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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗
DOE OSTI2016

Model polymer etching and surface modification by a time modulated RF plasma jet: role of atomic oxygen and water vapor

The surface interaction of a well-characterized time modulated radio frequency (RF) plasma jet with polystyrene, poly(methyl methacrylate) and poly(vinyl alcohol) as model polymers is investigated. The RF plasma jet shows fast polymer etching but mild chemical modification with a characteristic carbonate ester and NO formation on the etched surface. By varying the plasma treatment conditions including feed gas composition, environment gaseous composition, and treatment distance, we find that short lived species, especially atomic O for Ar/1% O 2 and 1% air plasma and OH for Ar/1% H 2 O plasma, play an essential role for polymer etching. For O 2 containing plasma, we find that atomic O initiates polymer etching and the etching depth mirrors the measured decay of O atoms in the gas phase as the nozzlesurface distance increases. Here, the etching reaction probability of an O atom ranging from 10 –4 to 10 –3 is consistent with low pressure plasma research. We also find that adding O 2 and H 2 O simultaneously into Ar feed gas quenches polymer etching compared to adding them separately which suggests the reduction of O and OH density in Ar/O 2 /H 2 O plasma.

atomic O↗
DOE OSTI2018

Combining CO 2 Reduction with Ethane Oxidative Dehydrogenation by Oxygen-Modification of Molybdenum Carbide

The surface properties that determine the selectivity of Mo 2 C catalysts in ethane oxidative dehydrogenation with CO 2 as a soft oxidant were investigated using a combination of pulse experiments and in-situ spectroscopic methods. Oxygen modification was discovered to be crucial for inhibiting the cleavage of the C–C bond in ethane and enhancing the production of ethylene. Here, the addition of the Fe promoter accelerated the formation of surface oxygen species and stabilized them from reduction by ethane, leading to a shorter induction period, higher ethylene yield, and improved stability.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Modification of cell wall polysaccharide guides cell division in Streptococcus mutans

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1985

Description, validation, and modification of the Guyton model for space-flight applications. Part A. Guyton model of circulatory, fluid and electrolyte control. Part B. Modification of the Guyton model for circulatory, fluid and electrolyte control

The mathematical model that has been a cornerstone for the systems analysis of space-flight physiological studies is the Guyton model describing circulatory, fluid and electrolyte regulation. The model and the modifications that are made to permit simulation and analysis of the stress of weightlessness are described.

Leonard, J. I.↗
DOE OSTI2015

Targeted Single-Site MOF Node Modification: Trivalent Metal Loading via Atomic Layer Deposition

Postsynthetic functionalization of metal organic frameworks (MOFs) enables the controlled, high-density incorporation of new atoms on a crystallographically precise framework. Leveraging the broad palette of known atomic layer deposition (ALD) chemistries, ALD in MOFs (AIM) is one such targeted approach to construct diverse, highly functional, few-atom clusters. We here demonstrate the saturating reaction of trimethylindium (InMe3) with the node hydroxyls and ligated water of NU-1000, which takes place without significant loss of MOF crystallinity or internal surface area. We computationally identify the elementary steps by which trimethylated trivalent metal compounds (ALD precursors) react with this Zr-based MOF node to generate a uniform and well characterized new surface layer on the node itself, and we predict a final structure that is fully consistent with experimental X-ray pair distribution function (PDF) analysis. We further demonstrate tunable metal loading through controlled number density of the reactive handles (-OH and -OH2) achieved through node dehydration at elevated temperatures.

atomic layer deposition in MOF↗
DOE OSTI2018

Li-rich Li[Li1/6Fe1/6Ni1/6Mn1/2]O2 (LFNMO) Cathodes: Atomic Scale Insight on the Mechanisms of Cycling Decay and of the Improvement due to Cobalt Phosphate Surface Modification

Lithium-rich Li[Li1/6Fe1/6Ni1/6Mn1/2]O2(0.4Li2MnO3-0.6LiFe1/3Ni1/3Mn1/3O2, LFNMO) is a new member of the xLi2MnO3·(1-x)LiMO2 family of high capacity - high voltage LIB cathodes. Unfortunately, it suffers from the severe degradation during cycling both in terms of reversible capacity and operating voltage. We are the first to document the corresponding degradation occurring in LFNMO at an atomic scale using aberration- corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) , as well as tracing the elemental crossover to the Li metal anode using XPS. We also demonstrate that a phosphate coating significantly boosts LFNMO cycling stability and rate capability. Due to cycling, the unmodified LFNMO undergoes extensive elemental dissolution (especially Mn) and O loss, forming Kirkendall-type voids. The associated structural degradation is from the as-synthesized R-3m layered structure to a disordered rock-salt phase. Prior to cycling, the phosphate coating shares the crystallography of the parent material. During cycling, a 2-3 nm thick disordered Co-based rock-salt structure is formed on the Mod-LFNMO surface, while the bulk material retains R-3m crystallography. Electrochemical impedance spectroscopy (EIS) analysis highlights how the phosphide treatment stabilizes the charge transfer resistance (RCT), the CEI resistance (RCEI), and the lithium ion diffusion coefficient (DLi). XPS analysis demonstrates that the coating also reduces the amount of cross-over Mn, Fe and especially Ni deposited on the Li metal anode, which is expected to lead to a more stable SEI layer during cycling. These combined cathode - anode findings significantly advance the microstructural design principles for next generation Li-rich cathode materials and coatings.

: high voltage cathode, Li - and Mn - rich cathode↗
DOE OSTI2021

Oxidation and Associated Pore Structure Modification During Experimental Alteration of Granite

Weathering plays a crucial role in a number of environmental processes, and the microstructure and evolution of multi-scale pore space is a critically important factor in the weathering of geological formations. In igneous rocks the infiltration of meteoric water into initially relatively dry material can cause the rock to begin to disaggregate, increasing porosity and surface area, and allowing further disaggregation and weathering to occur. These processes, in turn, allow biota to colonize the rock, further enhancing the weathering rate. In some igneous rocks this may be driven by oxidation of primary minerals. One such mineral, biotite, has been repeatedly mentioned as a cause of cracking during oxidation. However, the scale-dependence of the processes by which this occurs are poorly understood. We cannot, therefore, accurately extrapolate laboratory reaction rates to the field in predictive numerical models. In order to better understand the effects of oxidation and test the hypothesis that fracture and disaggregation are initiated by swelling of oxidizing biotites, we reacted granite cores in a selenic acid-rich aqueous solution at 200°C for up to 438 days. Elevated temperatures and selenic acid were used to provide relatively fast reaction rates and highly oxidizing conditions in sealed reaction vessels. These experiments were analyzed using a combination of imaging, X-ray diffraction, Mössbauer spectroscopy, and small- and ultra-small angle neutron scattering to interrogate porosity and microfracture formation. The experimental results show little observable biotite swelling, but significant transport and growth of iron oxides and/or clays along grain boundaries throughout the sample. Significant increases in porosity were also observed at the sample rim, likely associated with feldspar alteration. Fractures and transport were observed throughout the core, suggesting that stresses due to crystallization pressures caused by the growing iron phases may be the initiating factors in granite weathering, possibly followed by biotite swelling after sufficient permeability is achieved.

Anovitz, Lawrence M.↗