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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Utah FORGE: Earth Model Native State Simulation Results

Utah FORGE phase 2C Native State Simulation zip contains the data used for the boundary conditions and subsequent native state simulation results obtained using the simulation code FALCON. Data are from the nodes of the simulation domain, with used a uniform 50m spacing over a 2500 X 2500 X 2750m domain approximately centered on the FORGE footprint. There is also a read me text file, that is included, containing metadata. The Reservoir Porosity and Upscale DFN Permeability zip contains the data used for the spatial distribution of the anisotropic permeability and porosity used in the native state simulation of the Utah FORGE site. Please contact Robert Podgorney at the Idaho National Laboratory with questions, robert.podgorney@inl.gov. There is also a read me text file included containing metadata.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

Biomechanical Analysis of Multilevel Posterior Cervical Spinal Fusion Constructs

Study Design: Controlled Laboratory Study Objective: To compare multilevel posterior cervical fusion (PCF) constructs stopping at C7, T1, and T2 under cyclic load to determine the range of motion (ROM) between the lowest instrumented level and lowest instrumented-adjacent level (LIV-1). Summary of Background Data: PCF is a mainstay of treatment for various cervical spine conditions. The transition between the flexible cervical spine and rigid thoracic spine can lead to construct failure at the cervicothoracic junction. There is little evidence to determine the most appropriate level at which to stop a multilevel PCF. Methods: Fifteen human cadaveric cervicothoracic spines were randomly assigned to 1 of 3 treatment groups: PCF stopping at C7, T1, or T2. Specimens were tested in their native state, following a simulated PCF, and after cyclic loading. Specimens were loaded in flexion-extension), lateral bending, and axial rotation. Three-dimensional kinematics were recorded to evaluate ROM. Results: The C7 group had greater flexion-extension motion than the T1 and T2 groups following instrumentation (10.17±0.83 degree vs. 2.77±1.66 degree and 1.06±0.55 degree, P <0.001), and after cyclic loading (10.42±2.30 degree vs. 2.47±0.64 degree and 1.99±1.23 degree, P <0.001). There was no significant difference between the T1 and T2 groups. The C7 group had greater lateral bending ROM than both thoracic groups after instrumentation (8.81±3.44 degree vs. 3.51±2.52 degree, P =0.013 and 1.99±1.99 degree, P =0.003) and after cyclic loading. The C7 group had greater axial rotation motion than the thoracic groups (4.46±2.27 degree vs. 1.26±0.69 degree, P =0.010; and 0.73±0.74 degree, P =0.003) following cyclic loading. Conclusion: Motion at the cervicothoracic junction is significantly greater when a multilevel PCF stops at C7 rather than T1 or T2. This is likely attributable to the transition from a flexible cervical spine to a rigid thoracic spine. Although this does not account for in vivo fusion, surgeons should consider extending multilevel PCF constructs to T1 when feasible. Level of Evidence: Not applicable.

Neurosciences & Neurology↗
DOE OSTI2019

Utah FORGE Phase Native State FALCON Model Files

The submission includes FALCON input file and mesh for the an initial pressure-temperature simulation, and a second set for pressure-temperature-displacement simulation. All simulations are steady state. Data and input for the FORGE Phase 2 native state model were compiled from historic and FORGE specific characterization efforts. The simulations look to find the in-situ pressure, temperature, and stress distributions in the vicinity of the Utah FORGE site. The purpose of the native state model was to establish a baseline for all other modeling analyses—so that the whole modeling team can start from a consistent set of conditions which makes for comparison of results more straightforward and meaningful. Requires the FALCON simulator which can be found in the "FALCON Simulator" link in the submission. Instructions for compiling and running FALCON can be found on the FORGE branch of the FALCON git repository in the README.

15 GEOTHERMAL ENERGY↗
DOE OSTI2018

Fallon FORGE: Thermal-Hydrological-Mechanical Models

Archive contains thermal-mechanical simulation input/output files. Included are files which fall into the following categories: ( 1 ) Spreadsheets with various input parameter calculations ( 2 ) Final Simulation Inputs ( 3 ) Native-State Thermal-Hydrological Model Input File Folders ( 4 ) Native-State Thermal-Hydrological-Mechanical Model Input Files ( 5 ) THM Model Stimulation Cases See 'File Descriptions.xlsx' resource below for additional information on individual files.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields

High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The 10–14% differences affect molecular dynamics simulations of protein folding. • Shortening C–H bonds by 10–14% can improve protein folding simulations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

QUASI-ANHARMONIC ANALYSIS REVEALS INTERMEDIATE STATES IN THE NUCLEAR CO-ACTIVATOR RECEPTOR BINDING DOMAIN ENSEMBLE. In: Biocomputing 2012

