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Results for “Directed evolution”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

High Throughput expression and characterization of laccases in Saccharomyces cerevisiae

Laccases are oxidative enzymes containing 4 conserved copper heteroatoms. Laccases catalyze cleavage of bonds in lignin using radical chemistry, yet their exact specificity for bonds (such as the β-O-4 or C-C) in lignin remains unknown and may vary with the diversity of laccases across fungi, plants and bacteria. Bond specificity may perhaps even vary for the same enzyme across different reaction conditions. Determining these differences has been difficult due to the fact that heterologous expression of soluble, active laccases has proven difficult. Here we describe the successful heterologous expression of functional laccases in two strains of Saccharomyces cerevisiae, including one we genetically modified with CRISPR. We phylogenically map the enzymes that we successfully expressed, compared to those that did not express. We also describe differences protein sequence differences and pH and temperature profiles and their ability to functionally express, leading to a potential future screening platform for directed evolution of laccases and other ligninolytic enzymes such as peroxidases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Enzyme Engineering for Expanded Product Scope (CRADA Final Report)

As part of the Cyclotron Road program, Aralez Inc. investigated methods for producing chemicals sustainably, with a particular focus on engineering enzymes to make novel chemical products or accept new substrates that aren’t found in nature. We used directed evolution and other protein engineering techniques to create enzymes that perform abiological chemistry or make chemical products through a non-natural synthetic route. This work was an important step towards increasing the scope of compounds that can be manufactured in a sustainable fashion, which in turn will alleviate the high energy consumption, costly emissions, and waste that are hallmarks of current methods in chemical manufacturing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The moderately defficient enzyme: Catalysis-related damage in vivo and its repair

Enzymes have in vivo lifespans. Analysis of lifespans – lifetime totals of catalytic turnovers – suggests that non-survivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme lifespan might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements is lacking: there are too few measurements of in vivo lifespan, and existing information on the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach to identify, predict, and validate instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability, and could change thinking about which enzymes die young in vivo, and why.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The moderately defficient enzyme: Catalysis-related damage in vivo and its repair

Enzymes have in vivo lifespans. Analysis of lifespans – lifetime totals of catalytic turnovers – suggests that non-survivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme lifespan might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements is lacking: there are too few measurements of in vivo lifespan, and existing information on the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach to identify, predict, and validate instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability, and could change thinking about which enzymes die young in vivo, and why.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

In situ observation of short- and long-timescale material property evolution under extreme conditions

Directly observing the evolution of material performance in-situ under extreme conditions remains a great challenge. Emergent behavior, such as the transition from incubation to steady state void swelling, is often difficult to capture in these conditions. To fill this gap, transient grating spectroscopy (TGS) has been used to collect multi-property information in-situ under high temperature exposure to ion beam irradiation. This all-optical method returns elastic and thermal transport properties with second-scale time resolution. Here, recent work using this methodology to track the evolution of Ni-based solid-solution alloys using the in situ ion irradiation TGS (I3TGS) beamline will be described. Tracking material property evolution during long exposure times (hours) provides a clear indication of when void swelling has occurred. On short timescales (seconds to minutes), observing rapid changes in thermoelastic properties as defect generation is initiated allows a unique window into bulk transient defect populations which are otherwise difficult to observe.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Direct observation of kink evolution due to Hund’s coupling on approach to metal-insulator transition in NiS 2- x Se x

Understanding characteristic energy scales is a fundamentally important issue in the study of strongly correlated systems. In multiband systems, an energy scale is affected not only by the effective Coulomb interaction but also by the Hund’s coupling. Direct observation of such energy scale has been elusive so far in spite of extensive studies. Here, we report the observation of a kink structure in the low energy dispersion of NiS 2- x Se x and its characteristic evolution with x , by using angle resolved photoemission spectroscopy. Dynamical mean field theory calculation combined with density functional theory confirms that this kink originates from Hund’s coupling. We find that the abrupt deviation from the Fermi liquid behavior in the electron self-energy results in the kink feature at low energy scale and that the kink is directly related to the coherence-incoherence crossover temperature scale. Our results mark the direct observation of the evolution of the characteristic temperature scale via kink features in the spectral function, which is the hallmark of Hund’s physics in the multiorbital system.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.

