Results for “mechanical engineering” — Page 63

DOE OSTI2023

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗

DOE OSTI2022

Coalescence dynamics of prismatic dislocation loops due to vacancy supersaturation

Recovery processes in metals with a high defect concentration are at the heart of a structural alloy's usability in engineering applications. However, such processes take place via nonconservative mechanisms mediated by point defect diffusion and are governed by their interactions with the underlying microstructure. Indeed, one of the main challenges in studying recovery processes is their intrinsic multiscale complexity, which often negates the direct use of experimental techniques. Here, in this Research Letter, we study the mechanism of dislocation loop coalescence in metals by simulating the interaction dynamics between vacancies and prismatic loops using a stochastic framework that seamlessly bridges point defect kinetics with dislocation mechanics. Our simulations reveal two fundamental discoveries: first, that climb processes are governed by local fluctuations that are not captured by continuum elastodiffusion models, and, second, that prismatic loops create internal traps for vacancies, leading to the formation of rings around the perimeter of the loops that affect how coalescence takes place. Our results show an excellent agreement with in situ experimental observations of loop coalescence in Fe under irradiation.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Code for the manuscript "Mori-Zwanzig Modal Decomposition"

We would like to create an open source repository in LANL's github on code written in Julia, in which we implement and extend the data-driven Mori-Zwanzig method for extracting large-scale spatio-temporal structures from data, which we call MZMD. This method is an extension of Dynamic Mode Decomposition (DMD) in which Mori-Zwanzig memory kernels are included into the associated companion matrix. In the code we would like to release, we apply MZMD to a flow over a cylinder with Reynolds number 100 rather than the much larger data set used in the associated manuscript. DMD is used extensively in the fluid dynamics community mainly for extracting large scale spatio-temporal structures (patters) from flow data. This is useful for understanding the key mechanisms that generate certain complex dynamical process relevant in engineering design. In MZMD, we improve upon DMD by adding the Mori-Zwanzig memory kernels, and show this improvement is especially important in strongly nonlinear regions of the flow.

Woodward, Michael↗

DOE OSTI2022

Achromat Design for Multi-Pulse Test Line

This note describes the design of a 90° achromatic bend on DARHT Axis 2 to support multi-pulse target studies. The achromatic bend consists of two 45° dipole magnets with a focusing quadrupole centered between the dipoles. The optical design of the achromat is described followed by a discussion of the sensitivity to space charge and variations in the beam energy. The preliminary design of the magnets is then described with a description of the electro-mechanical parameters.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego User Manual (V.5.6)

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego Theory Manual - Version 5.8

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego User Manual - Version 5.8

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego Verification Manual - Version 5.8

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego Verification Manual (V.5.10)

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2022

SIERRA Low Mach Module: Fuego Theory Manual (V.5.10)

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

DOE OSTI2024

DECOVALEX-2023: Task F2 Salt Final Report

The subject of Task F of DECOVALEX-2023 concerns performance assessment modelling of radioactive waste disposal in deep mined repositories. The primary objectives of Task F are to build confidence in the models, methods, and software used for performance assessment (PA) of deep geologic nuclear waste repositories, and/or to bring to the fore additional research and development needed to improve PA methodologies. In Task F2- (salt), these objectives have been accomplished through staged development and comparison of the models and methods used by participating teams in their PA frameworks. Coupled-process submodels and deterministic simulations of the entire PA model for a reference scenario for waste disposal in domal salt have been conducted. The task specification has been updated continuously since the initiation of the project to reflect the staged development of the conceptual repository model and performance metrics. Thermal, hydrological, mechanical, and chemical properties of individual components of the engineered and natural system were chosen for relevance by participating teams. The salt reference case system was characterized using data and measurements collected at relevant underground research laboratories (URLs), field sites, and simulation results from teams with specialized modelling capability. Participating teams made a wide range of model assumptions from compartmentalized networks to full 3D models of the salt formation. No single contributed model includes full-fidelity representation of all the features, events, and processes (FEPs) detailed in the task specification, but almost all features and processes are represented in at least one model. Despite differences in the modelling strategies developed by participating teams, all models indicate that salt compaction and radionuclide diffusion are key processes in the repository, and for the FEPs and model scenario considered, little of the disposed radionuclides will migrate beyond the repository seal over the 100,000 year simulations. In general, the model output quantities have the largest differences over the short term and near the waste. The models tend to be more similar further from waste and at later time. Disparities between the models are believed to be due to differing simplifications from the task specification, some of which are chosen simplifications to reduce complexity, and some are restrictions imposed by the modelling tools. A second round of this task has been accepted for DECOVALEX-2027 in conjunction with Task F1 on crystalline PA modelling. The future round includes waste package heating, improved modelling of salt creep closure, additional comparisons of coupled-process sub-models, and the impact of repository engineering design on radionuclide migration in the repository. Participants will also propose and finalize a set of uncertain inputs for the reference case simulations, propagate these uncertainties in a set of realizations, and conduct sensitivity analyses on the simulation results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Probing Light-Dependent Regulation of the Calvin Cycle Using a Multi-Omics Approach

