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At least 1,495 records · Page 83

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DOE OSTI2025

Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. Here, we validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Tuning antimicrobial properties of biomimetic nanopatterned surfaces

Here, nature has amassed an impressive array of structures that afford protection from microbial colonization/infection when displayed on the exterior surfaces of organisms. Here, controlled variation of the features of mimetics derived from etched silicon allows for tuning of their antimicrobial efficacy. Materials with nanopillars up to 7 μm in length are extremely effective against a wide range of microbial species and exceed the performance of natural surfaces; in contrast, materials with shorter/blunter nanopillars (<2 μm) selectively killed specific species. Using a combination of microscopies, the mechanisms by which bacteria are killed are demonstrated, emphasizing the dependence upon pillar density and tip geometry. Additionally, real-time imaging reveals how cells are immobilized and killed rapidly. Generic or selective protection from microbial colonization could be conferred to surfaces [for, e.g., internal medicine, implants (joint, dental, and cosmetic), food preparation, and the agricultural industry] patterned with these materials as coatings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Coalescence-controlled and coalescence-free growth regimes during deposition of pulsed metal vapor fluxes on insulating surfaces

The morphology and physical properties of thin films deposited by vapor condensation on solid surfaces are predominantly set by the processes of island nucleation, growth, and coalescence. When deposition is performed using pulsed vapor fluxes, three distinct nucleation regimes are known to exist depending on the temporal profile of the flux. These regimes can be accessed by tuning deposition conditions; however, their effect on film microstructure becomes marginal when coalescence sets in and erases morphological features obtained during nucleation. By preventing coalescence from being completed, these nucleation regimes can be used to control microstructure evolution and thus access a larger palette of film morphological features. Recently, we derived the quantitative criterion to stop coalescence during continuous metal vapor flux deposition on insulating surfaces—which typically yields 3-dimensional growth—by describing analytically the competition between island growth by atomic incorporation and the coalescence rate of islands [Lü et al., Appl. Phys. Lett. 105, 163107 (2014)]. Here, we develop the analytical framework for entering a coalescence-free growth regime for metal vapor deposition on insulating substrates using pulsed vapor fluxes, showing that there exist three distinct criteria for suppressing coalescence that correspond to the three nucleation regimes of pulsed vapor flux deposition. The theoretical framework developed herein is substantiated by kinetic Monte Carlo growth simulations. Our findings highlight the possibility of using atomistic nucleation theory for pulsed vapor deposition to control morphology of thin films beyond the point of island density saturation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Current-phase relations of InAs nanowire Josephson junctions: From interacting to multimode regimes

Gate-tunable semiconductor-superconductor nanowires with superconducting leads form exotic Josephson junctions that are a highly desirable platform for two types of qubits: Those with topological superconductivity (Majorana qubits) and those based on tunable anharmonicity (gatemon qubits). Controlling their behavior, however, requires understanding their electrostatic environment and electronic structure. Here we study gated InAs nanowires with epitaxial aluminum shells. By measuring current-phase relations and comparing them with analytical and numerical calculations, we show that we can tune the number of modes, determine the transparency of each mode, and tune into regimes in which electron-electron interactions are apparent, indicating the presence of a quantum dot. To take into account electrostatic and geometrical effects, we perform microscopic self-consistent Schrodinger-Poisson numerical simulations, revealing the energy spectrum of Andreev states in the junction as well as their spatial distribution. Here, our work systematically demonstrates the effect of device geometry, gate voltage, and phase bias on mode behavior, providing insights into ongoing experimental efforts and predictive device design.

36 MATERIALS SCIENCE↗

DOE OSTI2014

TU-C-17A-04: BEST IN PHYSICS (THERAPY) - A Supervised Framework for Automatic Contour Assessment for Radiotherapy Planning of Head- Neck Cancer

Purpose: Precise contour delineation of tumor targets and critical structures from CT simulations is essential for accurate radiotherapy (RT) treatment planning. However, manual and automatic delineation processes can be error prone due to limitations in imaging techniques and individual anatomic variability. Tedious and laborious manual verification is hence needed. This study develops a general framework for automatically assessing RT contours for head-neck cancer patients using geometric attribute distribution models (GADMs). Methods: Geometric attributes (centroid and volume) were computed from physician-approved RT contours of 29 head-neck patients. Considering anatomical correlation between neighboring structures, the GADM for each attribute was trained to characterize intra- and interpatient structure variations using principal component analysis. Each trained GADM was scalable and deformable, but constrained by the principal attribute variations of the training contours. A new hierarchical model adaptation algorithm was utilized to assess the RT contour correctness for a given patient. Receiver operating characteristic (ROC) curves were employed to evaluate and tune system parameters for the training models. Results: Experiments utilizing training and non-training data sets with simulated contouring errors were conducted to validate the framework performance. Promising assessment results of contour normality/abnormality for the training contour-based data were achieved with excellent accuracy (0.99), precision (0.99), recall (0.83), and F-score (0.97), while corresponding values of 0.84, 0.96, 0.83, and 0.9 were achieved for the non-training data. Furthermore, the areas under the ROC curves were above 0.9, validating the accuracy of this test. Conclusion: The proposed framework can reliably identify contour normality/abnormality based upon intra- and inter-structure constraints derived from clinically-approved contours. It also allows physicians to analytically determine the system parameters to fit various clinic requirements (e.g. as-low-as-possible false positives). It has great potential for improving RT work flow. More geometric attributes and training sets will be investigated to improve framework performance in the future.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion↗

