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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 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Morphologies of ABC Triblock Terpolymer Melts Containing Poly(Cyclohexadiene): Effects of Conformational Asymmetry

We have synthesized linear ABC triblock terpolymers containing poly(1,3-cyclohexadiene), PCHD, as an end block and characterized their morphologies in the melt. Specifically, we have studied terpolymers containing polystyrene (PS), polybutadiene (PB), and polyisoprene (PI) as the other blocks. Systematically varying the ratio of 1,2- /1,4-microstructures of poly(1,3-cyclohexadiene), we have studied the effects of conformational asymmetry among the three blocks on the morphologies using transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and self-consistent field theory (SCFT) performed with PolySwift++. Our work reveals that the triblock terpolymer melts containing a high percentage of 1,2-microstructures in the PCHD block are disordered at 110 °C for all the samples, independent of sequence and volume fraction of the blocks. In contrast, the triblock terpolymer melts containing a high percentage of 1,4-microstructure form regular morphologies known from the literature. The accuracy of the SCFT calculations depends on calculating the χ parameters that quantify the repulsive interactions between different monomers. Simulations using χ values obtained from solubility parameters and group contribution methods are unable to reproduce the morphologies as seen in the experiments. However, SCFT calculations accounting for the enhancement of the χ parameter with an increase in the conformational asymmetry lead to an excellent agreement between theory and experiments. Lastly, these results highlight the importance of conformational asymmetry in tuning the χ parameter and, in turn, morphologies in block copolymers.

36 MATERIALS SCIENCE↗
DOE OSTI2015

NMR diffusion-encoding with axial symmetry and variable anisotropy: Distinguishing between prolate and oblate microscopic diffusion tensors with unknown orientation distribution

We introduce a nuclear magnetic resonance method for quantifying the shape of axially symmetric microscopic diffusion tensors in terms of a new diffusion anisotropy metric, D{sub Δ}, which has unique values for oblate, spherical, and prolate tensor shapes. The pulse sequence includes a series of equal-amplitude magnetic field gradient pulse pairs, the directions of which are tailored to give an axially symmetric diffusion-encoding tensor b with variable anisotropy b{sub Δ}. Averaging of data acquired for a range of orientations of the symmetry axis of the tensor b renders the method insensitive to the orientation distribution function of the microscopic diffusion tensors. Proof-of-principle experiments are performed on water in polydomain lyotropic liquid crystals with geometries that give rise to microscopic diffusion tensors with oblate, spherical, and prolate shapes. The method could be useful for characterizing the geometry of fluid-filled compartments in porous solids, soft matter, and biological tissues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

SU-E-J-186: Acquiring and Assessing Upright CBCT Images for Future Treatment Planning

Purpose: To acquire upright CBCT images using the onboard imager of a Varian TrueBeam. An easy to implement upright imaging protocol could allow for widespread upright radiation therapy which would greatly benefit certain patients. These include thoracic cancer patients (because lung volume increases in a seated position) and patients who experience substantial discomfort during supine treatment. Methods: To acquire upright CBCT images, the gantry head remained stationary at 0 degrees with the KV imager arms extended to their lateral positions. Phantoms were placed upright at the end of the treatment couch. During a scan, the couch rotated from 270 to 90 degrees while continuous fluoroscopic projections were taken by the onboard imager. To extend the field-of-view, this sequence was performed twice: once with the KV detector longitudinally offset +14.5cm and once with it longitudinally offset −14.5cm. The resulting two image sets were stitched together before reconstruction. The imaging beam parameters were chosen to deliver a dose similar to that given during a simulation CT. Image quality was evaluated for spatial linearity, high and low contrast resolution, and HU linearity using CatPhan and anthropomorphic phantoms. A deformable registration technique was used to evaluate HU mapping from a simulation CT. Results: Spatial linearity and high contrast resolution were maintained in upright CBCT when compared to simulation CT. However, low contrast resolution and HU linearity degraded. Streak artifacts were caused by the limited 180 degree arc of the couch, and the stitching process created a sharp artifact at the center of the reconstruction. The deformable registration was robust in the HU mapping even with these artifacts and the loss of HU linearity. Conclusions: The image quality obtained from upright CBCT was sufficient for treatment planning. The success of this novel technique is an important step towards a future clinical protocol. This project was funded in part by Varian Medical Systems, Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗
DOE OSTI2013

