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Results for “TdT”

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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9 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3′ Terminal Structures for Enzymatic De Novo DNA Synthesis

Enzymatic oligonucleotide synthesis methods based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) promise to enable the de novo synthesis of long oligonucleotides under mild, aqueous conditions. Intermediates with a 3′ terminal structure (hairpins) will inevitably arise during synthesis, but TdT has poor activity on these structured substrates, limiting its usefulness for oligonucleotide synthesis. Here, we described two parallel efforts to improve the activity of TdT on hairpins: (1) optimization of the concentrations of the divalent cation cofactors and (2) engineering TdT for enhanced thermostability, enabling reactions at elevated temperatures. By combining both of these improvements, we obtained a ~10-fold increase in the elongation rate of a guanine-cytosine hairpin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Revealing intrinsic domains and fluctuations of moiré magnetism by a wide-field quantum microscope

Moiré magnetism featured by stacking engineered atomic registry and lattice interactions has recently emerged as an appealing quantum state of matter at the forefront of condensed matter physics research. Nanoscale imaging of moiré magnets is highly desirable and serves as a prerequisite to investigate a broad range of intriguing physics underlying the interplay between topology, electronic correlations, and unconventional nanomagnetism. Here we report spin defect-based wide-field imaging of magnetic domains and spin fluctuations in twisted double trilayer (tDT) chromium triiodide CrI 3 . We explicitly show that intrinsic moiré domains of opposite magnetizations appear over arrays of moiré supercells in low-twist-angle tDT CrI 3 . In contrast, spin fluctuations measured in tDT CrI 3 manifest little spatial variations on the same mesoscopic length scale due to the dominant driving force of intralayer exchange interaction. Our results enrich the current understanding of exotic magnetic phases sustained by moiré magnetism and highlight the opportunities provided by quantum spin sensors in probing microscopic spin related phenomena on two-dimensional flatland.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Comparison of three state-of-the-art crystal plasticity based deformation twinning models for magnesium alloys

In magnesium alloys, deformation twinning and its interactions with dislocation slip are responsible for a sigmoidal shape stress–strain behavior and an asymmetrical tension–compression yield strength in magnesium alloys. The sensitivity of twinning to the underlying microstructure renders the crystal plasticity method the most commonly adopted modeling approach for magnesium-twinning. This paper compares three state-of-the-art crystal plasticity-based twinning models from the literature, namely the elastic-viscoplastic self-consistent twinning-detwinning (EVPSC-TDT) model, crystal plasticity finite element model based on enhanced predominate twin reorientation approach (CPFE-ePTR), and the crystal plasticity finite element model based on “discrete twinning” approach (CPFE-DT). A polycrystalline microstructure is simulated with all three methods to compare the resulting stress–strain curves and lattice strains to those from the experimentally measured data. All three methods showed the capability of capturing the experimental results with different levels of accuracy. Additionally, the EVPSC-TDT method avoids solving the finite element matrices and showed the highest computational efficiency. The CPFE-ePTR model shows a higher accuracy in capturing the lattice strain. The CPFE-DT relies on high-resolution finite element mesh and is much slower than the other two methods, but it captured the local deformation concentration and stress reversal phenomena near the twin band, which was not possible with the other two methods. Based on the comparison, guidance for the selection of the appropriate model based on the specific modeling target is provided in this paper.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Thermodynamic theory of crystal plasticity: Formulation and application to polycrystal fcc copper

We present a thermodynamic description of crystal plasticity. Our formulation is based on the Langer-Bouchbinder-Lookman thermodynamic dislocation theory (TDT), which asserts the fundamental importance of an effective temperature that describes the state of configurational disorder and therefore the dislocation density of the crystalline material. We extend the TDT description from isotropic plasticity to crystal plasticity with many slip systems. Finite-element simulations show favourable comparison with experiments on polycrystal fcc copper under uniaxial compression, tension, and simple shear. Here, the thermodynamic theory of crystal plasticity thus provides a thermodynamically consistent and physically rigorous description of dislocation motion in crystals. We also discuss new insights about the interaction of dislocations belonging to different slip systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Rapid Identification of Synthetic Routes to Functional Metastable Phases Using X-ray Probed Laser Anneal Mapping (XPLAM) Time-Temperature Quench Maps

