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DOE OSTI2024

CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications

In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Feedstock to Function (F2F) v1

The Feedstock to Function (F2F) tool was designed to help scientists and companies explore viable biofuels and bioproducts early in the R&D cycle to support more productive experimentation, while reducing early-stage exploration from months/years to days/weeks (feedstock-to-function.lbl.gov). The tool focuses on using machine learning to predict biomass-derived molecule properties, while evaluating the cost, benefits, and risks of promising molecules for sustainable aviation fuels. The tool successfully predicts (within 15% of experimental values) high-throughput aviation properties for over 10,000 molecules while enabling users to explore new possibilities and opportunities rapidly and effortlessly. It also links to lightweight life-cycle analysis and techno-economic tools for cost and emissions analyses. Predicted molecule properties include melting point, boiling point, flash point, yield sooting index, and heat of combustion. To date, F2F is more expansive and outperforms several other molecule property prediction models while enabling users (scientists, companies, and policy makers) to explore new possibilities and opportunities rapidly and effortlessly. F2F provides the foundation for developing an adaptive computational tool that predicts properties, cost, benefits, and risk of promising new and uncertified alternative jet fuel pathways and their blending effects.

Rapp, Vi↗

DOE OSTI2019

Phase-field model for diffusion-induced grain boundary migration: An application to battery electrodes

Diffusion-induced grain boundary migration is a phenomenon in which a grain boundary moves in response to the driving forces generated by diffusing solute species. For example, diffusing solute species change the atomic volume in the host material, either by filling a vacancy with a misfitting solute atom or by expanding host lattices through interstitial diffusion. These volume changes are inhomogeneous and are stored as elastic energy in the material that drives grain boundaries. In this paper, we introduce our previously developed Cahn-Hilliard–phase-field-crystal model (CH-PFC) as a computational tool to investigate diffusion-induced grain boundary migration in crystalline materials. This multiscale phase-field model couples the composition field of a diffusing species with the crystallographic texture of a host material. We apply the CH-PFC model to battery electrodes and investigate whether interstitial solute diffusion induces grain growth in FePO 4 /LiFePO 4 electrodes. To this end, we compute grain growth in 60 FePO 4 electrodes by conducting two parallel trials: In the first trial, we cycle the electrode and calculate diffusion-induced grain growth. In the second trial, we do not cycle the electrode and calculate curvature-driven grain growth. We find a statistically significant grain growth in the cycled electrodes and negligible grain growth in the noncycled electrodes. Altogether, we show that the CH-PFC model not only predicts electrode microstructures as a function of the Li composition, but also predicts the crystallographic features of an electrode during battery operation.

36 MATERIALS SCIENCE↗

NASA NTRS1994

Discrete-Layer Piezoelectric Plate and Shell Models for Active Tip-Clearance Control

The objectives of this work were to develop computational tools for the analysis of active-sensory composite structures with added or embedded piezoelectric layers. The targeted application for this class of smart composite laminates and the analytical development is the accomplishment of active tip-clearance control in turbomachinery components. Two distinct theories and analytical models were developed and explored under this contract: (1) a discrete-layer plate theory and corresponding computational models, and (2) a three dimensional general discrete-layer element generated in curvilinear coordinates for modeling laminated composite piezoelectric shells. Both models were developed from the complete electromechanical constitutive relations of piezoelectric materials, and incorporate both displacements and potentials as state variables. This report describes the development and results of these models. The discrete-layer theories imply that the displacement field and electrostatic potential through-the-thickness of the laminate are described over an individual layer rather than as a smeared function over the thickness of the entire plate or shell thickness. This is especially crucial for composites with embedded piezoelectric layers, as the actuating and sensing elements within these layers are poorly represented by effective or smeared properties. Linear Lagrange interpolation polynomials were used to describe the through-thickness laminate behavior. Both analytic and finite element approximations were used in the plane or surface of the structure. In this context, theoretical developments are presented for the discrete-layer plate theory, the discrete-layer shell theory, and the formulation of an exact solution for simply-supported piezoelectric plates. Finally, evaluations and results from a number of separate examples are presented for the static and dynamic analysis of the plate geometry. Comparisons between the different approaches are provided when possible, and initial conclusions regarding the accuracy and limitations of these models are given.

