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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Microstructure Clones

Background: A material’s microstructure drives its material performance. Contemporary crystal plasticity experiments compare full-field strain measurements of polycrystal specimens to models. Because each specimen is unique, it is impossible to know which features of the observed deformation are deterministic vs statistical; thus, differences between model and experiment may or may not be significant. Objective: This paper introduces the invention of microstructure clones. Microstructure clones are 2D oligocrystal specimens that have nearly identical microstructures to remedy the aforementioned experimental limitations. Having specimens with nearly identical microstructures will allow for multiple destructive tests of a microstructure (either as repeats or intentionally different experiments), an ability to “see the future” by providing insight into how a specimen will deform, variability quantification, and experimental investigations of response to small microstructural changes. Methods: This work introduces microstructure clones. Repeatability of these clones is demonstrated in tensile bars of pure nickel. Local strain measurements from digital image correlation are compared between clone specimens and compared to results from a crystal plasticity finite element model. Results: Two sets of microstructure clones were tested in this study and displayed very consistent deformation responses within each clone set. Small observed differences in deformation invite investigation into microstructure stochasticity and the effect of small microstructural and loading differences. Conclusions: Microstructure clones represent a significant shift in understanding structure–property relationships. This work reshapes experimental crystal plasticity to allow for experiments that control for specific variables, quantification of microstructural stochasticity (and other sources of stochasticity), and opportunities for replicating experiments.

Crystal Plasticity↗
DOE OSTI2025

SpecSims: A Scalable Speculative Tree-based Simulation Cloning Framework for Finite Memory Machines

Simulation cloning is a technique in which cloned simulations whose state spaces differ partially from their parent simulation due to intervening events are spawned at runtime and concurrently advanced. It is a powerful method to carry out what-if analysis by speculatively exploring and evaluating the impact of various permutations of intervening cascade of events. Due to the exponential growth in the number of possible clones even for a small number of distinct intervening events, the practical efficacy of the approach is often severely limited by the maximum available memory of the computing host. In this paper, we introduce a novel speculative simulation cloning framework that executes a simulation cloning campaign capable of efficiently exploring an exponentially large space of clone simulations created by permutation of intervening events under a finite memory constraint. We provide a theoretical analysis of the runtime characteristics of our proposed approach and highlight its novel advantages such as memory-aware and as-long-as-needed execution. Furthermore, in support of our analytical findings and to demonstrate its practical feasibility, we implement a prototype of the cloning framework on a shared memory system and report its performance characteristics in the context of a heat diffusion simulation, and a power grid simulation subject to cascading disruptions from geomagnetic disturbances.

Simulation framework↗
DOE OSTI2025

Single-qubit multi-party transmission using universal symmetric quantum cloning

This study considers the hypothetical quantum network case where Alice wishes to transmit one qubit of information (specifically a pure quantum state) to M parties, where M is some large number. The remote receivers locally perform single-qubit quantum state tomography on the transmitted qubits in order to compute the quantum state within some error rate (dependent on the tomography technique and the number of transmitted qubits). We show that with the use of an intermediate optimal symmetric universal quantum cloning machine (between Alice and the remote receivers) as a repeater-type node in a hypothetical quantum network, Alice can send significantly fewer qubits compared to direct transmission of the message qubits to each of the M remote receivers. This is possible due to two properties of quantum cloning. The first is that single qubit quantum clones retain the same Bloch angle as the initial quantum state. This means that if the mixed state of the quantum clone can be computed to high enough accuracy, the original pure quantum state can be inferred by extrapolating that vector to the surface of the Bloch sphere. The second property is that the state overlap of approximate quantum clones, with respect to the original pure quantum state, quickly converges (specifically for 1 → M , the limit of the fidelity as M goes to infinity is $\frac{2}{3}$). This means that Alice can prepare a constant number of qubits (which are then passed through the quantum cloning machine) in order to achieve a desired error rate if M is large enough. Combined, these two properties mean that for a large M , Alice can prepare many orders of magnitude fewer qubits in order to achieve the same single qubit transmission accuracy compared to the naive direct qubit transmission approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Rapid Construction of an Infectious Clone of the Zika Virus, Strain ZKC2