Biosensors↗
DOE OSTI2025

Understanding Structural and Compositional Evolution during NMC Cathode Direct Recycling via Solid-State NMR

Recycling end-of-life lithium-ion batteries (LIBs) to recover high-value cathode materials such as LiNixMnyCozO2 (NMC) is driven by economical, geopolitical, and sustainability needs. There has been recent interest in direct recycling methods to improve efficiency and recovery of materials, including ionothermal, hydothermal, solid-state, or redox mediator methods. In conjunction with recycling process development, detailed structural characterization is necessary in order to understand the mechanisms and efficacy of cathode recycling steps. Solid-state nuclear magnetic resonance (NMR) spectroscopy is a unique tool that can probe Li coordination, bulk and surface environments, and transition metal ordering in recycled and upcycled NMC cathodes. Here, 6,7Li, 1H, and 19F NMR spectroscopy to probe structural and compositional changes as well as surface impurities that may form during each step in NMC direct recycling is utilized. During relithiation, Li reinsertion into the NMC lattice is observed. During upcycling, where the goal is to increase the Ni content in the NMC, incorporation of Ni-rich phases into the bulk Li environment is observed. Surface impurities formed during processing were also identified. These studies provide valuable information for optimizing recycling processes to reach targeted cathode composition and structure that can enable electrochemical performance comparable to or better than pristine materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Full 3D Kinetic Modeling and Quantification of Positive Streamer Evolution in an Azimuthally Swept Pin-to-Plane Wedge Geometry

Cathode-directed streamer evolution in near atmospheric air is modeled in 3D pin-to-plane geometries using a 3D kinetic Particle-In-Cell (PIC) code that simulates particle-particle collisions via the Direct Simulation Monte Carlo (DSMC) method. Due to the computational challenges associated with a complete 360° volumetric domain, a practical alternative was achieved using a wedge domain and a range of azimuthal angles was explored (5°, 15°, 30°, and 45°) to study possible effects on the streamer growth and propagation due to the finite wedge angle. A DC voltage of 6 kV is administered to a hemispherical anode of radius 100 μm, with a planar cathode held at ground potential, generating an over-volted state with an electric field of 4 MV/m across a 1500 μm gap. The domain is seeded with an initial ion and electron density of 10 18 m -3 at 1 eV temperature confined to a spherical region of radius 100 μm centered at the tip of the anode. The air chemistry model [1] includes standard Townsend breakdown mechanisms (electron-neutral elastic, excitation, ionization, attachment, and detachment collision chemistry and secondary electron emission) as well as streamer mechanisms (photoionization and ion-neutral collisions) via tracking excited state neutrals which can then either quench via collisions or spontaneously emit a photon based on specific Einstein-A coefficients [2, 3]. In this work, positive streamer dynamics are formally quantified for each wedge angle in terms of electron velocity and density as temporal functions of coordinates r, Φ, and z. Applying a random plasma seed for each simulation, particles of interest are tracked with near femtosecond temporal resolution out to 1.4 ns and spatially binned. This process is repeated six times and results are averaged. Prior 2D studies have shown that the reduced electric field, E/n, can significantly impact streamer evolution [4]. We extend the analysis to 3D wedge geometries, to limit computational costs, and examine the wedge angle’s effect on streamer branching, propagation, and velocity. Results indicate that the smallest wedge angle that produced an acceptably converged solution is 30°. The potential effects that a mesh, when under-resolved with respect to the Debye length, can impart on streamer dynamics and numerical heating were not investigated, and we explicitly state here that the smallest cell size was approximately 10 times the minimum λ D in the streamer channel at late times. This constraint on cell size was the result of computational limitations on total mesh count.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Direct numerical simulation of hypersonic turbulent boundary layers: effect of spatial evolution and Reynolds number

