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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Occurrence of NDM-1-producing Morganella morganii and Proteus mirabilis in a single patient in Portugal: probable in vivo transfer by conjugation

Abstract Objectives To decipher the genetics of acquisition of carbapenemase-encoding genes identified in two carbapenem-resistant Enterobacteriaceae recovered from a single patient in Portugal. Methods Carbapenemase genes were searched by PCR assays and mating-out assays were performed to further characterize the plasmid support of the carbapenemase genes. Genetic characterization of the plasmid supports was performed by whole-plasmid sequencing using the Illumina technology. Results We identified here two NDM-1-producing isolates, namely a Morganella morganii and a Proteus mirabilis, sharing the same blaNDM-1-positive plasmid. This 154 kb plasmid belonged to the IncA/C2 type, recently renamed IncC, and co-harboured two AmpC β-lactamase genes, namely blaCMY-4 and blaDHA-1, in addition to the 16S rRNA methylase gene armA encoding high-level resistance to aminoglycosides. In addition, the M. morganii isolate produced the CTX-M-33 extended-spectrum β-lactamase possessing weak carbapenemase activity, encoded by another plasmid. Conclusions We showed here that, in addition to KPC-type and OXA-181 carbapenemases, which have been identified as widespread in this country, another concern is the emergence of NDM-1-producing enterobacterial isolates in Portugal. We demonstrated here the in vivo plasmid transfer of a blaNDM-1-positive plasmid leading to dissemination of this carbapenemase gene within different enterobacterial species in a single patient.

Aires-de-Sousa, Marta↗
DOE OSTI2025

Antitoxin control of optimal transcriptional repression in the atypical HigB–HigA toxin–antitoxin system from Proteus vulgaris

Abstract Bacterial toxin–antitoxin (TA) pairs transcriptionally autoregulate their expression via a repression/derepression mechanism in response to changing environmental conditions. The structural diversity of TA systems influences the mechanisms of transcriptional regulation. Here, we define the molecular mechanism for the plasmid-encoded HigB–HigA TA pair originally identified in a post-operative infection with antibiotic-resistant Proteus vulgaris. We determine DNA binding and promoter activity by the HigB–HigA complex supported by structural biology and molecular dynamics simulations of an elusive DNA operator–TA repressor complex. To define the optimal oligomeric TA repressor–DNA operator complex required for derepression, we engineered a dedicated trimeric HigB–HigA2 complex that represses transcription more than 26-fold as compared to the tetrameric HigB2–HigA2. These results expand the known diversity of how the HigB–HigA TA family is autoregulated.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Proteus

Proteus enables Just-In-Time (JIT) compilation and optimization of C/C++ code using LLVM.

Georgakoudis, Giorgis↗
NASA NTRS1991

Verification of the proteus two-dimensional Navier-Stokes code for flat plate and pipe flows

The Proteus Navier-Stokes Code is evaluated for 2-D/axisymmetric, viscous, incompressible, internal, and external flows. The particular cases to be discussed are laminar and turbulent flows over a flat plate, laminar and turbulent developing pipe flows, and turbulent pipe flow with swirl. Results are compared with exact solutions, empirical correlations, and experimental data. A detailed description of the code set-up, including boundary conditions, initial conditions, grid size, and grid packing is given for each case.

Conley, Julianne M.↗
NASA NTRS1991

Verification of the Proteus two-dimensional Navier-Stokes code for flat plate and pipe flows

The Proteus Navier-Stokes Code is evaluated for two-dimensional/axisymmetric, viscous, incompressible, internal and external flows. The particular cases to be discussed are laminar and turbulent flows over a flat plate, laminar and turbulent dveloping pipe flows and turbulent pipe flow with swirl. Results are compared with exact solutions, empirical correlations and experimental data. A detailed description of the code set-up, including boundary conditions, intitial conditions, grid size and grid packing is given for each case.

Conley, Julianne M.↗
NASA NTRS1993

Proteus two-dimensional Navier-Stokes computer code, version 2.0. Volume 2: User's guide

A computer code called Proteus 2D was developed to solve the two-dimensional planar or axisymmetric, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body-fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. This is the User's Guide, and describes the program's features, the input and output, the procedure for setting up initial conditions, the computer resource requirements, the diagnostic messages that may be generated, the job control language used to run the program, and several test cases.

Towne, Charles E.↗
NASA NTRS1993

Proteus two-dimensional Navier-Stokes computer code, version 2.0. Volume 1: Analysis description

A computer code called Proteus 2D was developed to solve the two-dimensional planar or axisymmetric, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body-fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. This is the Analysis Description, and presents the equations and solution procedure. The governing equations, the turbulence model, the linearization of the equations and boundary conditions, the time and space differencing formulas, the ADI solution procedure, and the artificial viscosity models are described in detail.

Towne, Charles E.↗
NASA NTRS1993

Proteus three-dimensional Navier-Stokes computer code, version 1.0. Volume 2: User's guide

A computer code called Proteus 3D was developed to solve the three-dimensional, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body-fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. This User's Guide describes the program's features, the input and output, the procedure for setting up initial conditions, the computer resource requirements, the diagnostic messages that may be generated, the job control language used to run the program, and several test cases.

Towne, Charles E.↗
NASA NTRS1993

Proteus three-dimensional Navier-Stokes computer code, version 1.0. Volume 3: Programmer's reference

A computer code called Proteus 3D was developed to solve the three-dimensional, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. The Programmer's Reference contains detailed information useful when modifying the program. The program structure, the Fortran variables stored in common blocks, and the details of each subprogram are described.