The molten globule nuclear receptor co-activator binding domain (NCBD) of CREB binding protein (CBP) selectively recruits transcription co-activators (TCAs) during the formation of the transcription preinitiation complex. NCBD:TCA interactions have been implicated in several cancers, however, the mechanisms of NCBD:TCA recognition remain uncharacterized. NCBD:TCA intermolecular recognition has challenged traditional investigation as both NCBD and several of its corresponding TCAs are intrinsically disordered. Using 40μs of explicit solvent molecular dynamics simulations, we relate the conformational diversity of ligand-free NCBD to its bound configurations. We introduce two novel techniques to quantify the conformational heterogeneity of ligand-free NCBD, dihedral quasi-anharmonic analysis (dQAA) and hierarchical graph-based diffusive clustering. With this integrated approach we find that three of four ligand-bound states are natively accessible to the ligand-free NCBD simulations with root-mean squared deviation (RMSD) less than 2Å These conformations are accessible via diverse pathways while a rate-limiting barrier must be crossed in order to access the fourth bound state.

BURGER, VIRGINIA M.↗
DOE OSTI2012

Quasi-Anharmonic Analysis Reveals Intermediate States In The Nuclear Co-Activator Receptor Binding Domain Ensemble

The molten globule nuclear receptor co-activator binding domain (NCBD) of CREB binding protein (CBP) selectively recruits transcription co-activators (TCAs) during the formation of the transcription preinitiation complex. NCBD:TCA interactions have been implicated in several cancers, however, the mechanisms of NCBD:TCA recognition remain uncharacterized. NCBD:TCA intermolecular recognition has challenged traditional investigation as both NCBD and several of its corresponding TCAs are intrinsically disordered. Using 40 {micro}s of explicit solvent molecular dynamics simulations, we relate the conformational diversity of ligand-free NCBD to its bound configurations. We introduce two novel techniques to quantify the conformational heterogeneity of ligand-free NCBD, dihedral quasi-anharmonic analysis (dQAA) and hierarchical graph-based diffusive clustering. With this integrated approach we find that three of four ligand-bound states are natively accessible to the ligand-free NCBD simulations with root-mean squared deviation (RMSD) less than 2 {angstrom}. These conformations are accessible via diverse pathways while a rate-limiting barrier must be crossed in order to access the fourth bound state.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Subsurface Characterization and Machine Learning Predictions at Brady Hot Springs Results

Geothermal power plants typically show decreasing heat and power production rates over time. Mitigation strategies include optimizing the management of existing wells - increasing or decreasing the fluid flow rates across the wells - and drilling new wells at appropriate locations. The latter is expensive, time-consuming, and subject to many engineering constraints, but the former is a viable mechanism for periodic adjustment of the available fluid allocations. Data and supporting literature from a study describing a new approach combining reservoir modeling and machine learning to produce models that enable strategies for the mitigation of decreased heat and power production rates over time for geothermal power plants. The computational approach used enables translation of sets of potential flow rates for the active wells into reservoir-wide estimates of produced energy and discovery of optimal flow allocations among the studied sets. In our computational experiments, we utilize collections of simulations for a specific reservoir (which capture subsurface characterization and realize history matching) along with machine learning models that predict temperature and pressure timeseries for production wells. We evaluate this approach using an "open-source" reservoir we have constructed that captures many of the characteristics of Brady Hot Springs, a commercially operational geothermal field in Nevada, USA. Selected results from a reservoir model of Brady Hot Springs itself are presented to show successful application to an existing system. In both cases, energy predictions prove to be highly accurate: all observed prediction errors do not exceed 3.68% for temperatures and 4.75% for pressures. In a cumulative energy estimation, we observe prediction errors that are less than 4.04%. A typical reservoir simulation for Brady Hot Springs completes in approximately 4 hours, whereas our machine learning models yield accurate 20-year predictions for temperatures, pressures, and produced energy in 0.9 seconds. This paper aims to demonstrate how the models and techniques from our study can be applied to achieve rapid exploration of controlled parameters and optimization of other geothermal reservoirs. Includes a synthetic, yet realistic, model of a geothermal reservoir, referred to as open-source reservoir (OSR). OSR is a 10-well (4 injection wells and 6 production wells) system that resembles Brady Hot Springs (a commercially operational geothermal field in Nevada, USA) at a high level but has a number of sufficiently modified characteristics (which renders any possible similarity between specific characteristics like temperatures and pressures as purely random). We study OSR through CMG simulations with a wide range of flow allocation scenarios. Includes a dataset with 101 simulated scenarios that cover the period of time between 2020 and 2040 and a link to the published paper about this project, where we focus on the Machine Learning work for predicting OSR's energy production based on the simulation data, as well as a link to the GitHub repository where we have published the code we have developed (please refer to the repository's readme file to see instructions on how to run the code). Additional links are included to associated work led by the USGS to identify geologic factors associated with well productivity in geothermal fields. Below are the high-level steps for applying the same modeling + ML process to other geothermal reservoirs: 1. Develop a geologic model of the geothermal field. The location of faults, upflow zones, aquifers, etc. need to be accounted for as accurately as possible 2. The geologic model needs to be converted to a reservoir model that can be used in a reservoir simulator, such as, for instance, CMG STARS, TETRAD, or FALCON 3. Using native state modeling, the initial temperature and pressure distributions are evaluated, and they become the initial conditions for dynamic reservoir simulations 4....