Direct numerical simulations (DNS) are performed to investigate the spatial evolution of flat-plate zero-pressure-gradient turbulent boundary layers over long streamwise domains ( >300δ i , with δ i the inflow boundary-layer thickness) at three different Mach numbers, 2.5, 4.9 and 10.9, with the surface temperatures ranging from quasiadiabatic to highly cooled conditions. The settlement of turbulence statistics into a fully developed equilibrium state of the turbulent boundary layer has been carefully monitored, either based on the satisfaction of the von Kármán integral equation or by comparing runs with different inflow turbulence generation techniques. The generated DNS database is used to characterize the streamwise evolution of multiple important variables in the high-Mach-number, cold-wall regime, including the skin friction, the Reynolds analogy factor, the shape factor, the Reynolds stresses, and the fluctuating wall quantities. The data confirm the validity of many classic and newer compressibility transformations at moderately high Reynolds numbers (up to friction Reynolds number Re τ ≈1200 ) and show that, with proper scaling, the sizes of the near-wall streaks and superstructures are insensitive to the Mach number and wall cooling conditions. The strong wall cooling in the hypersonic cold-wall case is found to cause a significant increase in the size of the near-wall turbulence eddies (relative to the boundary-layer thickness), which leads to a reduced-scale separation between the large and small turbulence scales, and in turn to a lack of an outer peak in the spanwise spectra of the streamwise velocity in the logarithmic region.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Single-Step Direct Laser Writing of Multimetal Oxygen Evolution Catalysts from Liquid Precursors

We investigate a laser direct-write method to synthesize and deposit metastable, mixed transition metal oxides and evaluate their performance as oxygen evolution reaction catalysts. This laser processing method enabled the rapid synthesis of diverse heterogeneous alloy and oxide catalysts directly from cost-effective solution precursors, including catalysts with a high density of nanocrystalline metal alloy inclusions within an amorphous oxide matrix. The nanoscale heterogenous structures of the synthesized catalysts were consistent with reactive force-field Monte Carlo calculations. By evaluating the impact of varying transition metal oxide composition ratios, we created a stable Fe 0.63 Co 0.19 Ni 0.18 O x /C catalyst with a Tafel slope of 38.23 mV dec -1 and overpotential of 247 mV, a performance similar to that of IrO 2 . Synthesized Fe 0.63 Co 0.19 Ni 0.18 O x /C and Fe 0.14 Co 0.46 Ni 0.40 O x /C catalysts were experimentally compared in terms of catalytic performance and structural characteristics to determine that higher iron content and a less crystalline structure in the secondary matrix decreases the charge transfer resistance and thus is beneficial for electrocatalytic activity. Furthermore, this conclusion is supported by density-functional theory calculations showing distorted active sites in ternary metal catalysts are key for lowering overpotentials for the oxygen evolution reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus

Cytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but there are no clinically licensed vaccines to prevent infection, in part due to challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Surprisingly, we found that a single amino acid heavy chain mutation A33N, which was an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the non-neutralizing UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution in a single donor and lay a foundation for using this B cell-lineage directed approach for the design of next-generation CMV vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Grain Structure Evolution in Fe-6Si During Directed Energy Deposition

The purpose of this study is to explore the effect of additive manufacturing (AM) process variables on the grain structure of Fe-6Si, a soft-magnetic alloy used in electrical machine and grid applications. Samples were fabricated with laser engineered net shaping (LENS) with varying inter-pass timing and numbers of unidirectional passes. Here the results show that the grain structure was affected by both solidification and solid-state grain growth mechanisms. A model of the LENS process suggests that, although shorter inter-pass times encourage greater nucleation of new grains and therefore grain refinement during solidification, these conditions also help maintain high solid-state temperatures that allow for grain boundary motion to keep pace with the build rate. Grains formed under these conditions may span multiple layers, and the high-temperature gradient promotes directional growth. This new understanding of these microstructure evolution mechanisms will aid in using process conditions to control the competition between solidification and solid-state grain growth to create grain structures that may not be possible with conventional processing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Measurements of the Five-Dimensional Phase Space Distribution of an Intense Ion Beam

No simulation of intense beam transport has accurately reproduced measurements at the level of beam halo. One potential explanation of this discrepancy is a lack of knowledge of the initial distribution of particles in six-dimensional (6D) phase space. A direct 6D measurement of an ion beam was recently performed at the Spallation Neutron Source (SNS) Beam Test Facility (BTF), revealing nonlinear transverse-longitudinal correlations in the beam core that affect downstream evolution. Unfortunately, direct 6D measurements are limited in resolution and dynamic range; here, we discuss the use of three slits and one screen to measure a 5D projection of the 6D phase space distribution, overcoming these limitations at the cost of one dimension. We examine the measured 5D distribution before and after transport through the BTF and compare to particle-in-cell simulations. We also discuss the possibility of reconstructing the 6D distribution from 5D and 4D projections.

