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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Magnetic domain engineering in SrRuO3 thin films

Abstract Magnetic domain engineering in ferromagnetic thin films is a very important route toward the rational design of spintronics and memory devices. Although the magnetic domain formation has been extensively studied, artificial control of magnetic domain remains challenging. Here, we present the control of magnetic domain formation in paradigmatic SrRuO 3 /SrTiO 3 heterostructures via structural domain engineering. The formation of structural twin domains in SrRuO 3 films can be well controlled by breaking the SrTiO 3 substrate symmetry through engineering miscut direction. The combination of x-ray diffraction analysis of structural twin domains and magnetic imaging of reversal process demonstrates a one-to-one correspondence between structural domains and magnetic domains, which results in multi-step magnetization switching and anomalous Hall effect in films with twin domains. Our work sheds light on the control of the magnetic domain formation via structural domain engineering, which will pave a path toward desired properties and devices applications.

Materials Science↗
DOE OSTI2014

Formation mechanism of chalcogenide nanocrystals confined inside genetically engineered virus-like particles

Engineered virus-like particles (VLP) are attractive for fabricating nanostructured materials for applications in diverse areas such as catalysis, drug delivery, biomedicine, composites, etc. Basic understanding of the interaction between the inorganic guest and biomolecular host is thus important for the controlled synthesis of inorganic nanoparticles inside VLP and rational assembly of ordered VLP-based hierarchical nanostructures. We have investigated in detail the formation mechanism and growth kinetics of semiconducting nanocrystals confined inside genetically engineered bacteriophage P22 VLP using semiconducting CdS as a prototypical example. The selective nucleation and growth of CdS at the engineered sites is found to be uniform during the early stage, followed by a more stochastic growth process. Furthermore, kinetic studies reveal that the presence of an engineered biotemplate helps in significantly retarding the reaction rate. These findings provide guidance for the controlled synthesis of a wide range of other inorganic materials confined inside VLP, and are of practical importance for the rational design of VLP-based hierarchical nanostuctures.

PHOTOCATALYSIS↗
DOE OSTI2014

More bang for your buck: Super-adiabatic quantum engines

The practical untenability of the quasi-static assumption makes any realistic engine intrinsically irreversible and its operating time finite, thus implying friction effects at short cycle times. An important technological goal is thus the design of maximally efficient engines working at the maximum possible power. We show that, by utilising shortcuts to adiabaticity in a quantum engine cycle, one can engineer a thermodynamic cycle working at finite power and zero friction. Our findings are illustrated using a harmonic oscillator undergoing a quantum Otto cycle.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Molecular engineering of fluorescein dyes as complementary absorbers in dye co-sensitized solar cells

Fluorescein dye derivatives exhibit extended optical absorption up to 500 nm, rendering these compounds suitable as co-absorbers in dye-sensitized solar cells (DSCs). A molecular engineering approach is presented, which embraces this intrinsic optical attribute of fluoresceins, while modifying the dye chemistry to enhance their light harvesting efficiency, in order to effectively tailor them for DSC applications. This approach first realizes relationships between the molecular structure and the optoelectronic properties for a series of five a priori known (parent) fluorescein dyes: 5-carboxyfluorescein (1), a mixture of m -carboxyfluorescein where m = 5 or 6 (2), 5-carboxyfluorescein diacetate (3), 6-carboxyfluorescein diacetate (4), a mixture of n -carboxy-2',7'-dichlorofluorescein diacetate where n = 5 or 6 (5). The first step in this approach combines, where available, experimental and computational methods so that electronic structure calculations can also be validated for representative fluorescein dyes. Such calculations can then be used reliably to predict the structure and properties of fluorescein dyes for cases where experimental data are lacking. Structure-function relationships established from this initial step inform the selection of parent dye 1 that is taken forward to the second step in molecular engineering: in silico chemical derivation to re-functionalize 1 for DSC applications. For this purpose, computational calculations are used to extend the charge conjugation in 1 between its donor and acceptor moieties. These structural modifications result in a bathochromic shift of the lowest excitation by ~1.3-1.9 eV (100-170 nm), making the dye optically absorb in the visible region. Further calculations on dye molecules adsorbed onto the surface of a TiO 2 cluster are used to investigate the dye sensitization behavior via dye adsorption energies and anchoring modes. The results of this theoretical investigation lead to two molecularly engineered fluoresceins being proposed to act as co-sensitizers together with a rhodamine dye. This combination of three dyes ensures chemical compatibility, panchromatic absorption, and restores optical absorption dipping otherwise observed in a DSC device at ~350-400 nm owing to the I-/I- 3 electrolyte. Altogether, the results of this study demonstrate that molecular engineering can be used to identify suitable chemical modifications for organic dyes with improved light harvesting properties for photovoltaic applications.