DOE OSTI2015

Fast Spatially Resolved Exhaust Gas Recirculation (EGR) Distribution Measurements in an Internal Combustion Engine Using Absorption Spectroscopy

One effective method of reducing NO x emissions while improving efficiency is exhaust gas recirculation (EGR) in internal combustion engines. But, insufficient mixing between fresh air and exhaust gas can lead to cycle-to-cycle and cylinder-to-cylinder nonuniform charge gas mixtures of a multi-cylinder engine, which can in turn reduce engine performance and efficiency. Furthermore, a sensor packaged into a compact probe was designed, built and applied to measure spatiotemporal EGR distributions in the intake manifold of an operating engine. The probe promotes the development of more efficient and higher-performance engines by resolving high-speed in situ CO 2 concentration at various locations in the intake manifold. Our study employed mid-infrared light sources tuned to an absorption band of CO 2 near 4.3 μm, an industry standard species for determining EGR fraction. The calibrated probe was used to map spatial EGR distributions in an intake manifold with high accuracy and monitor cycle-resolved cylinder-specific EGR fluctuations at a rate of up to 1 kHz.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Overcoming proton and 3 He intrinsic resonances in the AGS Booster with an ac dipole

Polarized 3 He collisions are part of future physics programs for RHIC and eRHIC. Due to optics perturbations from the AGS partial helical dipoles, it is desired to extract 3 He from the Booster at Gγ = –10.5, which involves crossing the 12 – ν y and the 6 + ν y intrinsic resonances. To overcome these resonances, an ac dipole is being designed to be installed in the Booster. The effect of an ac dipole is to generate artificial spin-resonance by inducing vertical betatron oscillations that guide the bunch through the horizontal fields of the quadrupoles. An experimental study with Au beam was performed to confirm that the available aperture is sufficient to accommodate these large vertical betatron oscillations. Simulations for 3 He crossing the aforementioned resonances have been performed and display the effectiveness of the ac dipole at spin-flipping in the Booster. Due to the rapid acceleration of the Booster, the ac dipole tune will change as much as 0.0028 over the course of an ac dipole cycle, which changes the amplitude of these betatron oscillations over the course of the cycle. Through simulation, it is shown that the varying betatron amplitude does not dilute the effectiveness of the ac dipole. Sextupoles are used to provide further control over the tune spread, where RF-dual harmonics are used to control the bunch length, and to reduce the momentum spread.

43 PARTICLE ACCELERATORS↗

DOE OSTI2017

ChemNet: A Transferable and Generalizable Deep Neural Network for Small-Molecule Property Prediction

With access to large datasets, deep neural networks through representation learning have been able to identify patterns from raw data, achieving human-level accuracy in image and speech recognition tasks. However, in chemistry, availability of large standardized and labelled datasets is scarce, and with a multitude of chemical properties of interest, chemical data is inherently small and fragmented. In this work, we explore transfer learning techniques in conjunction with the existing Chemception CNN model, to create a transferable and generalizable deep neural network for small-molecule property prediction. Our latest model, ChemNet learns in a semi-supervised manner from inexpensive labels computed from the ChEMBL database. When fine-tuned to the Tox21, HIV and FreeSolv dataset, which are 3 separate chemical tasks that ChemNet was not originally trained on, we demonstrate that ChemNet exceeds the performance of existing Chemception models, contemporary MLP models that trains on molecular fingerprints, and it matches the performance of the ConvGraph algorithm, the current state-of-the-art. Furthermore, as ChemNet has been pre-trained on a large diverse chemical database, it can be used as a universal “plug-and-play” deep neural network, which accelerates the deployment of deep neural networks for the prediction of novel small-molecule chemical properties.