Hoover, Austin↗
DOE OSTI2021

Anisotropy evolution of elastomeric foams during uniaxial compression measured via in-situ X-ray computed tomography

We have characterized the three-dimensional evolution of microstructural anisotropy of a family of elastomeric foams during uniaxial compression via in-situ X-ray computed tomography. Flexible polyurethane foam specimens with densities of 136, 160 and 240 kg/m 3 were compressed in uniaxial stress tests both parallel and perpendicular to the foam rise direction, to engineering strains exceeding 70%. The uncompressed microstructures show slightly elongated ellipsoidal pores, with elongation aligned parallel to the foam rise direction. The evolution of this microstructural anisotropy during deformation is quantified based on the autocorrelation of the image intensity, and verified via the mean intercept length as well as the shape of individual pores. Trends are consistent across all three methods. In the rise direction, the material remains transversely anisotropic throughout compression. Anisotropy initially decreases with compression, reaches a minimum, then increases up to large strains, followed by a small decrease in anisotropy at the largest strains as pores collapse. Compression perpendicular to the foam rise direction induces secondary anisotropy with respect to the compression axis, in addition to primary anisotropy associated with the foam rise direction. In contrast to compression in the rise direction, primary anisotropy initially increases with compression, and shows a slight decrease at large strains. These surprising non-monotonic trends and qualitative differences in rise and transverse loading are explained based on the compression of initially ellipsoidal pores. Microstructural anisotropy trends reflect macroscopic stress-strain and lateral strain response. These findings provide novel quantitative connections between three-dimensional microstructure and anisotropy in moderate density polymer foams up to large deformation, with important implications for understanding complex three-dimensional states of deformation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Revealing Coexisting Cu0–Cu+ Sites in Cu3N Nanoensembles for Selective CC Coupling of CO2 Under Low Overpotential

To address a long-existing debate on what copper species are responsible for efficient CC coupling, especially ethanol formation, in electrochemical CO2 reduction reaction, herein, a comprehensive study using Cu3N nanocubes with a uniform size and shape, alongside a single crystalline phase is reported. The Cu3N nanoensemble electrode has a remarkable Faradaic efficiency (FE) of 64% for ethanol production at a relatively low potential of -0.6 V versus reversible hydrogen electrode. Through in-operando X-ray absorption spectroscopy study, a dynamic phase evolution that directly correlates with changes in FE across varying applied potentials is observed. Notably, the nanoensemble with a composition of ≈71% Cu+ and 29% Cu0 is identified as being selective for ethanol formation at the low overpotential. Conversely, a predominantly metallic Cu phase formed at potentials more negative than -0.6 V favors the hydrogen evolution reaction. Density functional theory calculations at the Cu3N-Cu interface substantiate that the coexistence of Cu0-Cu+ not only energetically favors the ethanol reaction pathway but also destabilizes the intermediates for ethylene pathway.

*CH-CHO as an intermediate for ethanol production↗
DOE OSTI2026

Which way does the dendrite grow? Competition among epitaxy, preferred growth direction, and thermal gradients in powder bed fusion additive manufacturing

The as-processed microstructure of metal alloy parts manufactured through laser powder bed fusion (LPBF) is heavily derived from the cellular dendritic solidification. The growth direction of dendrites within the melt pool is determined through competition among epitaxial growth, preferred growth directions, and maximum thermal gradients. However, the dominant factor and the specific role of each in developing melt pool microstructures remain unknown. Here, in this study, we performed single laser track scans on an SS316L single crystal substrate and combined experimental characterization of microstructure and crystal orientations with Computational Fluid Dynamics simulations of thermal gradients to evaluate the role of each factor in determining dendritic growth direction and evolution. Our results reveal that epitaxial growth dominates microstructure development by preferentially growing along a single 〈100〉 variant of the single crystal substrate adjacent to the melt pool boundary. Under LPBF’s highly curved and rapidly evolving thermal field, this preferential dendrite variant selection and its continued growth from the melt pool boundary to the centerline are governed by the local temperature gradient magnitude at the solid-liquid interface, rather than by the instantaneous maximum temperature gradient direction alone. Using these findings, we successfully predict changes in the dendrite growth direction with changing laser scan direction on a single crystal substrate, and show that the geometric melt pool centerline can deviate from the microstructural centerline because asymmetric local temperature gradient magnitudes transiently limit growth, resulting in different dendrite travel distances on each side of the melt pool.

36 MATERIALS SCIENCE↗