US DOE Perspectives on Advisory Board Effectiveness - 13539

Federal missions on the Oak Ridge Reservation began with the Manhattan Project, and continues today with major facilities supporting the Nation's Science and National Security missions. While most of the land area on the Oak Ridge Reservation is free of environmental impacts from these activities, significant legacy contamination is associated with specific facilities and past waste management areas. In 1989, the Oak Ridge Reservation (ORR) was placed on National Priorities List, and DOE established its Office of Environmental Management that same year. Three years later, in 1992, the Federal Facility Agreement for the reservation was signed. Three years afterward, the Oak Ridge Site Specific Advisory Board was established to augment ongoing public involvement activities related to Oak Ridge Reservation cleanup activities. One of the early and most impactful decisions the board made was to organize the End Use Working Group. This broad-based group of board members, DOE representatives, and members of the public was formed in 1997 to study future uses for contaminated areas of the reservation. The group was instrumental in building consensus in the Oak Ridge community regarding the long-term end state of reservation lands. The group's recommendations were a fundamental input into Record's of Decision subsequently developed to establish cleanup requirements across the ORR, and they continue to influence decisions being made today. In developing its recommendations on end states, the End Use Working Group came to the realization that long-term stewardship of contaminated areas of the reservation would be necessary, in some cases in perpetuity. It was from this concept that the Oak Ridge SSAB's 15-year involvement in stewardship would begin. A stewardship committee formed by the End Use Working Group wrote Volume 1 of the Stakeholder Report on Stewardship. This document-and its companion Volume 2, which was written a year later-form a crucial foundation for stewardship planning in Oak Ridge and have been referenced around the DOE complex as other sites consider stewardship planning. From these two broad-based initiatives, the board's focus has evolved to increasingly hone in on more specific, project-based recommendations and initiatives. The Oak Ridge Reservation Site Specific Advisory Board has been a highly effective forum for soliciting community input on Oak Ridge Reservation cleanup. Experience in Oak Ridge indicates that the utility of Board recommendations is far higher when the Board is asked to focus on broad programmatic issues, and less useful when the Board attempts to provide advice and recommendations on matters related to technical or project management issues. In Oak Ridge the Board has helped shape the program on many levels including definition of end-state cleanup objectives, budget development, program sequencing, waste management, and decisions concerning preservation of history related to missions implemented on the Oak Ridge Reservation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

A two-level approach to large mixed-integer programs with application to cogeneration in energy-efficient buildings

We study a two-stage mixed-integer linear program (MILP) with more than 1 million binary variables in the second stage. We develop a two-level approach by constructing a semi-coarse model that coarsens with respect to variables and a coarse model that coarsens with respect to both variables and constraints. We coarsen binary variables by selecting a small number of prespecified on/off profiles. We aggregate constraints by partitioning them into groups and taking convex combination over each group. With an appropriate choice of coarsened profiles, the semi-coarse model is guaranteed to find a feasible solution of the original problem and hence provides an upper bound on the optimal solution. We show that solving a sequence of coarse models converges to the same upper bound with proven finite steps. This is achieved by adding violated constraints to coarse models until all constraints in the semi-coarse model are satisfied. We demonstrate the effectiveness of our approach in cogeneration for buildings. Here, the coarsened models allow us to obtain good approximate solutions at a fraction of the time required by solving the original problem. Extensive numerical experiments show that the two-level approach scales to large problems that are beyond the capacity of state-of-the-art commercial MILP solvers.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2014

Cervical Gross Tumor Volume Dose Predicts Local Control Using Magnetic Resonance Imaging/Diffusion-Weighted Imaging—Guided High-Dose-Rate and Positron Emission Tomography/Computed Tomography—Guided Intensity Modulated Radiation Therapy

Purpose: Magnetic resonance imaging/diffusion weighted-imaging (MRI/DWI)-guided high-dose-rate (HDR) brachytherapy and {sup 18}F-fluorodeoxyglucose (FDG) — positron emission tomography/computed tomography (PET/CT)-guided intensity modulated radiation therapy (IMRT) for the definitive treatment of cervical cancer is a novel treatment technique. The purpose of this study was to report our analysis of dose-volume parameters predicting gross tumor volume (GTV) control. Methods and Materials: We analyzed the records of 134 patients with International Federation of Gynecology and Obstetrics stages IB1-IVB cervical cancer treated with combined MRI-guided HDR and IMRT from July 2009 to July 2011. IMRT was targeted to the metabolic tumor volume and lymph nodes by use of FDG-PET/CT simulation. The GTV for each HDR fraction was delineated by use of T2-weighted or apparent diffusion coefficient maps from diffusion-weighted sequences. The D100, D90, and Dmean delivered to the GTV from HDR and IMRT were summed to EQD2. Results: One hundred twenty-five patients received all irradiation treatment as planned, and 9 did not complete treatment. All 134 patients are included in this analysis. Treatment failure in the cervix occurred in 24 patients (18.0%). Patients with cervix failures had a lower D100, D90, and Dmean than those who did not experience failure in the cervix. The respective doses to the GTV were 41, 58, and 136 Gy for failures compared with 67, 99, and 236 Gy for those who did not experience failure (P<.001). Probit analysis estimated the minimum D100, D90, and Dmean doses required for ≥90% local control to be 69, 98, and 260 Gy (P<.001). Conclusions: Total dose delivered to the GTV from combined MRI-guided HDR and PET/CT-guided IMRT is highly correlated with local tumor control. The findings can be directly applied in the clinic for dose adaptation to maximize local control.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering

Inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, herein we report the design of sequence-defined peptoids for biomimetic synthesis of flower-like gold nanosuperstruc-tures. We demonstrate that the peptoid-induced morphosyn-thesis of gold nanoflowers is sequence-dependent. By varying the hydrophobicity, number of carboxylate and amino groups, and side-chain positions of peptoids, we develop a rule of thumb for designing peptoids that yield gold nanoflowers. Through a combination of hyperspectral UV-Vis absorption micro-spectroscopy (H-UVVIS-AMS) and three-photon photoemission electron microscopy (TP-PEEM), we measured the plasmonic properties of individual nanoflowers. Whereas H-UVVIS-AMS experiments revealed well-defined plasmon resonances centered at ~528 nm, TP-PEEM measurements showed an unprecedented plasmonic enhancement as high as 105 for a single nanoflower. A com-bination of the unique plasmonic property and the high sta-bility endows the peptoid-engineered nanoflowers with po-tential applications in chemical and biological imaging. FY, YC, HJ and C-LC acknowledge support by the Materials Synthesis and Simulation Across Scales (MS3) Initiative, through the Laboratory Directed Research & Development (LDRD) fund at Pacific Northwest National Laboratory (PNNL). FY was also partially supported by fellowships from Shandong Provincial Education Association for International Exchanges. YG was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PZE acknowledges support from the Laboratory Directed Research and Development Program through a Linus Pauling Fellowship at PNNL. PNNL is multi-program national laboratory operated for the Department of Energy by Battelle under Contracts No. DE-AC05-76RL01830. The authors are most grateful to Alan Joly and Wayne Hess (PNNL) for their support with the PEEM measurements and several useful discussions.

Yan, Feng↗
DOE OSTI2017

Advanced Seismic Probabilistic Risk Assessment Methodology: Development of Beta 1.0 MASTODON Toolset

Design of nuclear power plant (NPP) facilities to resist natural hazards has been a part of the regulatory process from the beginning of the NPP industry in the United States, but has evolved substantially over time. The original set of approaches and methods was entirely deterministic in nature and focused on a traditional engineering margins-based approach. However, over time probabilistic and risk-informed approaches were also developed and implemented in US Nuclear Regulatory Commission guidance and regulation. A defense-in-depth framework has also been incorporated into US regulatory guidance over time. As a result, today, the US regulatory framework incorporates deterministic and probabilistic approaches for a range of different applications and for a range of natural hazard considerations. Although the US regulatory framework has continued to evolve over time, the tools, methods and data available to the US nuclear industry to meet the changing requirements have not kept pace. Notably, there is room for improvement in the tools and methods available for external event probabilistic risk assessment (PRA), which is the principal assessment approach used in risk-informed regulations and risk-informed decision-making applied to natural hazard assessment and design. Development of a new set of tools and methods that incorporate current knowledge, modern best practice, and state-of-the-art computational resources would lead to more reliable assessment of facility risk and risk insights (e.g., the plant elements and accident sequences that are most risk-significant), with less uncertainty and reduced conservatisms. Development of the next generation tools and methods for external events PRA is ongoing under the Risk Informed Safety Margins Characterization (RISMC) technical pathway. The RISMC toolkit development centers on integration of the tools and methods under a common framework, MOOSE. These tools and methods make use of existing and newly developed tools and methods, coupled with the experience and data gained in the past decades, to define and analyze more realistic risk assessment models. Specific focus in this report is on the capability to model seismic risk using advanced SPRA methods. Over the last year, significant capability has been added to Mastodon to simulate 3-D wave passage effects through nonlinear soil. Verification has demonstrated the capability of Mastodon to model wave passage effects in 1-D, 2-D, and 3-D. Methods have been developed to incorporate probabilistic floor response capabilities. Additional capability will be added to Mastodon over the next year to implement a robust gapping and sliding element for cyclic shaking, web-based verification and user manuals, stochastic finite elements, and frequency independent damping. Verification of added capabilities has occured in parallel with code writing activities.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2013