Zika virus (ZIKV) has had detrimental effects on global public health in recent years. This is because the management of the disease has been limited, in part because its pathogenic mechanisms are not yet completely understood. Infectious clones are an important tool that utilize reverse genetics; these can be used to modify the ZIKV genomic RNA at the DNA level. A homologous recombination clone was used to construct pWSK29, a low copy plasmid that contained sequences for a T7 promoter, the whole genome of ZIKV ZKC2 strain, and a hepatitis delta virus ribozyme. High fidelity PCR was then used to amplify the T7 transcription template. The transcript was then transfected into susceptible cells via lipofection to recover the ZIKV ZKC2 strain. Finally, the virulence of rZKC2 was evaluated both in vitro and in vivo . The rZKC2 was successfully obtained and it showed the same virulence as its parent, the ZIKV ZKC2 strain (pZKC2), both in vitro and in vivo . The 3730 (NS2A-D62G) mutation site was identified as being important, since it had significant impacts on rZKC2 recovery. The 4015 (NS2A, A157V) mutation may reduce virus production by increasing the interferon type I response. In this study, one of the earliest strains of ZIKV that was imported into China was used for infectious clone construction and one possible site for antiviral medication development was discovered. The use of homologous recombination clones, of PCR products as templates for T7 transcription, and of lipofection for large RNA transfection could increase the efficiency of infectious clone construction. Our infectious clone provides an effective tool which can be used to explore the life cycle and medical treatment of ZIKV.

Qin, Zhiran↗
DOE OSTI2023

eYGFPuv-Assisted Transgenic Selection in Populus deltoides WV94 and Multiplex Genome Editing in Protoplasts of P. trichocarpa × P. deltoides Clone ‘52-225’

Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone ‘52-225’ (P. trichocarpa × P. deltoides clone ‘52-225’). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning

The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4-5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

An Ab Initio Multiple Cloning Method for Non-Adiabatic Excited-State Molecular Dynamics in NWChem

The recently developed ab-initio multiple cloning (AIMC) approach based on the multicongurational Ehrenfest (MCE) method provides a powerful and accurate way of describing the excited-state dynamics of molecular systems. The AIMC method is a controlled approximation to non-adiabatic dynamics with a particular strength in the proper description of decoherence effects due to branching of vibrational wavepackets at a level crossing. In this work, we report a new implementation of the AIMC algorithm in the open source NWChem computational chemistry program. The framework combines linear-response time-dependent density functional theory with Ehrenfest mean-eld theory to determine the equations of motion for classical trajectories. The multi-dimensional wave function is decomposed into a superposition of Gaussian coherent states guided by Ehrenfest trajectories (i.e., MCE approach), which can clone with fully quantum mechanical amplitudes and phases. By using an efficient time-derivative based non-adiabatic coupling approach within the AIMC method, all observable are calculated on-the-y in the non-adiabatic molecular dynamics process. As a representative example, we apply our implementation to study the ultrafast photoinduced electronic and vibrational energy transfer in a pyridine molecule. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer are discussed. This new AIMC implementation provides a high-level non-adiabatic molecular dynamics framework for simulating photoexcited dynamics in complex molecular systems and experimentally relevant ultrafast spectroscopic probes, such as nonlinear coherent optical and X-ray signals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