Heyliger, P. R.↗

DOE OSTI2012

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity

Background: Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or “signature genes”) present in groups of closely related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose. Results: Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http:// phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study. Conclusions: PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Comparison of steady-state analytical wake models implemented in wind farm analysis software

A common set of mathematical wind turbine wake models are implemented in a few, well-adopted computational tools for wind farm wake modelling. Although the referenced mathematical formulations are common, implementation details may lead to differences in results. This study presents a systematic comparison of the implementation of mathematical wake models in open source, Python-based wind turbine wake modelling software, and a set of the models are directly compared. Despite aligning only the mathematical model parameters and retaining the default computational model parameters, good agreement is found across most of the model implementations, and additional agreement is expected upon further parameters alignment.

17 WIND ENERGY↗

DOE OSTI2012

RCrane: semi-automated RNA model building

RCrane is a new tool for the partially automated building of RNA crystallographic models into electron-density maps of low or intermediate resolution. This tool helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1998

Combined Numerical/Analytical Perturbation Solutions of the Navier-Stokes Equations for Aerodynamic Ejector/Mixer Nozzle Flows

In spite of rapid advances in both scalar and parallel computational tools, the large number of variables involved in both design and inverse problems make the use of sophisticated fluid flow models impractical, With this restriction, it is concluded that an important family of methods for mathematical/computational development are reduced or approximate fluid flow models. In this study a combined perturbation/numerical modeling methodology is developed which provides a rigorously derived family of solutions. The mathematical model is computationally more efficient than classical boundary layer but provides important two-dimensional information not available using quasi-1-d approaches. An additional strength of the current methodology is its ability to locally predict static pressure fields in a manner analogous to more sophisticated parabolized Navier Stokes (PNS) formulations. To resolve singular behavior, the model utilizes classical analytical solution techniques. Hence, analytical methods have been combined with efficient numerical methods to yield an efficient hybrid fluid flow model. In particular, the main objective of this research has been to develop a system of analytical and numerical ejector/mixer nozzle models, which require minimal empirical input. A computer code, DREA Differential Reduced Ejector/mixer Analysis has been developed with the ability to run sufficiently fast so that it may be used either as a subroutine or called by an design optimization routine. Models are of direct use to the High Speed Civil Transport Program (a joint government/industry project seeking to develop an economically.viable U.S. commercial supersonic transport vehicle) and are currently being adopted by both NASA and industry. Experimental validation of these models is provided by comparison to results obtained from open literature and Limited Exclusive Right Distribution (LERD) sources, as well as dedicated experiments performed at Texas A&M. These experiments have been performed using a hydraulic/gas flow analog. Results of comparisons of DREA computations with experimental data, which include entrainment, thrust, and local profile information, are overall good. Computational time studies indicate that DREA provides considerably more information at a lower computational cost than contemporary ejector nozzle design models. Finally. physical limitations of the method, deviations from experimental data, potential improvements and alternative formulations are described. This report represents closure to the NASA Graduate Researchers Program. Versions of the DREA code and a user's guide may be obtained from the NASA Lewis Research Center.

