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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Third international challenge to model the medium- to long-range transport of radioxenon to four Comprehensive Nuclear-Test-Ban Treaty monitoring stations

In 2015 and 2016, atmospheric transport modeling challenges were conducted in the context of the Comprehensive Nuclear-Test-Ban Treaty (CTBT) verification, however, with a more limited scope with respect to emission inventories, simulation period and number of relevant samples (i.e., those above the Minimum Detectable Concentration (MDC)) involved. Therefore, a more comprehensive atmospheric transport modeling challenge was organized in 2019. Stack release data of Xe-133 were provided by the Institut National des Radioéléments/IRE (Belgium) and the Canadian Nuclear Laboratories/CNL (Canada) and accounted for in the simulations over a three (mandatory) or six (optional) months period. Best estimate emissions of additional facilities (radiopharmaceutical production and nuclear research facilities, commercial reactors or relevant research reactors) of the Northern Hemisphere were included as well. Model results were compared with observed atmospheric activity concentrations at four International Monitoring System (IMS) stations located in Europe and North America with overall considerable influence of IRE and/or CNL emissions for evaluation of the participants’ runs. Participants were prompted to work with controlled and harmonized model set-ups to make runs more comparable, but also to increase diversity. It was found that using the stack emissions of IRE and CNL with daily resolution does not lead to better results than disaggregating annual emissions of these two facilities taken from the literature if an overall score for all stations covering all valid observed samples is considered. A moderate benefit of roughly 10% is visible in statistical scores for samples influenced by IRE and/or CNL to at least 50% and there can be considerable benefit for individual samples. Effects of transport errors, not properly characterized remaining emitters and long IMS sampling times (12–24 h) undoubtedly are in contrast to and reduce the benefit of high-quality IRE and CNL stack data. Complementary best estimates for remaining emitters push the scores up by 18% compared to just considering IRE and CNL emissions alone. Despite the efforts undertaken the full multi-model ensemble built is highly redundant. An ensemble based on a few arbitrary runs is sufficient to model the Xe-133 background at the stations investigated. The effective ensemble size is below five. An optimized ensemble at each station has on average slightly higher skill compared to the full ensemble. However, the improvement (maximum of 20% and minimum of 3% in RMSE) in skill is likely being too small for being exploited for an independent period.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Technique for comprehensive head and neck irradiation using 3-dimensional conformal proton therapy

Owing to the technical and logistical complexities of matching photon and proton treatment modalities, we developed and implemented a technique of comprehensive head and neck radiation using 3-dimensional (3D) conformal proton therapy. A monoisocentric technique was used with a 30-cm snout. Cervical lymphatics were treated with 3 fields: a posterior-anterior field with a midline block and a right and a left posterior oblique field. The matchline of the 3 cervical nodal fields with the primary tumor site fields was staggered by 0.5 cm. Comparative intensity-modulated photon plans were later developed for 12 previously treated patients to provide equivalent target coverage, while matching or improving on the proton plans' sparing of organs at risk (OARs). Dosimetry to OARs was evaluated and compared by treatment modality. Comprehensive head and neck irradiation using proton therapy yielded treatment plans with significant dose avoidance of the oral cavity and midline neck structures. When compared with the generated intensity-modulated radiation therapy (IMRT) plans, the proton treatment plans yielded statistically significant reductions in the mean and integral radiation dose to the oral cavity, larynx, esophagus, and the maximally spared parotid gland. There was no significant difference in mean dose to the lesser-spared parotid gland by treatment modality or in mean or integral dose to the spared submandibular glands. A technique for cervical nodal irradiation using 3D conformal proton therapy with uniform scanning was developed and clinically implemented. Use of proton therapy for cervical nodal irradiation resulted in large volume of dose avoidance to the oral cavity and low dose exposure to midline structures of the larynx and the esophagus, with lower mean and integral dose to assessed OARs when compared with competing IMRT plans.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. Additionally, we developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Comprehensive Model of Single Particle Pulverized Coal Combustion Extended to Oxy-Coal Conditions