Many material systems have known or predicted functional phases that are metastable at standard temperature and pressure. While substantial advances have been made in the high-throughput and combinatorial synthesis of materials with a range of stoichiometries, investigation of thermal processing remains largely the domain of iterative uniform anneals or static gradients. Here we develop X-ray probed laser anneal mapping (XPLAM), a high throughput technique coupling spatially resolved X-ray diffraction with microsecond to millisecond laser gradient anneals to produce temperature–dwell–transformation (TDT) diagrams of the phase as a function of quench time and temperature. In addition to showing regimes where specific metastable phases form preferentially, TDT diagrams provide insight into the submillisecond kinetics of solid–solid phase transitions. This is a unique tool for mapping reaction pathways for metastable phases. As a first demonstration of XPLAM, we study Bi2O3, which has a rich set of polytypes, including the d-phase with an exceptionally high oxygen ion conductivity. We demonstrate the first annealing-driven synthesis of room temperature d-Bi2O3. We expect XPLAM to prove a powerful technique for rapid identification of synthetic routes to metastable phases and to generate the exhaustive data sets required for machine learning-guided exploration of materials processing.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes

Abstract Combining surface‐initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI‐TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush‐functionalized DNA nanostructures. We demonstrate that SI‐TcEP can site‐specifically pattern DONs with brushes containing both natural and non‐natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse‐grained simulations predict the conformation of the brush‐functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush‐functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site‐specific growth of polynucleotide brushes. The ability to site‐specifically decorate DONs with brushes of natural and non‐natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

Yang, Yunqi↗
DOE OSTI2021

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes

Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. Here we demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Thermomechanical conversion in metals: dislocation plasticity model evaluation of the Taylor-Quinney coefficient

Using a partitioned-energy thermodynamic framework which assigns energy to that of atomic configurational stored energy of cold work and kinetic-vibrational, in this study we derive an important constraint on the Taylor-Quinney coefficient, which quantifies the fraction of plastic work that is converted into heat during plastic deformation. Associated with the two energy contributions are two separate temperatures – the ordinary temperature for the thermal energy and the effective temperature for the configurational energy. We show that the Taylor-Quinney coefficient is a function of the thermodynamically defined effective temperature that measures the atomic configurational disorder in the material. Finite-element analysis of recently published experiments on the aluminum alloy 6016-T4 [1], using the thermodynamic dislocation theory (TDT), shows good agreement between theory and experiment for both stress-strain behavior and temporal evolution of the temperature. The simulations include both conductive and convective thermal energy loss during the experiments, and significant thermal gradients exist within the simulation results. Computed values of the differential Taylor-Quinney coefficient are also presented and suggest a value which differs between materials and increases with increasing strain.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Development of a three-dimensional APOLLO3 neutrons deterministic scheme for the CABRI reactor

CABRI is an experimental reactor to study the fuel behavior during reactivity injection transients. These transients being highly multiphysics, the development of suitable modeling and simulation tools to simulate them is important for the optimization of the tests and the control of the experimental conditions. This paper focuses on the development of an APOLLO3 deterministic core calculation tool dedicated to the CABRI transient analysis. It represents the first stage of the incremental process for the implementation of a multiphysics time-dependent modeling of the CABRI transient. The neutron calculation scheme is based on a classical two-step approach. The first step consists of a 281-energy group calculation flux with the TDT-MOC (Method Of Characteristics) solver for cross-section space and energy (23 groups) collapsing for the CABRI different assembly clusters. The bias on a 2D core neutron calculation due to the self-shielding calculation and collapsing on a restricted pattern are investigated thanks to a comparison with a direct full 2D calculation on a quarter of core. The second step relies on a pin-resolved transport 3D transport core calculation with the SN solver MINARET. A progressive numerical validation process is followed to quantify the calculation biases on reactivity and reaction rates at each step using reference calculations with the stochastic code TRIPOLI4. The next development stage toward a multiphysics scheme will be the implementation of the 3D-kinetics equation resolution and the coupling with a core thermal-hydraulics model. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