DeChant, Lawrence Justin↗

DOE OSTI2017

VERA Core Physics Benchmark Progression Problem Results for VERA 3.6

This report contains a comparison of results obtained with VERA 3.6 Release Candidate 0 for the Core Physics Benchmark Progression Problems 1 through 9 to both computational tools and measured data from Watts Bar Unit 1 (WBN1). (Ref. 1 and Ref. 2) These problems progress from single pin cell analyses to full core depletion calculations. VERA results obtained for Problems 1 through 5 are compared against results obtained using the SCALE 6.2 Beta code KENO-VI. Results for Problem 6 and 7 are compared against those obtained using a coupled neutronic and thermal-hydraulic combination of the KAPL software MC21 and the CASL tool CTF. (Ref. 3, Ref. 4 and Ref. 5) VERA results from problems 5 and 9 are compared to data from WBN1. For all of the analyses contained in this report, VERA provided similar results to other state-of-the-art software programs and real reactor data. This indicates that the program is capable of modeling a full-scale PWR in a more discretized and computationally efficient manner than any other reactor physics program. Since the descriptions of the Core Physics Benchmark Progression Problems and the logic behind their selection is discussed in-depth elsewhere it is not covered in the scope of this document. Additionally, in-depth discussions of the software programs used in this analysis are not provided for the same rationale.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2008

Validation of High-Fidelity CFD Simulations for Rocket Injector Design

Computational fluid dynamics (CFD) has the potential to improve the historical rocket injector design process by evaluating the sensitivity of performance and injector-driven thermal environments to the details of the injector geometry and key operational parameters. Methodical verification and validation efforts on a range of coaxial injector elements have shown the current production CFD capability must be improved in order to quantitatively impact the injector design process. This paper documents the status of a focused effort to compare and understand the predictive capabilities and computational requirements of a range of CFD methodologies on a set of single element injector model problems. The steady Reynolds-Average Navier-Stokes (RANS), unsteady Reynolds-Average Navier-Stokes (URANS) and three different approaches using the Large Eddy Simulation (LES) technique were used to simulate the initial model problem, a single element coaxial injector using gaseous oxygen and gaseous hydrogen propellants. While one high-fidelity LES result matches the experimental combustion chamber wall heat flux very well, there is no monotonic convergence to the data with increasing computational tool fidelity. Systematic evaluation of key flow field regions such as the flame zone, the head end recirculation zone and the downstream near wall zone has shed significant, though as of yet incomplete, light on the complex, underlying causes for the performance level of each technique. 1 Aerospace Engineer and Combustion CFD Team Leader, MS ER42, NASA MSFC, AL 35812, Senior Member, AIAA. 2 Professor and Director, Computational Combustion Laboratory, School of Aerospace Engineering, 270 Ferst Dr., Atlanta, GA 30332, Associate Fellow, AIAA. 3 Reilly Professor of Engineering, School of Mechanical Engineering, 585 Purdue Mall, West Lafayette, IN 47907, Fellow, AIAA. 4 Principal Member of Technical Staff, Combustion Research Facility, 7011 East Avenue, MS9051, Livermore, CA 94550, Associate Fellow, AIAA. 5 J. L. and G. H. McCain Endowed Chair, Mechanical Engineering, 104 Research Building East, University Park, PA 16802, Fellow, AIAA. American Institute of Aeronautics and Astronautics 1

Tucker, P. Kevin↗

NASA NTRS1997

RL10A-3-3A Rocket Engine Modeling Project

Two RL10A-3-3A rocket engines comprise the main propulsion system for the Centaur upper stage vehicle. Centaur is used with bod Titan and Atlas launch vehicles, carrying military and civilian payloads from high altitudes into orbit and beyond. The RL10 has delivered highly reliable service for the past 30 years. Recently, however, there have been two in-flight failures which have refocused attention on the RL10. This heightened interest has sparked a desire for an independent RL10 modeling capability within NASA and th Air Force. Pratt & Whitney, which presently has the most detailed model of the RL10, also sees merit in having an independent model which could be used as a cross-check with their own simulations. The Space Propulsion Technology Division (SPTD) at the NASA Lewis Research Center has developed a computer model of the RL10A-3-3A. A project team was formed, consisting of experts in the areas of turbomachinery, combustion, and heat transfer. The overall goal of the project was to provide a model of the entire RL10 rocket engine for government use. In the course of the project, the major engine components have been modeled using a combination of simple correlations and detailed component analysis tools (computer codes). The results of these component analyses were verified with data provided by Pratt & Whitney. Select modeling results and test data curves were then integrated to form the RL10 engine system model The purpose of this report is to introduce the reader to the RL10 rocket engine and to describe the engine system model. The RL10 engine and its application to U.S. launch vehicles are described first, followed by a summary of the SPTD project organization, goals, and accomplishments. Simulated output from the system model are shown in comparison with test and flight data for start transient, steady state, and shut-down transient operations. Detailed descriptions of all component analyses, including those not selected for integration with the system model, are included as appendices.

