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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Computational design of mechanically coupled axle-rotor protein assemblies

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here we explore the de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry. We find that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo–electron microscopy, we find that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.

Science & Technology - Other Topics↗
DOE OSTI2024

Computational design of non-porous pH-responsive antibody nanoparticles

Abstract Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1965

Guidance computer design

Some 22 years have elapsed since the first digital computer was completed. For the past several years, digital guidance computers have flown in airplanes, missiles, and rockets. Some of these vehicles are scarcely bigger than an early computer, whose performance is surpassed by the guidance computers they carry.

APOLLO SPACECRAFT↗
NASA NTRS1994

Modeling Improvements and Users Manual for Axial-flow Turbine Off-design Computer Code AXOD

An axial-flow turbine off-design performance computer code used for preliminary studies of gas turbine systems was modified and calibrated based on the experimental performance of large aircraft-type turbines. The flow- and loss-model modifications and calibrations are presented in this report. Comparisons are made between computed performances and experimental data for seven turbines over wide ranges of speed and pressure ratio. This report also serves as the users manual for the revised code, which is named AXOD.

Glassman, Arthur J.↗
DOE OSTI2021

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l - and d -amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC 50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.

42 ENGINEERING↗
DOE OSTI2022

Computational Design of Alloys for Energy Technologies

Advanced materials that maintain their mechanical performance under elevated temperatures, corrosive environments, and a range of static and evolving stresses are needed to improve the efficiency and reduce the environmental impact of a wide spectrum of energy technologies. For instance, cost-efficient alloys that can withstand high temperatures (e.g., 700 °C) have a critical role in improving the efficiency and economics of power generation to support decarbonization of the energy sector; such is true of both the nuclear and fossil energy sectors. Considering both the threats of the energy crisis, namely soaring costs of greenhouse gas emission-producing energy and climate change, it is essential to increase the pace of material discovery and enable rapid paths for material qualification to advance clean energy technologies. Conventionally, alloy development has followed a slow Edisonian process that uses repeated cycles of making, characterizing, and modifying to arrive at optimum composition and processing conditions to achieve the desired component performance. This optimization is followed by the necessary stepwise materials qualification. Furthermore, the increasing adoption of sound data management and physics-informed machine learning represents the next step in the acceleration of materials design and development. In the integrated computational materials engineering (ICME) approach, computational modeling and simulation data from different length and time scales can be combined with complex microstructural details from multimodal experimental characterization and selective property testing to close the design loop for rapid alloy development.

Computational Design Of Materials↗
NASA NTRS1976

Computer-aided design and computer science technology

A description is presented of computer-aided design requirements and the resulting computer science advances needed to support aerospace design. The aerospace design environment is examined, taking into account problems of data handling and aspects of computer hardware and software. The interactive terminal is normally the primary interface between the computer system and the engineering designer. Attention is given to user aids, interactive design, interactive computations, the characteristics of design information, data management requirements, hardware advancements, and computer science developments.

Fulton, R. E.↗
DOE OSTI2022

Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing

Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield and thereby brightness of a dim monomeric RFP (mRojoA, quantum yield = 0.02) by optimizing chromophore packing with aliphatic residues, which we hypothesized would reduce torsional motions causing non-radiative decay. Experimental characterization of the top 10 designed sequences yielded mSandy1 (λ em = 609 nm, quantum yield = 0.26), a variant with equivalent brightness to mCherry, a widely used RFP. We next used directed evolution to further increase brightness, resulting in mSandy2 (λ em = 606 nm, quantum yield = 0.35), the brightest Discosoma sp. derived monomeric RFP with an emission maximum above 600 nm reported to date. Crystallographic analysis of mSandy2 showed that the chromophore p-hydroxybenzylidene moiety is sandwiched between the side chains of Leu63 and Ile197, a structural motif that has not previously been observed in RFPs, and confirms that aliphatic packing leads to chromophore rigidification. Our results demonstrate that computational protein design can be used to generate bright monomeric RFPs, which can serve as templates for the evolution of novel far-red fluorescent proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1976

