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At least 379 records · Page 21

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DOE OSTI2025

Investigating Electron Conductivity Regimes in the Bacterial Cytochrome Wire OmcS

The anaerobic bacterium Geobacter sulfurreducens produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show OmcS wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. However, the mechanism by which this heme arrangement supports long-range electronic conduction remains unknown. Structure models from cryo-electron microscopy data show these wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. Existing computational models using static heme redox potentials and coupling energies fail to explain experimental observations, predicting conductances 10,000 to 100,000 times lower than measured values. Here, we investigate how dynamic disorder affects site energies, interheme coupling, and long-range electronic conductivity within these cytochrome wires. We introduce an approach to extract charge carrier site information directly from Kohn–Sham density functional theory, without employing projector schemes, and show that site and coupling energies are highly sensitive to changes in interheme geometry and the surrounding electrostatic environment. Unlike models that incorporate dynamic disorder as a thermally averaged quantity, our quantum charge carrier model incorporates proxies for dynamic disorder through decoherence corrections, yielding predicted diffusion coefficient closer to what is expected from experiment and comparable with other organic-based electronic materials. Based on these simulations, we propose that the instantaneous fluctuations of the local electrostatic environment can transiently lift energy degeneracies and delocalize charge carriers. Furthermore, these studies reveal how incorporating dynamic fluctuations associated with the environment resolves the discrepancy between theory and experiment in microbial cytochrome wires and highlight design principles for bioinspired, heme-based conductive materials.

Bioinorganic chemistry↗

NASA NTRS1979

Trends in reliability modeling technology for fault tolerant systems

Developments in reliability modeling for large fault tolerant avionic computing systems are presented. Issues of state size and complexity, fault coverage, and practical computation are addressed. A two-fold developmental effort is described based on the structural and fault coverage modeling approaches. A technique which was successfully applied to an 865 state pure death stationary Markov model is presented. Of particular interest is a short computer program which executes very quickly to produce reliability results of a large state space model. This model also incorporates fault coverage states for processor, memory, and bus line replaceable units. A second structural reliability modeling scheme is aimed at solving nonstationary Markov models. This technique provides the tool required for studying the reliability of systems with nonconstant failure rates and includes intermittent/transient faults, electronic hardware which exhibits decreasing failure rates, and hydromechanical devices which typically have wearout failure mechanisms. Several aspects of fault coverage, including modeling and data measurement of intermittent/transient faults and latent faults, are elucidated and illustrated. The CARE II (computer-aided reliability estimation) coverage is presented and shortcomings to be eliminated are discussed.

Bavuso, S. J.↗

NASA NTRS1976

Correlation of AH-1G airframe test data with a NASTRAN mathematical model

Test data was provided for evaluating a mathematical vibration model of the Bell AH-1G helicopter airframe. The math model was developed and analyzed using the NASTRAN structural analysis computer program. Data from static and dynamic tests were used for comparison with the math model. Static tests of the fuselage and tailboom were conducted to verify the stiffness representation of the NASTRAN model. Dynamic test data were obtained from shake tests of the airframe and were used to evaluate the NASTRAN model for representing the low frequency (below 30 Hz) vibration response of the airframe.

Cronkhite, J. D.↗

NASA NTRS1983

Outer atmospheres of cool stars. XIV - A model for the chromosphere and transition region of Beta Ceti (G9.5 III)

In the present chromospheric and transition region model for Beta Ceti, which is consistent with IUE spectra of the Mg II, C II, and C IV resonance lines, the Mg II h and k lines are treated in partial redistribution and the C II and C IV lines in complete redistribution. Computed line fluxes are presented for a range of models to show the range of permitted temperature structures. A comparison of the Beta Ceti model to models previously computed in a similar way for other stars shows a trend of decreasing chromospheric pressures and increasing geometric scales as single stars evolve across the transition region boundary. The present analysis also suggests that transition region pressures drastically decrease and geometric scales rapidly increase as single giant stars evolve to the right, toward the boudnary. Beta Ceti's exceptional X-ray brightness is discussed.

Eriksson, K.↗

NASA NTRS1990

A methodology for evaluating the reliability and risk of structures under complex service environments

The theoretical basis and numerical implementation of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress; Cruse et al., 1988), a computer code for probabilistic structural analyses of aerospace components, are described, with an emphasis on the use of NESSUS for reliability and risk assessment. Topics addressed include the structure of NESSUS, the material-properties model, computational procedures, probabilistic models of fatigue-crack initiation, risk/cost evaluation, fatigue-fracture analyses, and fatigue-crack propagation. Numerical results from typical applications are presented in extensive graphs and briefly characterized; the usefulness of NESSUS predictions for establishing inspection and retirement schedules and for component certification is indicated.