14 SOLAR ENERGY↗
DOE OSTI2023

Enhanced microbial production of protocatechuate from engineered sorghum using an integrated feedstock-to-product conversion technology

Building a stronger bioeconomy requires production capabilities that are largely generated through microbial genetic engineering. Plant feedstocks can additionally be genetically engineered to generate desirable feedstock traits and provide precursors for direct microbial conversion into desired products. The oleaginous yeast Rhodosporidium toruloides is a promising organism for this type of conversion as it can grow on a wide range of deconstructed biomass and consume a variety of carbon sources. Here, we leveraged R. toruloides native p-coumaric acid consumption pathway to accumulate protocatechuate (PCA) from 4-hydroxybenzoate (4HBA) released from a sorghum feedstock line genetically engineered to overproduce 4HBA. We did so by generating and evaluating an R. toruloides strain that accumulates PCA, RSΔ12623. We then show that at two scales a cholinium lysinate pretreatment with enzymatic saccharification successfully extracts 95% of the 4HBA from the engineered sorghum biomass while producing deconstructed lignin that can be more efficiently depolymerized in a subsequent thermochemical reaction. We also demonstrate that strain RSΔ12623 can convert more than 95% of 4HBA to PCA while consuming >95% of the glucose and >80% of the xylose present in sorghum hydrolysates. Finally, to evaluate the scalability of such fermentations, we conducted the conversion of 4HBA to PCA in a 2 L bioreactor under controlled conditions. Importantly, this work demonstrates the potential of purposefully producing aromatic precursors in planta that can be liberated during biomass deconstruction for direct microbial conversion to desirable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Research Update: Interface-engineered oxygen octahedral tilts in perovskite oxide heterostructures

Interface engineering of structural distortions is a key for exploring the functional properties of oxide heterostructures and superlattices. In this paper, we report on our comprehensive investigations of oxygen octahedral distortions at the heterointerface between perovskite oxides SrRuO{sub 3} and BaTiO{sub 3} on GdScO{sub 3} substrates and of the influences of the interfacially engineered distortions on the magneto-transport properties of the SrRuO{sub 3} layer. Our state-of-the-art annular bright-field imaging in aberration-corrected scanning transmission electron microscopy revealed that the RuO{sub 6} octahedral distortions in the SrRuO{sub 3} layer have strong dependence on the stacking order of the SrRuO{sub 3} and BaTiO{sub 3} layers on the substrate. This can be attributed to the difference in the interfacial octahedral connections. We also found that the stacking order of the oxide layers has a strong impact on the magneto-transport properties, allowing for control of the magnetic anisotropy of the SrRuO{sub 3} layer through interface engineering. Our results demonstrate the significance of the interface engineering of the octahedral distortions on the structural and physical properties of perovskite oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2015

The materials used in bone tissue engineering

Bone tissue engineering looking for an alternative solution to the problem of skeletal injuries. The method is based on the creation of tissue engineered bone tissue equivalent with stem cells, osteogenic factors, and scaffolds - the carriers of these cells. For production of tissue engineered bone equivalent is advisable to create scaffolds similar in composition to natural extracellular matrix of the bone. This will provide optimal conditions for the cells, and produce favorable physico-mechanical properties of the final construction. This review article gives an analysis of the most promising materials for the manufacture of cell scaffolds. Biodegradable synthetic polymers are the basis for the scaffold, but it alone cannot provide adequate physical and mechanical properties of the construction, and favorable conditions for the cells. Addition of natural polymers improves the strength characteristics and bioactivity of constructions. Of the inorganic compounds, to create cell scaffolds the most widely used calcium phosphates, which give the structure adequate stiffness and significantly increase its osteoinductive capacity. Signaling molecules do not affect the physico-mechanical properties of the scaffold, but beneficial effect is on the processes of adhesion, proliferation and differentiation of cells. Biodegradation of the materials will help to fulfill the main task of bone tissue engineering - the ability to replace synthetic construct by natural tissues that will restore the original anatomical integrity of the bone.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Effective work function engineering for a TiN/XO(X = La, Zr, Al)/SiO{sub 2} stack structures

