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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4

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NASA NTRS1989

Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

Weber, Arthur L.↗

NASA NTRS1990

Low cost management of replicated data in fault-tolerant distributed systems

Many distributed systems replicate data for fault tolerance or availability. In such systems, a logical update on a data item results in a physical update on a number of copies. The synchronization and communication required to keep the copies of replicated data consistent introduce a delay when operations are performed. A technique is described that relaxes the usual degree of synchronization, permitting replicated data items to be updated concurrently with other operations, while at the same time ensuring that correctness is not violated. The additional concurrency thus obtained results in better response time when performing operations on replicated data. How this technique performs in conjunction with a roll-back and a roll-forward failure recovery mechanism is also discussed.

Joseph, Thomas A.↗

NASA NTRS1989

Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

Weber, Arthur L.↗

NASA NTRS1992

Self-replication of chemical systems based on recognition within a double or a triple helix - A realistic hypothesis

A scenario is proposed for the non-enzymatic self-replication of short RNA molecules. The self-replication of an oligopyrimidine strand is considered and the process of template-directed synthesis based on recognition within a double helix is discussed. Replication mechanisms are suggested for selected oligonucleotides. The mechanisms are based on Watson-Crick base pairing between complementary nucleotides as well as Hoogsteen base pairing between a duplex and the complementary third strand. It is suggested that self-replication based on these mechanisms may be accomplished but may result in a substantial amount of misinformation transfer when mixed oligonucleotides are used.

Kanavarioti, Anastassia↗

NASA NTRS2002

Who or What? Self-Replication and Function-Reproduction in the Origin of Life

In this presentation, we will present results on the fundamental properties of two classes of replicating systems: autocatalytic replicators that reproduce exact copies of a template molecule, and function reproducers that maintain a set of essential functions without replicating the identities of the functional moieties. We will describe the stability and behavior in-the-large of autocatalytic replicators. Most importantly, we have found no sharp distinction between an autocatalytic and a non-autocatalytic domain. We will also present a new derivation of von Kiedrowski's square-root rate law. Function - reproducers are proposed as an important component of protocells and we will present theoretical results on a simple model system that incorporates known peptide biophysics. For a wide range of parameters, we have shown that this type of system can improve its overall performance, even in the absence of any method for information storage. This type of system improvement is defined to be non-genomic evolution.

New, Michael H.↗

NASA NTRS2019

Deterministic Polishing of Replicating Grazing-Incidence Mandrels

In an effort to manufacture high-angular-resolution, grazing-incidence, x-ray optics, Marshall Space Flight Center (MSFC) is taking measures to improve its electroformed replicated optics. A key development is the use of computer-numerical control (CNC) polishing to deterministically improve the surface of electroless nickel mandrels used to replicate grazing- incidence optics. Metrology, control software and polishing parameters must function together seamlessly to reach the specifications required to replicate sub-arcsecond optics. Each change in polishing parameters effects the wear pattern of the polishing head. Using Richardson-Lucy deconvolution, the controller software fits the wear pattern to metrology data to calculate the changing feedrates across the mandrel. Here we present an overview of our process, and early results showing the effectiveness of deterministic polishing for replicated optics.

Davis, Jacqueline↗

DOE OSTI2026

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗

DOE OSTI2024

A comparison of model validation approaches for echo state networks using climate model replicates