Shiao, Michael C.↗

NASA NTRS1998

Algorithms for Efficient Computation of Transfer Functions for Large Order Flexible Systems

An efficient and robust computational scheme is given for the calculation of the frequency response function of a large order, flexible system implemented with a linear, time invariant control system. Advantage is taken of the highly structured sparsity of the system matrix of the plant based on a model of the structure using normal mode coordinates. The computational time per frequency point of the new computational scheme is a linear function of system size, a significant improvement over traditional, still-matrix techniques whose computational times per frequency point range from quadratic to cubic functions of system size. This permits the practical frequency domain analysis of systems of much larger order than by traditional, full-matrix techniques. Formulations are given for both open- and closed-loop systems. Numerical examples are presented showing the advantages of the present formulation over traditional approaches, both in speed and in accuracy. Using a model with 703 structural modes, the present method was up to two orders of magnitude faster than a traditional method. The present method generally showed good to excellent accuracy throughout the range of test frequencies, while traditional methods gave adequate accuracy for lower frequencies, but generally deteriorated in performance at higher frequencies with worst case errors being many orders of magnitude times the correct values.

Maghami, Peiman G.↗

NASA NTRS1997

Efficient Computation of Closed-loop Frequency Response for Large Order Flexible Systems

An efficient and robust computational scheme is given for the calculation of the frequency response function of a large order, flexible system implemented with a linear, time invariant control system. Advantage is taken of the highly structured sparsity of the system matrix of the plant based on a model of the structure using normal mode coordinates. The computational time per frequency point of the new computational scheme is a linear function of system size, a significant improvement over traditional, full-matrix techniques whose computational times per frequency point range from quadratic to cubic functions of system size. This permits the practical frequency domain analysis of systems of much larger order than by traditional, full-matrix techniques. Formulations are given for both open and closed loop loop systems. Numerical examples are presented showing the advantages of the present formulation over traditional approaches, both in speed and in accuracy. Using a model with 703 structural modes, a speed-up of almost two orders of magnitude was observed while accuracy improved by up to 5 decimal places.

Maghami, Peiman G.↗

DOE OSTI2025

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Multiscale mechanical design of the lightweight, stiff, and damage-tolerant cuttlebone: A computational study

Cuttlebone, the endoskeleton of cuttlefish, offers an intriguing biological structural model for designing low-density cellular ceramics with high stiffness and damage tolerance. Cuttlebone is highly porous (porosity ~93%) and lightweight (density less than 20% of seawater), constructed mainly by brittle aragonite (95 wt%), but capable of sustaining hydrostatic water pressures over 20 atmospheres and exhibits energy absorption capability under compression comparable to many metallic foams (~4.4 kJ/kg). Here, in this work, we computationally investigate how such remarkable mechanical efficiency is enabled by the multiscale structure of cuttlebone. Using the common cuttlefish, Sepia Officinalis, as a model system, we first conducted high-resolution synchrotron micro-computed tomography (µ-CT) and quantified the cuttlebone's multiscale geometry, including the 3D asymmetric shape of individual walls, the wall assembly patterns, and the long-range structural gradient of walls across the entire cuttlebone (ca. 38 chambers). The acquired 3D structural information enables systematic finite-element simulations, which further reveal the multiscale mechanical design of cuttlebone: at the wall level, wall asymmetry provides optimized energy absorption while maintaining high structural stiffness; at the chamber level, variation of walls (number, pattern, and waviness amplitude) contributes to progressive damage; at the entire skeletal level, the gradient of chamber heights tailors the local mechanical anisotropy of the cuttlebone for reduced stress concentration. Our results provide integrated insights into understanding the cuttlebone's multiscale mechanical design and provide useful knowledge for the designs of lightweight cellular ceramics.

36 MATERIALS SCIENCE↗

DOE OSTI2021

CaMn 3 IV O 4 Cubane Models of the Oxygen‐Evolving Complex: Spin Ground States S <9/2 and the Effect of Oxo Protonation

Abstract We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn 3 IV O 4 and YMn 3 IV O 4 complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen‐evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin‐state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn 3 IV O 4 complexes and variants with protonated oxo moieties need not be S =9/2. Desymmetrization of the pseudo ‐ C 3 ‐symmetric Ca(Y)Mn 3 IV O 4 core leads to a lower S =5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S =3/2 spin ground state is observed in CaMn 3 IV O 3 (OH). Our studies complement the observation that the interconversion between the low‐spin and high‐spin forms of the S 2 state is pH‐dependent, suggesting that the (de)protonation of bridging or terminal oxygen atoms in the OEC may be connected to spin‐state changes.