MultiGreen: A multiplexing architecture for GreenGate cloning

Genetic modification of plants fundamentally relies upon customized vector designs. The ever-increasing complexity of transgenic constructs has led to increased adoption of modular cloning systems for their ease of use, cost effectiveness, and rapid prototyping. GreenGate is a modular cloning system catered specifically to designing bespoke, single transcriptional unit vectors for plant transformation—which is also its greatest flaw. MultiGreen seeks to address GreenGate’s limitations while maintaining the syntax of the original GreenGate kit. The primary limitations MultiGreen addresses are 1) multiplexing in series, 2) multiplexing in parallel, and 3) repeated cycling of transcriptional unit assembly through binary intermediates. MultiGreen efficiently concatenates bespoke transcriptional units using an additional suite of level 1acceptor vectors which serve as an assembly point for individual transcriptional units prior to final, level 2, condensation of multiple transcriptional units. Assembly with MultiGreen level 1 vectors scales at a maximal rate of 2*⌈ log 6 n ⌉+3 days per assembly, where n represents the number of transcriptional units. Further, MultiGreen level 1 acceptor vectors are binary vectors and can be used directly for plant transformation to further maximize prototyping speed. MultiGreen is a 1:1 expansion of the original GreenGate architecture’s grammar and has been demonstrated to efficiently assemble plasmids with multiple transcriptional units. MultiGreen has been validated by using a truncated violacein operon from Chromobacterium violaceum in bacteria and by deconstructing the RUBY reporter for in planta functional validation. MultiGreen currently supports many of our in-house multi transcriptional unit assemblies and will be a valuable strategy for more complex cloning projects.

Science & Technology - Other Topics↗
DOE OSTI2024

Microstructure Clones

Microstructure drives component behavior. Contemporary crystal plasticity studies compare strain measurements of polycrystal specimens to models. Because each specimen is unique, it is impossible to know which differences are significant. In this project, we invented microstructure clones and explored their use in understanding crystal plasticity. Microstructure clones are specimens with nearly identical microstructures, which allows for multiple destructive tests of a microstructure, insight into how a specimen will deform, variability quantification, and the ability to measure the effects of microstructural changes. Several sets of microstructure clones, pure nickel tensile bars, were tested. The techniques of digital image correlation, crystal plasticity finite element analysis, high resolution electron backscatter diffraction, transmission electron microscopy, and dislocation dynamics were used to understand the structural behavior of these microstructures. This work reshapes the fields of crystal plasticity and structure-property relationships by providing a technique to control for specific variables, quantify microstructural stochasticity, and replicate experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Construction of chicken infectious anemia virus infectious clone and study on its pathogenicity

Chicken infectious anemia virus (CIAV) can be transmitted through contaminated live poultry vaccine. However, the pathogenicity of contaminated CIAV strains is rarely reported. Previously, the chickens showed the typical symptoms of anemia after using the attenuated live fowl pox virus (FPV) vaccine. Therefore, exogenous CIAV contamination was suspected. We detected anti-CIAV antibodies in SPF chicks vaccinated with the FPV vaccine. CIAV contamination was confirmed in the FPV vaccine, and the CIAV strain was named JS2020-FPV. This study aims to rescue JS2020-FPV by reverse genetic assays and investigate its pathogenicity. Firstly, double-copies infectious clone of JS2020-FPV was constructed. For the pathogenicity study, infectious clone of JS2020-FPV was used to inoculate 1-day-old SPF chicks. The typical symptoms of anemia were observed in the JS2020-PFV group 14 days post inoculation. The hematocrit and body weight of chicks in the JS2020-PFV group were significantly lower than those in the mock group. Notably, the thymus development index and antibody levels of NDV were lower in chicks in the JS2020-PFV group than those in the mock group. Different degrees of apoptosis of MSB1 and DF-1 were observed after inoculated with the JS2020-FPV VP3 recombinant fusion protein expressed by E. coli system, indicating that VP3 induced apoptosis in the transformed cells. Overall, the pathogenicity of the CIAV detected in the contaminated vaccine was confirmed by inoculating SPF chicks with the double-copies infectious DNA clone in this study. Our findings indicate that the dangers of vaccine contamination cannot be ignored.

Wang, Jinjin↗
DOE OSTI2021

TNT cloning system

Disclosed herein are vectors and components for a nucleic acid cloning system, and methods of use of the vectors and components in cloning nucleic acid fragments of interest. The cloning system includes two families of destination vectors which can be used in alternating form to systematically combine nucleic acid fragments of interest.