As global temperatures continue to rise, climate mitigation strategies such as stratospheric aerosol injections (SAI) are increasingly discussed, but the downstream effects of these strategies are not well understood. As such, there is interest in developing statistical methods to quantify the evolution of climate variable relationships during the time period surrounding an SAI. Feature importance applied to echo state network (ESN) models has been proposed as a way to understand the effects of SAI using a data-driven model. This approach depends on the ESN fitting the data well. If not, the feature importance may place importance on features that are not representative of the underlying relationships. Typically, time series prediction models such as ESNs are assessed using out-of-sample performance metrics that divide the times series into separate training and testing sets. However, this model assessment approach is geared towards forecasting applications and not scenarios such as the motivating SAI example where the objective is using a data driven model to capture variable relationships. Here, in this paper, we demonstrate a novel use of climate model replicates to investigate the applicability of the commonly used repeated hold-out model assessment approach for the SAI application. Simulations of an SAI are generated using a simplified climate model, and different initialization conditions are used to provide independent training and testing sets containing the same SAI event. The climate model replicates enable out-of-sample measures of model performance, which are compared to the single time series hold-out validation approach. For our case study, it is found that the repeated hold-out sample performance is comparable, but conservative, to the replicate out-of-sample performance when the training set contains enough time after the aerosol injection.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Dissolvable Template Nanoimprint Lithography: A Facile and Versatile Nanoscale Replication Technique

Nanoimprinting lithography (NIL) is a next-generation nanofabrication method, capable of replicating nanostructures from original master surfaces. In this work, we develop highly scalable, simple, and nondestructive NIL using a dissolvable template. Termed dissolvable template nanoimprinting lithography (DT-NIL), our method utilizes an economic thermoplastic resin to fabricate nanoimprinting templates, which can be easily dissolved in simple organic solvents. Additionally, we used the DT-NIL method to replicate cicada wings which have surface nanofeatures of ~100 nm in height. The master, template, and replica surfaces showed a >~94% similarity based on the measured diameter and height of the nanofeatures. The versatility of DT-NIL was also demonstrated with the replication of re-entrant, multiscale, and hierarchical features on fly wings, as well as hard silicon wafer-based artificial nanostructures. The DT-NIL method can be performed under ambient conditions with inexpensive materials and equipment. Our work opens the door to opportunities for economical and high-throughput nanofabrication processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles

$RAD51C$ is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural and related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog and define separable RAD51C replication stability roles informed by its three-dimensional structure, assembly, and unappreciated polymerization motif. Mapping of cancer patient mutations as a functional guide confirms ATP-binding matching RAD51 recombinase yet highlights distinct CX3 interfaces. Analyses of CRISPR/Cas9-edited human cells with $RAD51C$ mutations combined with single-molecule, single-cell and biophysics measurements uncover discrete CX3 regions for DNA replication fork protection, restart and reversal, accomplished by separable functions in DNA binding and implied 5’ RAD51 filament capping. Collective findings establish CX3 as a cancer-relevant replication stress response complex, show how HDR-proficient variants could contribute to tumor development, and identify regions to aid functional testing and classification of cancer mutations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Alternative Designs and Analyses for Destructive and Non-replicable Gauge R &R Studies

This article presents new designs and their analyses for destructive and non-replicable gauge R & R studies. Less restrictive assumptions about destructive measurements on “similar” parts and non-replicable measurements made over time or space than have been made previously in the literature are proposed; only couples of “nearly identical” parts are proposed for destructive measurements and quadruples involving two operators are proposed for non-replicable measurements that avoid having to estimate a common trend and removing it. In this work, these new designs based on balanced incomplete block designs and their analyses are illustrated with simulated examples that confirm that with them such measurements systems can be assessed.

42 ENGINEERING↗

DOE OSTI2023

Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast

Abstract Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.

Carvalho Borges, Pâmela C. (ORCID:0000000244919874↗

DOE OSTI2023

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A global lipid map defines a network essential for Zika virus replication

>Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we performed comprehensive lipidomics to create a lipid network map during ZIKV infection. We found that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein resulted in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocked ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Artificial Soiling Replication of Field Losses on Commercial Photovoltaic Modules