Artificial Intelligence↗

DOE OSTI2022

Thermally stable hydrocarbon-based anion exchange membrane and ionomers

An anion exchange membrane is composed of a copolymer of 1,1-diphenylethylene and one or more styrene monomers, such as 4-tert-butylstyrene. The copolymer includes a backbone substituted with a plurality of ionic groups coupled to phenyl groups on the backbone via hydrocarbyl tethers between about 1 and about 7 carbons in length. High-temperature conditions enabled by these copolymers enhance conductivity performance, making them particularly suitable for use in anion exchange membranes in fuel cells, electrolyzers employing hydrogen, ion separations, etc. The properties of the membranes can be tuned via the degree of functionalization of the phenyl groups and selection of the functional groups, such as quaternary ammonium groups. Several processes can be used to incorporate the desired ionic functional groups into the polymers, such as chloromethylation, radical bromination, Friedel-Crafts acylation and alkylation, sulfonation followed by amination, or combinations thereof.

Lee, Sangwoo↗

DOE OSTI2024

Thermally stable hydrocarbon-based anion exchange membrane and ionomers

Lee, Sangwoo↗

DOE OSTI2025

Coefficient-to-Basis Network: a fine-tunable operator learning framework for inverse problems with adaptive discretizations and theoretical guarantees

We propose a Coefficient-to-Basis Network (C2BNet), a novel framework for solving inverse problems within the operator learning paradigm. C2BNet efficiently adapts to different discretizations through fine-tuning, using a pre-trained model to significantly reduce computational cost while maintaining high accuracy. Unlike traditional approaches that require retraining from scratch for new discretizations, our method enables seamless adaptation without sacrificing predictive performance. Furthermore, we establish theoretical approximation and generalization error bounds for C2BNet by exploiting low-dimensional structures in the underlying datasets. Our analysis demonstrates that C2BNet adapts to low-dimensional structures without relying on explicit encoding mechanisms, highlighting its robustness and efficiency. To validate our theoretical findings, we conducted extensive numerical experiments that showcase the superior performance of C2BNet on several inverse problems. The results confirm that C2BNet effectively balances computational efficiency and accuracy, making it a promising tool to solve inverse problems in scientific computing and engineering applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Optimized mirror shape tuning using beam weightings based on distance, angle of incidence, reflectivity, and power

For glancing-incidence optical systems, such as short-wavelength optics used for nano-focusing, incorporating physical factors in the calculations used for shape optimization can improve performance. Wavefront metrology, including the measurement of a mirror's shape or slope, is routinely used as input for mirror figure optimization on mirrors that can be bent, actuated, positioned, or aligned. Modeling shows that when the incident power distribution, distance from focus, angle of incidence, and the spatially varying reflectivity are included in the optimization, higher Strehl ratios can be achieved. Following the works of Maréchal and Mahajan, optimization of the Strehl ratio (for peak intensity with a coherently illuminated system) occurs when the expectation value of the phase error's variance is minimized. We describe an optimization procedure based on regression analysis that incorporates these physical parameters. This approach is suitable for coherently illuminated systems of nearly diffraction-limited quality. Mathematically, this work is an enhancement of the methods commonly applied for ex situ alignment based on uniform weighting of all points on the surface (or a sub-region of the surface). It follows a similar approach to the optimization of apodized and non-uniformly illuminated optical systems. Significantly, it reaches a different conclusion than a more recent approach based on minimization of focal plane ray errors.

47 OTHER INSTRUMENTATION↗

DOE OSTI2015

Reconstructing householder vectors from Tall-Skinny QR

The Tall-Skinny QR (TSQR) algorithm is more communication efficient than the standard Householder algorithm for QR decomposition of matrices with many more rows than columns. However, TSQR produces a different representation of the orthogonal factor and therefore requires more software development to support the new representation. Further, implicitly applying the orthogonal factor to the trailing matrix in the context of factoring a square matrix is more complicated and costly than with the Householder representation. We show how to perform TSQR and then reconstruct the Householder vector representation with the same asymptotic communication efficiency and little extra computational cost. We demonstrate the high performance and numerical stability of this algorithm both theoretically and empirically. The new Householder reconstruction algorithm allows us to design more efficient parallel QR algorithms, with significantly lower latency cost compared to Householder QR and lower bandwidth and latency costs compared with Communication-Avoiding QR (CAQR) algorithm. Experiments on supercomputers demonstrate the benefits of the communication cost improvements: in particular, our experiments show substantial improvements over tuned library implementations for tall-and-skinny matrices. Furthermore, we also provide algorithmic improvements to the Householder QR and CAQR algorithms, and we investigate several alternatives to the Householder reconstruction algorithm that sacrifice guarantees on numerical stability in some cases in order to obtain higher performance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Tuning the Intermolecular Electrostatic Interaction toward High-Efficiency and Low-Cost Organic Solar Cells