Photoautotrophic microorganisms are increasingly explored for the conversion of atmospheric carbon dioxide into biomass and valuable products. The Calvin-Benson-Bassham (CBB) cycle is the primary metabolic pathway for net CO 2 fixation within oxygenic photosynthetic organisms. The cyanobacteria, Synechocystissp. PCC 6803, is a model organism for the study of photosynthesis and a platform for many metabolic engineering efforts. The CBB cycle is regulated by complex mechanisms including enzymatic abundance, intracellular metabolite concentrations, energetic cofactors and post-translational enzymatic modifications that depend on the external conditions such as the intensity and quality of light. However, the extent to which each of these mechanisms play a role under different light intensities remains unclear. In this work, we conducted non-targeted proteomics in tandem with isotopically non-stationary metabolic flux analysis (INST-MFA) at four different light intensities to determine the extent to which fluxes within the CBB cycle are controlled by enzymatic abundance. The correlation between specific enzyme abundances and their corresponding reaction fluxes is examined, revealing several enzymes with uncorrelated enzyme abundance and their corresponding flux, suggesting flux regulation by mechanisms other than enzyme abundance. Additionally, the kinetics of 13 C labeling of CBB cycle intermediates and estimated inactive pool sizes varied significantly as a function of light intensity suggesting the presence of metabolite channeling, an additional method of flux regulation. These results highlight the importance of the diverse methods of regulation of CBB enzyme activity as a function of light intensity, and highlights the importance of considering these effects in future kinetic models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Light-inducible protein degradation in E. coli with the LOVdeg tag

Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Light-inducible protein degradation in E. coli with the LOVdeg tag

Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.

Tague, Nathan (ORCID:0000000281146700)↗

DOE OSTI2021

Spectroscopic Signatures of MQ-Resins in Silicone Elastomers

Polysiloxane elastomers have a large application space due to their versatile cross-linking chemistry and highly tunable physical and mechanical properties. One approach for improving the mechanical integrity of commercial polysiloxane “silicone” elastomers while maintaining their optical transparency is the addition of small, silicone-resin molecules to the network. However, both the poly(dimethylsiloxane) (PDMS) network and the silicone-resin particles have an amorphous structure and complex chemistry, which makes the characterization of their structural properties and segmental network dynamics difficult. Here, we report the synthesis and characterization of a series of model silicone networks modified with a specific class of silicone-resin known as MQ-resin using Raman and advanced nuclear magnetic resonance (NMR) spectroscopy methods. Raman spectroscopy was successfully used to quantify the contribution of the MQ-resin to the network, to determine the type of MQ-resin present in the network, and to investigate the completeness of the network cross-linking reaction. Furthermore, solid-state and 1H double-quantum (DQ) NMR spectroscopies were used not only as a detection method for the MQ-resins but also to quantify changes in the segmental dynamics of the network as a function of MQ-resin concentration. The combination of Raman and NMR spectroscopies describes a series of samples where the MQ-resin particles and PDMS chains maintain their independent segmental dynamics up to high concentrations of MQ-resins (40–50% MQ), where the physical properties of the resin dominate the physical properties of the overall network. The results from our spectroscopic analyses are consistent with the results from macroscopic characterization techniques such as solvent uptake and mechanical testing. The spectroscopic insights into the structure–property relationships of PDMS-MQ composites presented in this study are a valuable tool not only for the synthesis and reverse engineering of future generations of commercial silicone elastomers but also for understanding the mechanisms of aging and degradation over the material lifetime.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Computationally efficient evaluation of optimum homogeneous charge compression ignition operating range with accelerated multizone engine cycle simulation

The very intensive calculations necessary to define a performance map requiring evaluation of over a hundred individual operating points can be efficiently conducted with accelerated multizone for engine cycle simulation, leading to a definition of regions of acceptable and optimum homogeneous charge compression ignition operation. Accelerated multizone for engine cycle simulation has the virtue of enabling accurate evaluation of many operating conditions based on thermal stratification data from a single fluid mechanics run at motored conditions. This is possible because thermal stratification is more sensitive to engine geometry than to operating conditions. In this article, accuracy of accelerated multizone for engine cycle simulation is demonstrated by comparison with experimental data for iso-octane homogeneous charge compression ignition operation over a broad range of lean equivalence ratios (0.14–0.28). The validated accelerated multizone for engine cycle simulation model is then applied to generating a performance map for an engine controlled by appropriately adjusting equivalence ratio and internal exhaust gas recirculation. Regions of acceptable and optimum combustion are identified. It is finally demonstrated that while indicated mean effective pressure remains low for optimum homogeneous charge compression ignition operation (1–4 bar), this is sufficient for a large fraction of typical driving in light-duty vehicles. Much driving including idle can therefore be done in homogeneous charge compression ignition mode at high efficiency and low (essentially zero) NOx and particulate matter emissions.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2025

Durable, pure water–fed, anion-exchange membrane electrolyzers through interphase engineering

Anion-exchange membrane water electrolyzers (AEMWEs) promise scalable, low-cost hydrogen production but are limited by the electrochemical instability of their anode ionomers. We report interphase engineering using inorganic-containing molecular additives that coassemble with ionomer, enabling pure water-fed AEMWEs to operate with a degradation rate <0.5 millivolt per hour at 2.0 amperes per square centimeter and 70°C-a >20-fold durability improvement. Analysis of different additives and ionomers shows that the stabilization mechanism involves cross-links between metal oxo/hydroxo oligomers and ionomers. Under operation, the inorganic additive enriches, forming an interphase near the water-oxidation catalyst that passivates the anode ionomer against continuous degradation while maintaining mechanical integrity and hydroxide conductivity. This additive-based interphase-engineering strategy provides a path to durable AEMWEs that operate without supporting electrolytes and is adaptable across diverse catalysts and ionomers for electrochemical technologies.

Hou, Shujin↗