A systematic method for computer design of supercritical airfoils in cascade

A computer code has been developed for the direct calculation of shockless transonic airfoils whose pressure distributions can be assigned within reasonable limits. The partial differential equations of two-dimensional inviscid gas dynamics are solved by analytic continuation into the domain of two independent complex characteristic coordinates. The domain of integration is mapped conformally onto the unit circle in the hodograph plane of one of these coordinates. It is possible to formulate a boundary value problem on this circle for the stream function that is well posed in the case of transonic flow. This enables the formulation of a procedure for the calculation of an airfoil on which the speed is prescribed as a function of the arc length

Garabedian, P.↗
NASA NTRS1996

Cassini Science Operations and Planning Computer Design

The Cassini Science Operations and Planning Computers (SOPC) are meant to give Cassini investigators and the Huygens Probe Operations Centre (HPOC) more directed control of and responsibility for their instruments and their data and to reduce mission operations cost.SOPCs give the investigators the ability to command their instrument directly, but also the responsibility to do so correctly.

Cassini↗
NASA NTRS1989

Computational design aspects of a NASP nozzle/afterbody experiment

This paper highlights the influence of computational methods on design of a wind tunnel experiment which generically models the nozzle/afterbody flow field of the proposed National Aerospace Plane. The rectangular slot nozzle plume flow field is computed using a three-dimensional, upwind, implicit Navier-Stokes solver. Freestream Mach numbers of 5.3, 7.3, and 10 are investigated. Two-dimensional parametric studies of various Mach numbers, pressure ratios, and ramp angles are used to help determine model loads and afterbody ramp angle and length. It was found that the center of pressure on the ramp occurs at nearly the same location for all ramp angles and test conditions computed. Also, to prevent air liquefaction, it is suggested that a helium-air mixture be used as the jet gas for the highest Mach number test case.

Ruffin, Stephen M.↗
DOE OSTI2022

Computational Design of a Simple Flyer Plate Launcher

The response of materials to shock loading is important to understand for a variety of applications. When shock physics emerged during and after WWII, direct explosive loading or explosively driven plate impact was the primary tool for these studies. Subsequent decades have seen the widespread use of large caliber guns for plate impact studies, laser-shock facilities and pulsed power facilities. INL currently lacks a gun suitable for plate impact or explosives casting and machining facilities; however, it does possess explosives use and handling capabilities. An option for performing plate impact experiments was needed, therefore continuum scale models were utilized to explore a few simple donor-acceptor explosive plane wave lens designs, one of which could be hand packed with plastic explosives to launch flyer plates. 2D simulations were performed to study different geometries in an effort to minimize the difference in shock arrival across the central portion of a small copper flyer plate. A shock wave arrival time difference under 50 ns across 50 percent of the center of the flyer was achieved with a few designs. This work summarizes the computational models and results.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with up 85 compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Altogether, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Off-design computer code for calculating the aerodynamic performance of axial-flow fans and compressors

An off-design axial-flow compressor code is presented and is available from COSMIC for predicting the aerodynamic performance maps of fans and compressors. Steady axisymmetric flow is assumed and the aerodynamic solution reduces to solving the two-dimensional flow field in the meridional plane. A streamline curvature method is used for calculating this flow-field outside the blade rows. This code allows for bleed flows and the first five stators can be reset for each rotational speed, capabilities which are necessary for large multistage compressors. The accuracy of the off-design performance predictions depend upon the validity of the flow loss and deviation correlation models. These empirical correlations for the flow loss and deviation are used to model the real flow effects and the off-design code will compute through small reverse flow regions. The input to this off-design code is fully described and a user's example case for a two-stage fan is included with complete input and output data sets. Also, a comparison of the off-design code predictions with experimental data is included which generally shows good agreement.

Schmidt, James F.↗