Tuskan, Gerald A.↗
DOE OSTI2023

TNT cloning system

Disclosed herein are vectors and components for a nucleic acid cloning system, and methods of use of the vectors and components in cloning nucleic acid fragments of interest. The cloning system includes two families of destination vectors which can be used in alternating form to systematically combine nucleic acid fragments of interest.

Tuskan, Gerald A.↗
DOE OSTI2022

Dirac Fermion Cloning, Moiré Flat Bands, and Magic Lattice Constants in Epitaxial Monolayer Graphene

Tuning interactions between Dirac states in graphene has attracted enormous interest because it can modify the electronic spectrum of the 2D material, enhance electron correlations, and give rise to novel condensed-matter phases such as superconductors, Mott insulators, Wigner crystals, and quantum anomalous Hall insulators. Previous works predominantly focus on the flat band dispersion of coupled Dirac states from different twisted graphene layers. Here in this work, a new route to realizing flat band physics in monolayer graphene under a periodic modulation from substrates is proposed. Graphene/SiC heterostructure is taken as a prototypical example and it is demonstrated experimentally that the substrate modulation leads to Dirac fermion cloning and, consequently, the proximity of the two Dirac cones of monolayer graphene in momentum space. Theoretical modeling captures the cloning mechanism of the Dirac states and indicates that moiré flat bands can emerge at certain magic lattice constants of the substrate, specifically when the period of modulation becomes nearly commensurate with the ($\sqrt{3}$ x $\sqrt{3}$) R30° supercell of graphene. Our results show that epitaxial single monolayer graphene on suitable substrates is a promising platform for exploring exotic many-body quantum phases arising from interactions between Dirac electrons.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Massive expansion of multiple clones in the mouse hematopoietic system long after whole-body X-irradiation

Clonal hematopoiesis (CH) is prevalent in the elderly and associates with hematologic malignancy and cardiovascular disease. Although the risk of developing these diseases increases with radiation doses in atomic-bomb survivors, the causal relationship between radiation exposure and CH is unclear. This study investigated whether radiation exposure induces CH in mice 12–18 months after 3-Gy whole-body irradiation. We found radiation-associated increases in peripheral blood myeloid cells and red blood cell distribution width (RDW). Deep sequencing of bone marrow and non-hematopoietic tissue cells revealed recurrent somatic mutations specifically in the hematopoietic system in 11 of 12 irradiated mice but none in 6 non-irradiated mice. The irradiated mice possessed mutations with variant allele frequencies (VAFs) of > 0.02 on an average of 5.8 per mouse; mutations with VAFs of > 0.1 and/or deletion were prevalent. Examining hematopoietic stem/progenitor cells in two irradiated mice revealed several mutations co-existing in the same clones and multiple independent clones that deliver 60–80% of bone marrow nuclear cells. Our results indicate development of massive CH due to radiation exposure. Moreover, we have characterized mutations in radiation-induced CH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cloning the Dirac cones of bilayer graphene to the zone center by selenium adsorption

Dirac cones can foster extraordinary electronic effects, as exemplified by the case of graphene layers. Angle-resolved photoemission reveals that adsorption of selenium (Se) vapor on bilayer graphene creates a symmetric hybrid clone of the Dirac cones at the zone center. A detailed analysis aided by first-principles calculations shows that the adsorbed layer consists of an ordered array of Se 8 molecules. The uncovered cloning mechanism illustrates a method to generate electronic features of scientific and technological interests by gentle surface modification via van der Waals adsorption.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Annotated genome sequence of a fast-growing diploid clone of red alder ( Alnus rubra Bong.)

Abstract Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield

Abstract Background In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species. Methods A total of 116 CRAB isolates (2010–15), together with representatives of a previously described CRAB collection (4 isolates, 2001–06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis. Results A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001–04), OXA-40-producing ST98Oxf (2002–06), OXA-23-producing ST208Oxf (2006–10) and OXA-23-producing ST218Oxf (2010–15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5–28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000). Conclusions Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen–host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.

Silva, Liliana↗