comprehensive Picture of the Mobility Potential of a Location

Accessibility in a geo-spatial context refers to the ease of reaching a variety of opportunities from a given location. Accessibility theories (and resulting metrics) have traditionally focused on quantifying access to specific opportunities (such as jobs), or focused on specific modes (such as car, bike, etc.). Such approaches often fall short of providing a comprehensive picture of the true accessibility potential of a location as a combination of multiple modes to multiple types of destinations. Addressing this drawback, a novel metric labeled the ‘Mobility Energy Productivity (MEP) Metric’ was developed at the National Renewable Energy Laboratory to quantify the mobility potential of a location to connect people to goods, services, and employment using a variety of modes, while accounting for time, energy, and affordability. The MEP metric has been integrated with advance travel behavior models to compute the changes in mobility potential for various future scenarios, such as introduction of automated vehicles, and/or electric vehicles—but does so at the aggregate, or average-citizen level. The MEP in its initial iteration is not customized to the particular socio-economic contingents, or even to an individual whose modal availability or pattern of trip making may substantially differ from the average. Addressing this gap, this research effort extends the MEP framework from a static state to a more tailored and dynamic state, one in which an individual, or group can customize the metric for their unique characteristics, such as modes, activity patterns, and time-of-day preferences. The extended MEP metric framework can now be integrated to assess the customized mobility energy productivity of an individual.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

DOE OSTI2021

Calibration of a versatile multi-energy soft x-ray diagnostic for WEST long pulse plasmas

A compact multi-energy soft x-ray diagnostic is being installed on the W Environment in Steady-state Tokamak (WEST), which was designed and built to test ITER-like tungsten plasma facing components in a long pulse (~1000 s) scenario. The diagnostic consists of a pinhole camera fielded with the PILATUS3 photon-counting Si-based detector (≲100 kpixel). The detector has sensitivity in the range 1.6–30 keV and enables energy discrimination, providing a higher energy resolution than conventional systems with metal foils and diodes with adequate space and time resolution (≲1 cm and 2 ms). The lower-absorption cut-off energy is set independently on each one of the ~100 kpixels, providing a unique opportunity to measure simultaneously the plasma emissivity in multiple energy ranges and deduce a variety of plasma parameters (e.g., T e , n Z , and ΔZ eff ). The energy dependence of each pixel is calibrated here over the range 3–22 keV. The detector is exposed to a variety of monochromatic sources—fluorescence emission from metallic targets—and for each pixel, the lower energy threshold is scanned to calibrate the energy dependence. The data are fit to a responsivity curve (“S-curve”) that determines the mapping between the possible detector settings and the energy response for each pixel. Here, the calibration is performed for three energy ranges: low (2.3–6 keV), medium (4.5–13.5 keV), and high (5.4–21 keV). We determine the achievable energy resolutions for the low, medium, and high energy ranges as 330 eV, 640 eV, and 950 eV, respectively. The main limitation for the energy resolution is found to be the finite width of the S-curve.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

High-Fidelity Accelerated Design of High-performance Electrochemical Systems

Large-scale electrification is vital to addressing the climate crisis, but several scientific and technological challenges remain to fully electrify both the chemical industry and transportation. In both of these areas, new electrochemical materials will be critical, but their development currently relies heavily on human-time-intensive experimental trial and error and computationally expensive first-principles, meso-scale and continuum simulations. To accelerate this process, our team has developed the AutoMat platform. AutoMat can accelerate development of new electrochemical materials along two avenues: first, automated input generation and management of simulations at multiple lengthscales as well as “handoff” of outputs from one lengthscale as inputs to the next; and second, replacement of the most computationally intensive simulation processes with machine-learned surrogate models. The crux of our team’s effort was not “reinventing the wheel” by developing entirely new techniques, but rather building a “superhighway” that allows existing state-of-the-art techniques to run faster and more smoothly than before. AutoMat can utilize tools spanning from first-principles quantum chemistry computations to automated robotic experimentation, and is driven by design space search techniques to reduce the number of iterations through the full simulation loop by rapidly targeting promising regions of design spaces such as single-atom alloy catalysts or blends of liquid electrolytes.