In this study, we demonstrated that work function engineering is possible over a wide range (+200 mV to −430 mV) in a TiN/XO (X = La, Zr, or Al)/SiO{sub 2} stack structures. From ab initio simulations, we selected the optimal material for the work function engineering. The work function engineering mechanism was described by metal diffusion into the TiN film and silicate formation in the TiN/SiO{sub 2} interface. The metal doping and the silicate formation were confirmed by transmission electron microscopy and energy dispersive spectroscopy line profiling, respectively. In addition, the amount of doped metal in the TiN film depended on the thickness of the insertion layer XO. From the work function engineering technique, which can control a variety of threshold voltages (Vth), an improvement in transistors with different V{sub th} values in the TiN/XO/SiO{sub 2} stack structures is expected.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Entanglement engineering of optomechanical systems by reinforcement learning

Entanglement is fundamental to quantum information science and technology, yet controlling and manipulating entanglement—so-called entanglement engineering—for arbitrary quantum systems remains a formidable challenge. There are two difficulties: the fragility of quantum entanglement and its experimental characterization. We develop a model-free deep reinforcement-learning (RL) approach to entanglement engineering, in which feedback control together with weak continuous measurement and partial state observation is exploited to generate and maintain desired entanglement. We employ quantum optomechanical systems with linear or nonlinear photon–phonon interactions to demonstrate the workings of our machine-learning-based entanglement engineering protocol. In particular, the RL agent sequentially interacts with one or multiple parallel quantum optomechanical environments, collects trajectories, and updates the policy to maximize the accumulated reward to create and stabilize quantum entanglement over an arbitrary amount of time. The machine-learning-based model-free control principle is applicable to the entanglement engineering of experimental quantum systems in general.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels

Engineered antibody fragments (Fabs) have made major impacts on structural biology research, particularly to aid structural determination of membrane proteins. Nonetheless, Fabs generated by traditional monoclonal technology suffer from challenges of routine production and storage. Starting from the known IgG paratopes of an antibody that binds to the “turret loop” of the KcsA K+ channel, we engineered a synthetic Fab (sFab) based upon the highly stable Herceptin Fab scaffold, which can be recombinantly expressed in Escherichia coli and purified with single-step affinity chromatography. This synthetic Fab was used as a crystallization chaperone to obtain crystals of the KcsA channel that diffracted to a resolution comparable to that from the parent Fab. Furthermore, we show that the turret loop can be grafted into the unrelated voltage-gated Kv1.2–Kv2.1 channel and still strongly bind the engineered sFab, in support of the loop grafting strategy. Macroscopic electrophysiology recordings show that the sFab affects the activation and conductance of the chimeric voltage-gated channel. These results suggest that straightforward engineering of antibodies using recombinant formats can facilitate the rapid and scalable production of Fabs as structural biology tools and functional probes. The impact of this approach is expanded significantly based on the potential portability of the turret loop to a myriad of other K+ channels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