Towne, Charles E.↗
NASA NTRS1993

Proteus two-dimensional Navier-Stokes computer code, version 2.0. Volume 3: Programmer's reference

A computer code called Proteus 2D was developed to solve the two-dimensional planar or axisymmetric, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body-fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. The Programmer's Reference contains detailed information useful when modifying the program. The program structure, the Fortran variables stored in common blocks, and the details of each subprogram are described.

Towne, Charles E.↗
NASA NTRS1993

Proteus three-dimensional Navier-Stokes computer code, version 1.0. Volume 1: Analysis description

A computer code called Proteus 3D has been developed to solve the three dimensional, Reynolds averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort has been to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation have been emphasized. The governing equations are solved in generalized non-orthogonal body-fitted coordinates by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. This is the Analysis Description, and presents the equations and solution procedure. It describes in detail the governing equations, the turbulence model, the linearization of the equations and boundary conditions, the time and space differencing formulas, the ADI solution procedure, and the artificial viscosity models.

Towne, Charles E.↗
DOE OSTI2024

Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism

Tryptophan indole lyase (TIL; [E.C. 4.1.99.1]) is a bacterial pyridoxal-5′-phosphate (PLP)-dependent enzyme that catalyzes reversible β-elimination of indole from L-tryptophan. The mechanism of elimination of indole from L-tryptophan starts with the formation of an external aldimine of the substrate and PLP, followed by deprotonation of the α-CH of the substrate, forming a resonance-stabilized quinonoid intermediate. Proton transfer to C3 of the indole ring and carbon–carbon bond cleavage of the quinonoid intermediate provide indole and aminoacrylate bound to PLP, which then releases indole, followed by iminopyruvate. We have now determined the X-ray crystal structures of TIL complexes with (3S)-dioxindolyl-l-alanine, an inhibitor, and with substrates L-tryptophan, 7-aza-L-tryptophan, and S-ethyl-l-cysteine (SEC) in the presence of benzimidazole (BZI), an isostere of the product indole. These structures show a mixture of gem-diamine, external aldimine, quinonoid, and aminoacrylate intermediates, in both open and closed active site conformations. In the closed conformations of L-tryptophan, (3S)-dioxindolyl-l-alanine, and 7-aza-L-tryptophan complexes, hydrogen bonds form between Asp-133 with N1 of the ligand heterocyclic ring and NE2 of His-458 in the small domain of TIL. This hydrogen bond also forms in the BZI complex with the aminoacrylate intermediates formed from both L-tryptophan and SEC. The closed quinonoid complex of 7-aza-L-tryptophan shows that the azaindole ring in the closed conformation is bent out of plane of the Cβ–C3 bond by about 40°, putting it in a geometry that leads toward the transition-state geometry. Thus, both conformational dynamics and substrate activation play critical roles in the reaction mechanism of the TIL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Development of the PROTEUS and ANSYS Coupled System for Simulating Heat Pipe Cooled Micro Reactors

The objective of this project is to develop the coupled system of PROTEUS/ANSYS for simulating a heat pipe cooled micro reactor. As an initial effort, while figuring out controlling ANSYS Mechanical with Workbench, the coupled system of PROTEUS/FLUENT in the CORBA environment were tried to demonstrate the coupled simulation for a transient problem of a heat pipe cooled micro reactor. Finally, the coupled system of PROTEUS/ANSYS was constructed using APDL commands in the CORBA environment, instead of ANSYS Workbench, since we found that ANSYS with the current version of Workbench Python scripting did not provide capabilities necessary for simulating a transient problem.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2023

PROTEUS: Machine Learning Driven Resilience for Extreme-scale Systems

The objective of this project is to design, develop, and evaluate scalable software to enhance resilience, data checkpointing, program restart, and analysis. The proposed tasks are to 1) develop scalable machine learning techniques to learn temporal change patterns in a scalable and in-situ manner, and to minimize data movement and maximize learning locally closest to data; 2) design a concise data representation and indexing mechanism to capture the distribution of changes in data that can guarantee point-wise user-defined tolerable errors while reducing the data storage requirements by an order of magnitude or more; 3) develop data reduction techniques as library modules; 4) exploit local SSD for minimizing data movement in storage hierarchy; 5) develop anomaly detection algorithms that can predict corruptions based on learning of emerging patterns; 6) develop software libraries to be incorporated within widely used data formats and APIs; and 7) evaluate the proposed software using DOE scientific applications. The outcomes of the proposed work are to satisfy many synergistic data reduction and resilience requirements for large-scale data intensive applications executed on extreme-scale computing systems. The developed mechanism for error-bound data approximation is directly applicable to existing scientific applications. Through machine learning from historical events and change distribution, this work will enable anomaly detection for DOE computer facility.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Verifying LLM generative agents reflect human behavior in contested information environments to effectively simulate disinformation campaigns (Proteus)

Disinformation poses a significant and evolving threat to today’s online environment. Individuals encounter challenges in detecting disinformation, subsequently influencing their behavior and decision-making processes. Our research examines the potential use of large language model (LLM) generative agents (LGAs) to replicate human behavior to better understand how disinformation is spread in online environments. Using human subjects research, we first investigate how personality traits, individual differences, and demographic factors relate to decision-making in simulated online disinformation environments. Then, we examine whether LGAs can effectively replicate human responses in the same simulated online environments when assigned personality traits, demographic characteristics and behavioral attributes. Our findings indicate that LGAs can align with human decisions in these scenarios; however, alignment is contingent upon scenario context, persona settings and LLM selection. Results provide valuable insights for methodology refinement in future research and in utilizing LGAs to model complex national security challenges such as disinformation campaigns.

97 MATHEMATICS AND COMPUTING↗