25 ENERGY STORAGE↗

DOE OSTI2024

Active Learning for Metamaterial Optimization on HPC and QC Integrated Systems

Active learning algorithms, integrating machine learning, quantum computing and optics simulation in an iterative loop, offer a promising approach to optimizing metamaterials. However, these algorithms can face difficulties in optimizing highly complex structures due to computational limitations. High-performance computing (HPC) and quantum computing (QC) integrated systems can address these issues by enabling parallel computing. In this study, we develop an active learning algorithm working on HPC-QC integrated systems. We evaluate the performance of optimization processes within active learning (i.e., training a machine learning model, problem-solving with quantum computing, and evaluating optical properties through wave-optics simulation) for highly complex metamaterial cases. Our results showcase that utilizing multiple cores on the integrated system can significantly reduce computational time, thereby enhancing the efficiency of optimization processes. Therefore, we expect that leveraging HPC-QC integrated systems helps effectively tackle large-scale optimization challenges in general.

Kim, Seongmin↗

NASA NTRS1984

Two-dimensional computer simulation of EMVJ and grating solar cells under AMO illumination

A computer program, SCAP2D (Solar Cell Analysis Program in 2-Dimensions), is used to evaluate the Etched Multiple Vertical Junction (EMVJ) and grating solar cells. The aim is to demonstrate how SCAP2D can be used to evaluate cell designs. The cell designs studied are by no means optimal designs. The SCAP2D program solves the three coupled, nonlinear partial differential equations, Poisson's Equation and the hole and electron continuity equations, simultaneously in two-dimensions using finite differences to discretize the equations and Newton's Method to linearize them. The variables solved for are the electrostatic potential and the hole and electron concentrations. Each linear system of equations is solved directly by Gaussian Elimination. Convergence of the Newton Iteration is assumed when the largest correction to the electrostatic potential or hole or electron quasi-potential is less than some predetermined error. A typical problem involves 2000 nodes with a Jacobi matrix of order 6000 and a bandwidth of 243.

Gray, J. L.↗

NASA NTRS1999

Performance and Application of Parallel OVERFLOW Codes on Distributed and Shared Memory Platforms

The presentation discusses recent studies on the performance of the two parallel versions of the aerodynamics CFD code, OVERFLOW_MPI and _MLP. Developed at NASA Ames, the serial version, OVERFLOW, is a multidimensional Navier-Stokes flow solver based on overset (Chimera) grid technology. The code has recently been parallelized in two ways. One is based on the explicit message-passing interface (MPI) across processors and uses the _MPI communication package. This approach is primarily suited for distributed memory systems and workstation clusters. The second, termed the multi-level parallel (MLP) method, is simple and uses shared memory for all communications. The _MLP code is suitable on distributed-shared memory systems. For both methods, the message passing takes place across the processors or processes at the advancement of each time step. This procedure is, in effect, the Chimera boundary conditions update, which is done in an explicit "Jacobi" style. In contrast, the update in the serial code is done in more of the "Gauss-Sidel" fashion. The programming efforts for the _MPI code is more complicated than for the _MLP code; the former requires modification of the outer and some inner shells of the serial code, whereas the latter focuses only on the outer shell of the code. The _MPI version offers a great deal of flexibility in distributing grid zones across a specified number of processors in order to achieve load balancing. The approach is capable of partitioning zones across multiple processors or sending each zone and/or cluster of several zones into a single processor. The message passing across the processors consists of Chimera boundary and/or an overlap of "halo" boundary points for each partitioned zone. The MLP version is a new coarse-grain parallel concept at the zonal and intra-zonal levels. A grouping strategy is used to distribute zones into several groups forming sub-processes which will run in parallel. The total volume of grid points in each group are approximately balanced. A proper number of threads are initially allocated to each group, and in subsequent iterations during the run-time, the number of threads are adjusted to achieve load balancing across the processes. Each process exploits the multitasking directives already established in Overflow.

