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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 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid–Amino Acid Bond Pair Concept

SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid–amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD–ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Comparing Numerical Models of the TALOS Wave Energy Converter

In this study, we present the development of a numerical model of the TALOS Wave Energy Converter (WEC) in WEC-Sim and compare it with existing numerical in-house models from Lancaster and results from DNV's Sesam code. The objective of this work is to validate the performance of the TALOS WEC using WEC-Sim and compare the results with those obtained from other numerical models. The TALOS WEC is a promising technology for the generation of clean, renewable energy from ocean waves. The development of a reliable numerical model for the TALOS WEC is crucial for its design and optimization. To achieve this, we have implemented the TALOS WEC in WEC-Sim and compared the results to in-house models from Lancaster and to results from DNV's Sesam code. Our results show good agreement with the results from Lancaster and DNV, demonstrating the accuracy and reliability of the numerical model developed in WEC-Sim. This work advances the field of wave energy conversion by providing a verified numerical model of the TALOS WEC, which can be used for further optimization and design studies.

CFD↗
DOE OSTI2022

Midfidelity model verification for a point-absorbing wave energy converter with linear power take-off

In the preliminary design stage of a wave energy converter (WEC), researchers need fast and reliable simulation tools. High-fidelity numerical models are usually employed to study the wave-structure interaction, but the computational cost is demanding. As an alternative, midfidelity models can provide simulations in the order of real time. In this study, we operate Uppsala University’s WEC in a relatively mild sea state and model it using WEC-Sim. The model is verified based on OpenFOAM simulations. To analyze the ability of the midfidelity model to capture WEC dynamics, we investigate the system separately with 1, 2, and 3 degrees of freedom. We examine the contribution of viscous phenomena, and study both linear and weakly nonlinear solutions provided by WEC-Sim. Our results indicate that the viscous effects can be neglected in heave and surge motion, but not for pitch. We also find that the weakly nonlinear WEC-Sim solution successfully agrees with the computational fluid dynamics, whereas the linear solution could suggest misleading results.

16 TIDAL AND WAVE POWER↗
DOE OSTI2019

Data from: Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production

Over 13 million ha of former cropland are enrolled in the US Conservation Reserve Program (CRP), providing well-recognized biodiversity, water quality, and carbon (C) sequestration benefits that could be lost on conversion back to agricultural production. Here we provide measurements of the greenhouse gas consequences of converting CRP land to continuous corn, corn–soybean, or perennial grass for biofuel production. No-till soybeans preceded the annual crops and created an initial carbon debt of 10.6 Mg CO2 equivalents (CO2e)·ha−1 that included agronomic inputs, changes in C stocks, altered N2O and CH4 fluxes, and foregone C sequestration less a fossil fuel offset credit. Total debt, which includes future debt created by additional changes in soil C stocks and the loss of substantial future soil C sequestration, can be constrained to 68 Mg CO2e·ha−1 if subsequent crops are under permanent no-till management. If tilled, however, total debt triples to 222 Mg CO2e·ha−1 on account of further soil C loss. Projected C debt repayment periods under no-till management range from 29 to 40 y for corn–soybean and continuous corn, respectively. Under conventional tillage repayment periods are three times longer, from 89 to 123 y, respectively. Alternatively, the direct use of existing CRP grasslands for cellulosic feedstock production would avoid C debt entirely and provide modest climate change mitigation immediately. Incentives for permanent no till and especially permission to harvest CRP biomass for cellulosic biofuel would help to blunt the climate impact of future CRP conversion.

09 BIOMASS FUELS↗
NASA NTRS1964

Lathe converted for grinding aspheric surfaces

A standard overarm tracing lathe converted by the addition of an independently driven diamond grinding wheel is used for grinding aspheric surfaces. The motion of the wheel is controlled by the lathe air tracer following the template which produces the desired aspheric profile.

Larmer, J. W.↗
NASA NTRS1966

Compact actuator converts rotary to linear motion

Compact motor mounted on a stationary base converts rotary to linear motion. The motor rotates a gear train assembly so that the end of an arm attached to the assembly moves in a linear path.

Ford, A. G.↗