Secondary fusion coupled deuteron/triton transport simulation and thermal-to-fusion neutron convertor measurement

A Monte Carlo tool RSMC (Reaction Sequence Monte Carlo) was developed to simulate deuteron/triton transportation and reaction coupled problem. The 'Forced particle production' variance reduction technique was used to improve the simulation speed, which made the secondary product play a major role. The mono-energy 14 MeV fusion neutron source was employed as a validation. Then the thermal-to-fusion neutron convertor was studied with our tool. Moreover, an in-core conversion efficiency measurement experiment was performed with {sup 6}LiD and {sup 6}LiH converters. Threshold activation foils was used to indicate the fast and fusion neutron flux. Besides, two other pivotal parameters were calculated theoretically. Finally, the conversion efficiency of {sup 6}LiD is obtained as 1.97x10{sup -4}, which matches well with the theoretical result. (authors)

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress

Microalgae that are of interest for biofuel production must be able to tolerate environmental changes that occur in outdoor cultivation systems. While algal cultures may experience daily temperature fluctuations and seasonal environmental changes, the underlying mechanisms that control and regulate physiological responses and adaptation to environmental pressures are largely unknown. Systems-level characterization enabled by functional genomics can help identify biochemical pathways that promote stability and productivity of algae in various environmental conditions. Monoraphidium minutum 26B-AM, a freshwater green microalga, was identified as a top performer in biomass production in winter season screens. We sequenced the genome of M. minutum 26B-AM and applied our multi-omics pipeline to profile this high potential strain under high salt and cold temperature perturbations. Through comparative analysis, including other green algae in the class Chlorophyceae, we identified gene families unique to the genus Monoraphidium, including a desaturase that has been linked to cold tolerance in plants. We observed that osmolytes, such as trehalose, proline and betaine, accumulate under salt stress, coinciding with upregulation of genes involved in biosynthesis of these metabolites. From the genome annotation, we reconstructed a metabolic model to provide a detailed map of the metabolic pathways and can be used to simulate growth and reaction fluxes. This multi-omics analysis provides a foundation to explore algal strain potential for biofuel applications, guides strain engineering, and expands our understanding of metabolic and regulatory mechanisms of algae in applied systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Tension-dependent free energies of nucleosome unwrapping

Here, nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Femtosecond-resolved observation of the fragmentation of buckminsterfullerene following X-ray multiphoton ionization

X-ray free-electron lasers have, over the past decade, opened up the possibility of understanding the ultrafast response of matter to intense X-ray pulses. In earlier research on atoms and small molecules, new aspects of this response were uncovered, such as rapid sequences of inner-shell photoionization and Auger ionization. Here, we studied a larger molecule, buckminsterfullerene (C 60 ), exposed to 640 eV X-rays, and examined the role of chemical effects, such as chemical bonds and charge transfer, on the fragmentation following multiple ionization of the molecule. To provide time resolution, we performed femtosecond-resolved X-ray pump/X-ray probe measurements, which were accompanied by advanced simulations. The simulations and experiment reveal that despite substantial ionization induced by the ultrashort (20 fs) X-ray pump pulse, the fragmentation of C 60 is considerably delayed. This work uncovers the persistence of the molecular structure of C 60 , which hinders fragmentation over a timescale of hundreds of femtoseconds. Furthermore, we demonstrate that a substantial fraction of the ejected fragments are neutral carbon atoms. In conclusion, these findings provide insights into X-ray free-electron laser-induced radiation damage in large molecules, including biomolecules.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Direct observation of the exotic β – γ – α decay mode in the T z = – 1 nucleus Na 20

The exotic β – γ – α decay mode of 20 Na has been directly observed for the first time in the Day-one experiment at the Beijing Radioactive Ion-beam Facility. The 20 Na source was produced by using a 100-MeV proton beam bombarding a stack of microporous MgO thick target and delivered as an intense mass separated beam after online ionization. A high-efficiency simultaneous measurement of β, γ, and α transitions enables the β-delayed γ – γ and α – γ coincidence spectroscopy. Here three β – γ – α exotic decay sequences in 20 Na are discovered, which expands the rare decay modes observed in β decay. Moreover, a β – α –decay sequence to the 6130-keV 3 – state of 16 O is observed, which is likely through the 12367-keV 1 + state in 20 Ne. The experimentally deduced B(F) and B(GT) are compared to the shell-model calculation, the allowed β transition strengths can be well accounted for by using sd shell-model space interactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. Furthermore, we sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/ absence of M. cysteinexigens. In independent comparative phylogenomic analyses of fungal and bacterial genomes we find that they are consistent with an ancient origin for M. elongata M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Gap Resolution

Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.

Labutti, Kurt↗