HYPERACCRETING BLACK HOLE AS GAMMA-RAY BURST CENTRAL ENGINE. I. BARYON LOADING IN GAMMA-RAY BURST JETS

A hyperaccreting stellar-mass black hole has been long speculated as the best candidate for the central engine of gamma-ray bursts (GRBs). Recent rich observations of GRBs by space missions such as Swift and Fermi pose new constraints on GRB central engine models. In this paper, we study the baryon-loading processes of a GRB jet launched from a black hole central engine. We consider a relativistic jet powered by {nu} {nu}-bar -annihilation or by the Blandford-Znajek (BZ) mechanism. We consider baryon loading from a neutrino-driven wind launched from a neutrino-cooling-dominated accretion flow. For a magnetically dominated BZ jet, we consider neutron drifting from the magnetic wall surrounding the jet and subsequent positron capture and proton-neutron inelastic collisions. The minimum baryon loads in both types of jet are calculated. We find that in both cases a more luminous jet tends to be more baryon poor. A neutrino-driven ''fireball'' is typically ''dirtier'' than a magnetically dominated jet, while a magnetically dominated jet can be much cleaner. Both models have the right scaling to interpret the empirical {Gamma}-L{sub iso} relation discovered recently. Since some neutrino-driven jets have too much baryon loading as compared with the data, we suggest that at least a good fraction of GRBs should have a magnetically dominated central engine.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

A test of the millisecond magnetar central engine model of gamma-ray bursts with swift data

A rapidly spinning, strongly magnetized neutron star (magnetar) has been proposed as one possible candidate of the central engine of gamma-ray bursts (GRBs). We systematically analyze the Swift/XRT light curves of long GRBs detected before 2013 August, and characterize them into four categories based on how likely they may harbor a magnetar central engine: Gold, Silver, Aluminum, and Non-magnetar. We also independently analyze the data of short GRBs with a putative magnetar central engine. We then perform a statistical study of various properties of the magnetar samples and the non-magnetar sample, and investigate whether the data are consistent with the hypothesis that there exist two types of central engines. By deriving the physical parameters of the putative magnetars, we find that the observations of the Gold and Silver samples are generally consistent with the predictions of the magnetar model. For a reasonable beaming factor for long GRBs, the derived magnetar surface magnetic field B{sub p} and initial spin period P {sub 0} fall into the reasonable range. Magnetar winds in short GRBs, on the other hand, are consistent with being isotropic. No GRB in the magnetar sample has a beam-corrected total energy exceeding the maximum energy budget defined by the initial spin energy of the magnetar, while some non-magnetar GRBs do violate such a limit. With beaming correction, on average the non-magnetar sample is more energetic and luminous than the magnetar samples. Our analysis hints that millisecond magnetars are likely operating in a good fraction, but probably not all, GRBs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

RELATIVISTIC SUPERNOVAE HAVE SHORTER-LIVED CENTRAL ENGINES OR MORE EXTENDED PROGENITORS: THE CASE OF SN 2012ap

Deep, late-time X-ray observations of the relativistic, engine-driven, type Ic SN 2012ap allow us to probe the nearby environment of the explosion and reveal the unique properties of relativistic supernova explosions (SNe). We find that on a local scale of ∼0.01 pc the environment was shaped directly by the evolution of the progenitor star with a pre-explosion mass-loss rate of M-dot <5×10{sup −6} M{sub ⊙} yr{sup −1}, in line with gamma-ray bursts (GRBs) and the other relativistic SN 2009bb. Like sub-energetic GRBs, SN 2012ap is characterized by a bright radio emission and evidence for mildly relativistic ejecta. However, its late-time (δt ≈ 20 days) X-ray emission is ∼100 times fainter than the faintest sub-energetic GRB at the same epoch, with no evidence for late-time central engine activity. These results support theoretical proposals that link relativistic SNe like 2009bb and 2012ap with the weakest observed engine-driven explosions, where the jet barely fails to break out. Furthermore, our observations demonstrate that the difference between relativistic SNe and sub-energetic GRBs is intrinsic and not due to line-of-sight effects. This phenomenology can either be due to an intrinsically shorter-lived engine or to a more extended progenitor in relativistic SNe.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Dispersion-engineered χ(2) nanophotonics: a flexible tool for nonclassical light

Abstract This article reviews recent progress in quasi-phasematched χ ( 2 ) nonlinear nanophotonics, with a particular focus on dispersion-engineered nonlinear interactions. Throughout this article, we establish design rules for the bandwidth and interaction lengths of various nonlinear processes, and provide examples for how these processes can be engineered in nanophotonic devices. In particular, we apply these rules towards the design of sources of non-classical light and show that dispersion-engineered devices can outperform their conventional counterparts. Examples include ultra-broadband optical parametric amplification as a resource for measurement-based quantum computation, dispersion-engineered spontaneous parametric downconversion as a source of separable biphotons, and synchronously pumped nonlinear resonators as a potential route towards single-photon nonlinearities.