Organic solar cells (OSCs) have achieved much progress with rapidly increasing power conversion efficiencies (PCEs). It should be noted that the top-performance OSCs are generally consisted of active materials with complex chemical structures, resulting in high costs. Here, combining the material design and morphology control, high-efficiency OSCs are fabricated by a low-cost donor: acceptor blend. A completely non-fused electron acceptor named Tz is designed and synthesized via introducing thiazole units on both sides of a bithiophene core, which shows an outstanding PCE of 13.3% with a typical polythiophene donor. More importantly, optimization guidelines are presented to get excellent morphology for low-cost donor:acceptor systems. Three polythiophenes are selected, poly(3-hexylthiophene) and its two derivatives with electron-withdrawing substitutions (PDCBT and PDCBT-2F), as donors to fabricate the cell devices. The computational and experimental data reveal that decreasing the electrostatic interaction between polythiophene and Tz is the key to getting a suppressed miscibility and thus a high phase purity. Finally, this study provides insight into the molecular design and donor:acceptor matching requirements for high-efficiency and low-cost OSCs.

14 SOLAR ENERGY↗

DOE OSTI2023

Achieving stable all-solid-state lithium-metal batteries by tuning the cathode-electrolyte interface and ionic/electronic transport within the cathode

All-solid-state batteries with sulfide electrolytes and high-nickel layered oxide cathodes attract much interest due to their high specific energy. However, their cycling performance is primarily influenced by the interface between the sulfide electrolyte and the high-Ni layered oxide particles, which requires the use of composite cathodes with high ionic and electronic conductivities to achieve a kinetically stable interface inside the cathode. Here, we apply Ti 2 O 3 particles to the high-Ni cathode LiNi 0.8 Co 0.1 Mn 0.1 O 2 (NCM811), where Ti 2 O 3 not only acts as an electronic conductor to provide a fast diffusion path for electrons in the composite cathode, but also absorbs the lattice oxygen released from NCM811 cathode during cycling, stabilizing the Li 6 PS 5 Cl/NCM811 interface and suppressing electrolyte oxidation. The as-modified cathode exhibits an initial specific capacity of 192 mAh g -1 and retains 166 mAh g -1 after 140 cycles at 0.1C rate with a good capacity retention of 86.5%. Furthermore, the composite cathode displays high rate capability even at 1C rate. By contrast, the unmodified Li 6 PS 5 Cl/NCM811 cathode shows poor cycling performance with only 130 mAh g -1 remaining after 130 cycles. This work provides a new direction for the design of cathodes for all-solid-state batteries that can deliver high specific energy with long cycle life.

25 ENERGY STORAGE↗

DOE OSTI2015

Cosmic discordance: are Planck CMB and CFHTLenS weak lensing measurements out of tune?

We examine the level of agreement between low-redshift weak lensing data and the cosmic microwave background using measurements from the Canada–France–Hawaii Telescope Lensing Survey (CFHTLenS) and Planck+Wilkinson Microwave Anisotropy Probe (WMAP) polarization. We perform an independent analysis of the CFHTLenS six bin tomography results of Heymans et al. We extend their systematics treatment and find the cosmological constraints to be relatively robust to the choice of non-linear modelling, extension to the intrinsic alignment model and inclusion of baryons. We find that when marginalized in the Ωm–σ8 plane, the 95 percent confidence contours of CFHTLenS and Planck+WMAP only just touch, but the discrepancy is less significant in the full six-dimensional parameter space of Λ cold dark matter (ΛCDM). Allowing a massive active neutrino or tensor modes does not significantly resolve the tension in the full n-dimensional parameter space. Our results differ from some in the literature because we use the full tomographic information in the weak lensing data and marginalize over systematics. We note that adding a sterile neutrino to ΛCDM brings the 2D marginalized contours into greater overlap, mainly due to the extra effective number of neutrino species, which we find to be 0.88 ± 0.43 (68 per cent) greater than standard on combining the data sets. We discuss why this is not a completely satisfactory resolution, leaving open the possibility of other new physics or observational systematics as contributing factors. We provide updated cosmology fitting functions for the CFHTLenS constraints and discuss the differences from ones used in the literature.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Performance of the 650 MHZ SRF Cavity Tuner for PIP-II Project

The PIP-II linac will include fifty seven 650MHz SRF cav-ities. Each cavity will be equipped with tuner for coarse and fine frequency tuning. Design and operations parame-ters will be discussed. Results from room temperature tests with prototype tuner installed on a 650MHz βG=0.90 ellip-tical cavity will be presented.

43 PARTICLE ACCELERATORS↗