Here, this study demonstrates the capabilities of an indoor artificial soiling approach developed to closely replicate the natural, cyclic soil accumulation processes in the field-dust suspension, deposition, and sedimentation/cementation-for a subtropical climate. In this work, a near-field environment is replicated in an artificial soiling cubic chamber through controlled regulation of humidity, temperature, dust type, and dust concentration, based on site-specific historical climate data. Two different models (MA and MB) of full-size commercial photovoltaic modules from a single manufacturer, installed side by side in the mid-Atlantic United States, were retrieved and subjected to artificial soiling experiments and various characterization measurements, including short-circuit current, colorimetry, reflectance, X-ray fluorescence, laser diffraction, and optical microscopy. Both in the field and in our improved field-representative artificial soiling tests, the MA model experienced roughly twice the soiling loss as the MB model. To closely replicate the field soiling losses for a site-specific climate, it is critical to include: 1) The use of field-collected dust with identical dust chemistry and particle distribution instead of standardized ISO 12103 Arizona Road dusts, 2) the use of only a small amount of field-collected dust inside the chamber during the deposition process (e.g., 0.15 g), and 3) the preconditioning of the surface coating for the partial/full dose of UV stress as experienced in the field during sunlight exposure and the abrasion as experienced in the field during regular module cleaning activities, if/as needed. The field-representative artificial soiling method developed here could potentially be adopted for rank ordering of various antisoiling coatings developed by researchers and industry stakeholders.

14 SOLAR ENERGY↗

DOE OSTI2021

Processing Aleatory and Epistemic Uncertainties in Experimental Data From Sparse Replicate Tests of Stochastic Systems for Real-Space Model Validation

This paper presents a practical methodology for propagating and processing uncertainties associated with random measurement and estimation errors (that vary from test-to-test) and systematic measurement and estimation errors (uncertain but similar from test-to-test) in inputs and outputs of replicate tests to characterize response variability of stochastically varying test units. Also treated are test condition control variability from test-to-test and sampling uncertainty due to limited numbers of replicate tests. These aleatory variabilities and epistemic uncertainties result in uncertainty on computed statistics of output response quantities. The methodology was developed in the context of processing experimental data for “real-space” (RS) model validation comparisons against model-predicted statistics and uncertainty thereof. The methodology is flexible and sufficient for many types of experimental and data uncertainty, offering the most extensive data uncertainty quantification (UQ) treatment of any model validation method the authors are aware of. It handles both interval and probabilistic uncertainty descriptions and can be performed with relatively little computational cost through use of simple and effective dimension- and order-adaptive polynomial response surfaces in a Monte Carlo (MC) uncertainty propagation approach. A key feature of the progressively upgraded response surfaces is that they enable estimation of propagation error contributed by the surrogate model. Sensitivity analysis of the relative contributions of the various uncertainty sources to the total uncertainty of statistical estimates is also presented. Finally, the methodologies are demonstrated on real experimental validation data involving all the mentioned sources and types of error and uncertainty in five replicate tests of pressure vessels heated and pressurized to failure. Simple spreadsheet procedures are used for all processing operations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Fabrication of low blaze angle gratings by replication and plasma etch

We suggest a new method of making ultra-low blaze angle gratings for synchrotron application. The method is based on reduction of the blaze angle of a master grating by replication followed by a plasma etch. A master blazed grating with a relatively large blaze angle is fabricated by anisotropic wet etching of a Si single crystal substrate. The surface of the master grating is replicated by a polymer material on top of a quartz substrate by nanoimprinting and then transferred into quartz by a plasma etch. Then a 2nd nanoimprint step is applied to transfer the saw-tooth surface into a resist layer on top of a Si grating substrate. The plasma etch through the patterned resist layer provides transfer of the grooves into the Si substrate and results in reduction of the blaze angle due to the difference in etch rates of the resist and Si. We investigated the impact of the replication process on the groove shape, facet surface roughness, and diffraction efficiency of the fabricated 200 lines/mm low blaze angle grating.

Park, Sooyeon↗

DOE OSTI2023

Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types

While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism.

59 BASIC BIOLOGICAL SCIENCES↗