Jankowski, Marc (ORCID:0000000318457415)↗
DOE OSTI2022

Expanding the genetic engineering toolbox for the metabolically flexible acetogen Eubacterium limosum

Abstract Acetogenic bacteria are an increasingly popular choice for producing fuels and chemicals from single carbon (C1) substrates. Eubacterium limosum is a promising acetogen with several native advantages, including the ability to catabolize a wide repertoire of C1 feedstocks and the ability to grow well on agar plates. However, despite its promise as a strain for synthetic biology and metabolic engineering, there are insufficient engineering tools and molecular biology knowledge to leverage its native strengths for these applications. To capitalize on the natural advantages of this organism, here we extended its limited engineering toolbox. We evaluated the copy number of three common plasmid origins of replication and devised a method of controlling copy number and heterologous gene expression level by modulating antibiotic concentration. We further quantitatively assessed the strength and regulatory tightness of a panel of promoters, developing a series of well-characterized vectors for gene expression at varying levels. In addition, we developed a black/white colorimetric genetic reporter assay and leveraged the high oxygen tolerance of E. limosum to develop a simple and rapid transformation protocol that enables benchtop transformation. Finally, we developed two new antibiotic selection markers—doubling the number available for this organism. These developments will enable enhanced metabolic engineering and synthetic biology work with E. limosum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum

The industrial amino acid production workhorse, Corynebacterium glutamicum naturally produces low levels of 2,3,5,6-tetramethylpyrazine (TMP), a valuable flavor, fragrance, and commodity chemical. Here, we demonstrate TMP production (~0.8 g L –1 ) in C. glutamicum type strain ATCC13032 via overexpression of acetolactate synthase and/or α-acetolactate decarboxylase from Lactococcus lactis in CGXII minimal medium supplemented with 40 g L –1 glucose. This engineered strain also demonstrated growth and TMP production when the minimal medium was supplemented with up to 40% (v v –1 ) hydrolysates derived from ionic liquid-pretreated sorghum biomass. Further, a key objective was to take the fully engineered strain developed in this study and interrogate medium parameters that influence the production of TMP, a critical post-strain engineering optimization. Design of experiments in a high-throughput plate format identified glucose, urea, and their ratio as significant components affecting TMP production. These two components were further optimized using response surface methodology. In the optimized CGXII medium, the engineered strain could produce up to 3.56 g L –1 TMP (4-fold enhancement in titers and 2-fold enhancement in yield, mol mol –1 ) from 80 g L –1 glucose and 11.9 g L –1 urea in shake flask batch cultivation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering Escherichia coli to produce medium chain oleochemicals from C 2 substrates

Many strategies to create a circular bioeconomy have been proposed. To be successful, CO 2 must be reduced with renewable energy into chemical building blocks, from which the chemical industry can be supported. Circular strategies include leveraging photosynthesis to produce sugar and lipid intermediates or renewable electricity to produce hydrogen or other electron carriers to support CO 2 reduction. Acetogens can anaerobically reduce CO 2 with H 2 to produce mixtures of small organic molecules in gas fermentations. We previously demonstrated that acetate, a common product of gas fermentation, can be converted to the model oleochemical dodecanol in engineered Escherichia coli. Here, we explored the conversion of ethanol and mixtures of ethanol and acetate to the same model oleochemicals. Co-feeding ethanol can supply both carbon and additional reducing power relative to acetate alone. In this work, we engineered E. coli to catabolize ethanol and expressed two distinct ethanol metabolism pathways in different operons and combined them with improved engineered acetate activation. We evaluated the performance of these operons in dodecanol-producing strains when fed ethanol or acetate and found ethanol to be a better carbon source when judged by product titers. The engineered strains fed ethanol produced about two-fold more dodecanol than the strains fed acetate. This increase was in part, due to change in product distribution. Cells fed ethanol produced predominantly dodecanol, whereas cells fed acetate generated a mixture of dodecanol and dodecanoic acid. Dodecanol titers were further improved by employing feeding strategies in controlled bioreactors.

Escherichia coli↗