Binder, Michael↗

NASA NTRS2004

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗

NASA NTRSDate not supplied

Toward Adjoint-Based Aeroacoustic Optimization for Propeller and Rotorcraft Applications

The goal of the present project is to build a multidisciplinary, rapid, robust, and accurate computational tool to optimize wing-mounted propeller designs. The full Farassat’s formulation F1Afor aeroacoustic analysis is implemented in the open-source software SU2.This extension enables the prediction of far-field noise generated by moving sources. The formulation is verified, for a stationary and rotating sphere in a wind tunnel and for a tiltrotor in forward flight, by comparing the acoustic predictions ofSU2 with the predictions computed by NASA’s aeroacoustics code ANOPP2. The algorithmic differentiation capability of SU2 provides discretely consistent, adjoint-based sensitivity analysis for this formulation. The adjoint-based sensitivities are verified through comparison with complex-step sensitivities

R Omur Icke↗

DOE OSTI2016

ZEM: Integrated Framework for Real-Time Data and Model Analyses for Robust Environmental Management Decision Making - 16438

Typically environmental management (EM) problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly analysis, assimilation and integration into a series of models with different complexity for various types of model-based analyses. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions). To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian-Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is predominantly coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org) and incorporates the MADS computational tools (Model Analysis and Decision Support; http://mads.lanl.gov). We demonstrate the application of ZEM for data and model analyses at the LANL Chromium site. The ZEM framework will be released as open-source code and can be applied to any environmental management site. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Ion-chain sympathetic cooling and gate dynamics

Sympathetic cooling is a technique often employed to mitigate motional heating in trapped-ion quantum computers. However, choosing system parameters such as number of coolants and cooling duty cycle for optimal gate performance requires evaluating trade-offs between motional errors and other slower errors such as qubit dephasing. The optimal parameters depend on cooling power, heating rate, and ion spacing in a particular system. In this study, we aim to analyze best practices for sympathetic cooling of long chains of trapped ions using analytical and computational methods. We use a case study to show that optimal cooling performance is achieved when coolants are placed at the center of the chain and provide a perturbative upper bound on the cooling limit of a mode given a particular set of cooling parameters. In addition, using computational tools, we analyze the trade-off between the number of coolant ions in a chain and the center-of-mass mode heating rate. We also show that cooling as often as possible when running a circuit is optimal when the qubit coherence time is otherwise long. These results provide a roadmap for how to choose sympathetic cooling parameters to maximize circuit performance in trapped-ion quantum computers using long chains of ions.

Cooling & trapping↗

DOE OSTI2018

WebGIobe - A cloud-based geospatial analysis framework for interacting with climate data

While climate models have evolved over time to produce high fidelity and high resolution climate forecasts, visualization and analysis of the output of the model simulations has been limited, typically constrained to single dimensional charts for visualization and basic aggregate statistics for analytics. Same is true for the large troves of observational data available from meteorological stations all over the world. For richer understanding of climate and the impact of climate change, one needs computational tools that allow researchers, policymakers, and general public, to interact with the climate data. In this paper, we describe, webGlobe, a browser based GIS framework for interacting with climate data, and other datasets available in similar format. webGlobe is a unique resource that allows unprecedented access to climate data through a browser. The framework also allows for deploying machine learning based analytical applications on the climate data without putting computational burden on the client. Instead, webGlobe uses a client-server framework, where the server, deployed on a cloud infrastructure, allows for dynamic allocation of resources for running compute-intensive applications. The capabilities of the framework will be discussed in context of a use case: identifying extreme events from real and simulated climate data using a Gaussian process based change detection algorithm.

Sharma, Arun↗

DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