Djomehri, M. Jahed↗

NASA NTRS1994

A simple suboptimal least-squares algorithm for attitude determination with multiple sensors

Three-axis attitude determination is equivalent to finding a coordinate transformation matrix which transforms a set of reference vectors fixed in inertial space to a set of measurement vectors fixed in the spacecraft. The attitude determination problem can be expressed as a constrained optimization problem. The constraint is that a coordinate transformation matrix must be proper, real, and orthogonal. A transformation matrix can be thought of as optimal in the least-squares sense if it maps the measurement vectors to the reference vectors with minimal 2-norm errors and meets the above constraint. This constrained optimization problem is known as Wahba's problem. Several algorithms which solve Wahba's problem exactly have been developed and used. These algorithms, while steadily improving, are all rather complicated. Furthermore, they involve such numerically unstable or sensitive operations as matrix determinant, matrix adjoint, and Newton-Raphson iterations. This paper describes an algorithm which minimizes Wahba's loss function, but without the constraint. When the constraint is ignored, the problem can be solved by a straightforward, numerically stable least-squares algorithm such as QR decomposition. Even though the algorithm does not explicitly take the constraint into account, it still yields a nearly orthogonal matrix for most practical cases; orthogonality only becomes corrupted when the sensor measurements are very noisy, on the same order of magnitude as the attitude rotations. The algorithm can be simplified if the attitude rotations are small enough so that the approximation sin(theta) approximately equals theta holds. We then compare the computational requirements for several well-known algorithms. For the general large-angle case, the QR least-squares algorithm is competitive with all other know algorithms and faster than most. If attitude rotations are small, the least-squares algorithm can be modified to run faster, and this modified algorithm is faster than all but a similarly specialized version of the QUEST algorithm. We also introduce a novel measurement averaging technique which reduces the n-measurement case to the two measurement case for our particular application, a star tracker and earth sensor mounted on an earth-pointed geosynchronous communications satellite. Using this technique, many n-measurement problems reduce to less than or equal to 3 measurements; this reduces the amount of required calculation without significant degradation in accuracy. Finally, we present the results of some tests which compare the least-squares algorithm with the QUEST and FOAM algorithms in the two-measurement case. For our example case, all three algorithms performed with similar accuracy.

Brozenec, Thomas F.↗

DOE OSTI2023

Pickaxe: a Python library for the prediction of novel metabolic reactions

Abstract Background Biochemical reaction prediction tools leverage enzymatic promiscuity rules to generate reaction networks containing novel compounds and reactions. The resulting reaction networks can be used for multiple applications such as designing novel biosynthetic pathways and annotating untargeted metabolomics data. It is vital for these tools to provide a robust, user-friendly method to generate networks for a given application. However, existing tools lack the flexibility to easily generate networks that are tailor-fit for a user’s application due to lack of exhaustive reaction rules, restriction to pre-computed networks, and difficulty in using the software due to lack of documentation. Results Here we present Pickaxe, an open-source, flexible software that provides a user-friendly method to generate novel reaction networks. This software iteratively applies reaction rules to a set of metabolites to generate novel reactions. Users can select rules from the prepackaged JN1224min ruleset, derived from MetaCyc, or define their own custom rules. Additionally, filters are provided which allow for the pruning of a network on-the-fly based on compound and reaction properties. The filters include chemical similarity to target molecules, metabolomics, thermodynamics, and reaction feasibility filters. Example applications are given to highlight the capabilities of Pickaxe: the expansion of common biological databases with novel reactions, the generation of industrially useful chemicals from a yeast metabolome database, and the annotation of untargeted metabolomics peaks from an E. coli dataset. Conclusion Pickaxe predicts novel metabolic reactions and compounds, which can be used for a variety of applications. This software is open-source and available as part of the MINE Database python package ( https://pypi.org/project/minedatabase/ ) or on GitHub ( https://github.com/tyo-nu/MINE-Database ). Documentation and examples can be found on Read the Docs ( https://mine-database.readthedocs.io/en/latest/ ). Through its documentation, pre-packaged features, and customizable nature, Pickaxe allows users to generate novel reaction networks tailored to their application.

59 BASIC BIOLOGICAL SCIENCES↗