15 GEOTHERMAL ENERGY↗
DOE OSTI2014

Benchmarking all-atom simulations using hydrogen exchange

Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Spin-optomechanical cavity interfaces by deep subwavelength phonon-photon confinement

A central goal of quantum information science is transferring qubits between space, time, and modality. Spin-based systems in solids are promising quantum memories, but high-fidelity transfer of their quantum states to telecom optical fields remains challenging. Here, we introduce a phonon-mediated interface between spins in a diamond nanobeam optomechanical crystal and telecom optical fields by a simultaneous deep-subwavelength confinement of optical and acoustic fields with mode volumes $V_{\textrm{mech}}$$/Λ^3_\textrm{p} ~ 10^{-5}$ and $V_{\textrm{opt}}$$/λ^3 ~ 10^{−3}$, respectively. This confinement boosts the spin-mechanical coupling rate of Group-IV silicon vacancy (SiV − ) centers by an order of magnitude to ~ 32 MHz while retaining high acousto-optical couplings. The optical cavity couples to the spin irrespective of the emitter’s native excited states, avoiding spectral diffusion. Using Quantum Monte Carlo simulations, we estimate heralded entanglement fidelities exceeding 0.96 between two such interfaces. We anticipate broad utility beyond diamond emitter-telecom systems to most solid-state quantum memories.

Raniwala, Hamza [Massachusetts Inst. of Technology↗
DOE OSTI2017

Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations

Positional fluctuations of an atom in a protein can be described as motion in an effective local energy minimum created by the surrounding protein atoms. The dependence of atomic fluctuations on both temperature (T) and pressure (P) has been used to probe the nature of these minima, which are generally described as harmonic in experiments such as x-ray crystallography and neutron scattering. Here, a quasiharmonic analysis method is presented in which the P-T dependence of atomic fluctuations is in terms of an intrinsic isobaric thermal expansivity αP and an intrinsic isothermal compressibility κT. The method is tested on previously reported mean-square displacements from P-T molecular dynamics simulations of lysozyme, which were interpreted to have a pressure-independent dynamical transition Tg near 200 K and a change in the pressure dependence near 480 MPa. Our quasiharmonic analysis of the same data shows that the P-T dependence can be described in terms of αP and κT where below Tg, the temperature dependence is frozen at the Tg value. In addition, the purported transition at 480 MPa is reinterpreted as a consequence of the pressure dependence of Tg and the quasiharmonic frequencies. The former also indicates that barrier heights between substates are pressure dependent in these data. Furthermore, the insights gained from this quasiharmonic analysis, which was of the energy landscape near the native state of a protein, suggest that similar analyses of other simulations may be useful in understanding such phenomena as pressure-induced protein unfolding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation

The skin's permeability barrier consists of stacked lipid sheets of splayed ceramides, cholesterol and free fatty acids, positioned intercellularly in the stratum corneum. We report here on the early stage of skin barrier formation taking place inside the tubuloreticular system in the secretory cells of the topmost viable epidermis and in the intercellular space between viable epidermis and stratum corneum. The barrier formation process was analysed in situ in its near-native state, using cryo-EM combined with molecular dynamics modeling and EM simulation. Stacks of lamellae appear towards the periphery of the tubuloreticular system and they are closely associated with granular regions. Only models based on a bicontinuous cubic phase organization proved compatible with the granular cryo-EM patterns. Only models based on a dehydrated lamellar phase organization agreed with the lamellar cryo-EM patterns. The data support that human skin barrier formation takes place via a cubic to lamellar lipid phase transition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Prospects for simulating a qudit-based model of (1+1)D scalar QED

We present a gauge invariant digitization of (1+1)d scalar quantum electrodynamics for an arbitrary spin truncation for qudit-based quantum computers. We provide a construction of the Trotter operator in terms of a universal qudit-gate set. Here, the cost savings of using a qutrit based spin-1 encoding versus a qubit encoding are illustrated. We show that a simple initial state could be simulated on current qutrit based hardware using noisy simulations for two different native gate set.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets

The origin and the magnitude of the charge in a macroion are critical questions in mass spectrometry analysis coupled to electrospray and other ionization techniques that transfer analytes from the bulk solution into the gaseous phase via droplets. In many circumstances, it is the later stages of the existence of a macroion in the containing solvent drop before the detection that determines the final charge state. Experimental characterization of small (with linear dimensions of several nanometers) and short-lived droplets is quite challenging. Molecular simulations in principle may provide insight exactly in this challenging for experiments regime. We discuss the strengths and weaknesses of the molecular modeling of electrosprayed droplets using molecular dynamics. We illustrate the limitations of the molecular modeling in the analysis of large macroions and specifically proteins away from their native states. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