Lee, Heui Beom↗

DOE OSTI2021

CaMn 3 IV O 4 Cubane Models of the Oxygen‐Evolving Complex: Spin Ground States S <9/2 and the Effect of Oxo Protonation

Lee, Heui Beom↗

NASA NTRS1983

Mixture Models for Dependent Observations

Parametric mixture models appropriate for data presented in homogeneous blocks of varying sizes from several unidentified source populations are considered. For most applications, the data elements within each block are dependent. Models are proposed for multivariate normal data incorporating two types of dependence, exchangeability of elements within blocks, and a Markov structure for blocks. The consequences of assuming exchangeability, when in fact the Markov structure holds, are explored. Computational problems for each model are considered, and results of a simple test of the exchangeability hypothesis for LANDSAT data are presented.

Peters, C.↗

NASA NTRS1992

Assigning Damping Parameters To Component Dynamical Modes

Damping parameters found by solving nonlinear optimization problem. Paper discusses assignment of matrices of damping parameters to mathematical models of vibrations and rotations of interconnected flexible components of large, flexible structure. Such models truncated at component level to reduce amount of computation necessary to simulate dynamics of structure numerically at both component and system levels.

Lee, Allan Y.↗

NASA NTRS1979

The wave structures of the Eady model of baroclinic instability

By solving the linear quasi-geostrophic set of equations pertinent to the Eady model, the complex eigenvalues and the eigenfunctions are obtained. The propagation speed and the growth rate are computed. Quantitative information is provided about the wave structures for several unstable models, a marginally stable mode, and a stable mode. The peculiarities concerning the amplitude and the phase variations of the waves are noted as the wavenumber varies from the unstable region to the stable region. Physical interpretations of the interrelationships among the dynamical variables are given, with a view toward revealing important aspects of the energy transfer from the basic state to the growing waves.

Hyun, J. M.↗

NASA NTRS1999

User's Guide for ENSAERO_FE Parallel Finite Element Solver

A high fidelity parallel static structural analysis capability is created and interfaced to the multidisciplinary analysis package ENSAERO-MPI of Ames Research Center. This new module replaces ENSAERO's lower fidelity simple finite element and modal modules. Full aircraft structures may be more accurately modeled using the new finite element capability. Parallel computation is performed by breaking the full structure into multiple substructures. This approach is conceptually similar to ENSAERO's multizonal fluid analysis capability. The new substructure code is used to solve the structural finite element equations for each substructure in parallel. NASTRANKOSMIC is utilized as a front end for this code. Its full library of elements can be used to create an accurate and realistic aircraft model. It is used to create the stiffness matrices for each substructure. The new parallel code then uses an iterative preconditioned conjugate gradient method to solve the global structural equations for the substructure boundary nodes.

Eldred, Lloyd B.↗

DOE OSTI2020

Performance simulation of the soft gamma-ray concentrator

The soft gamma-ray concentrator is a telescope mission concept utilizing a suitable arrangement of bent multilayer structures of alternating low- and high-density materials. This lens is able to channel gamma-ray photons via total external reflection and concentrate the incident radiation to a point. The channeling technique offers the potential for concentrating gamma rays with focal lengths <10 m and energies >100 keV, beyond the reach of current grazing-incidence hard x-ray mirrors. For the performance estimation of such an instrument, we have developed a flexible set of computer modeling tools to compute the optical properties of multilayer structures, predict the channeling efficiency for a given multilayer configuration, and aid in the optimization of potential gamma-ray concentrator-based telescope designs. This modeling includes the multilayer optical properties calculated by the IMD software, the ray tracing using an IDL code, and the focal plane detector simulation by MEGAlib. We illustrate the potential of this approach by presenting simulated astronomical observations from a balloon-borne platform. The final result, including simulated effective area, instrument sensitivity, and polarization performance, shows that the gamma-ray concentrator will provide greatly increased sensitivity for next-generation soft gamma-ray missions with modest cost and complexity.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

On the extended chromosphere of Alpha Orionis

A detailed examination of the extended chromosphere of Alpha Orionis was performed in an attempt to characterize the matter-emitting processes of red giants and supergiants. The problem was approached using an Alfven wave driven stellar wind model to compute the density, temperature, and velocity structure of the wind. It is shown that the mechanical energy fluxes necessary to maintain the observed chromospheric temperatures are commensurate with the momentum deposition necessary to extend the chromosphere. The chromospheric model constructed is, however, inconsistent with the kinematics of the observed symmetric profiles, which could correspond to a fountain-type model that described infalling, rather than escaping, ejected material such as He.

Hartmann, L.↗