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive CFD simulations are valuable tools in evaluating and deploying oxy-fuel and other carbon capture technologies either as retrofit technologies or for new construction. But, accurate predictive simulations require physically realistic submodels with low computational requirements. In particular, comprehensive char oxidation and gasification models have been developed that describe multiple reaction and diffusion processes. Our work extends a comprehensive char conversion code (CCK), which treats surface oxidation and gasification reactions as well as processes such as film diffusion, pore diffusion, ash encapsulation, and annealing. In this work several submodels in the CCK code were updated with more realistic physics or otherwise extended to function in oxy-coal conditions. Improved submodels include the annealing model, the swelling model, the mode of burning parameter, and the kinetic model, as well as the addition of the chemical percolation devolatilization (CPD) model. We compare our results of the char combustion model to oxy-coal data, and further compared to parallel data sets near conventional conditions. A potential method to apply the detailed code in CFD work is given.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2018

NCAR Release of CAM‐SE in CESM2.0: A Reformulation of the Spectral Element Dynamical Core in Dry‐Mass Vertical Coordinates With Comprehensive Treatment of Condensates and Energy

Abstract It is the purpose of this paper to provide a comprehensive documentation of the new NCAR (National Center for Atmospheric Research) version of the spectral element (SE) dynamical core as part of the Community Earth System Model (CESM2.0) release. This version differs from previous releases of the SE dynamical core in several ways. Most notably the hybrid sigma vertical coordinate is based on dry air mass, the condensates are dynamically active in the thermodynamic and momentum equations (also referred to as condensate loading), and the continuous equations of motion conserve a more comprehensive total energy that includes condensates. Not related to the vertical coordinate change, the hyperviscosity operators and the vertical remapping algorithms have been modified. The code base has been significantly reduced, sped up, and cleaned up as part of integrating SE as a dynamical core in the CAM (Community Atmosphere Model) repository rather than importing the SE dynamical core from High‐Order Methods Modeling environment as an external code.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Abstract While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii , we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N -glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Global roll-out of comprehensive policy measures may aid in bridging emissions gap

Closing the emissions gap between Nationally Determined Contributions (NDCs) and the global emissions levels needed to achieve the Paris Agreement’s climate goals will require a comprehensive package of policy measures. National and sectoral policies can help fill the gap, but success stories in one country cannot be automatically replicated in other countries. They need to be adapted to the local context. Here, we develop a new Bridge scenario based on nationally relevant, short-term measures informed by interactions with country experts. These good practice policies are rolled out globally between now and 2030 and combined with carbon pricing thereafter. We implement this scenario with an ensemble of global integrated assessment models. We show that the Bridge scenario closes two-thirds of the emissions gap between NDC and 2°C scenarios by 2030 and enables a pathway in line with the 2 °C goal when combined with the necessary long-term changes, i.e. more comprehensive pricing measures after 2030. The Bridge scenario leads to a scale-up of renewable energy (reaching 52%-88% of global electricity supply by 2050), electrification of end-uses, efficiency improvements in energy demand sectors, and enhanced afforestation and reforestation. Our analysis suggests that early action via good-practice policies is less costly than a delay in global climate cooperation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A single-component water-lean post-combustion CO 2 capture solvent with exceptionally low operational heat and total costs of capture – comprehensive experimental and theoretical evaluation

A comprehensive evaluation of a recently developed water-lean amine-based solvent, namely N-(2-ethoxyethyl)-3-morpholinopropan-1-amine (2-EEMPA), has been performed to analyze its post-combustion CO 2 capture performance. This evaluation comprises (1) fundamental characterization of the solvent–CO 2 interaction using vapor–liquid equilibria, kinetics and viscosity measurements; (2) process characterization of the CO 2 capture performance as measured in a laboratory scale continuous flow system and via Aspen Plus® simulation using a flue gas simulant; as well as (3) a full techno economic analysis of the capture process at industrial scale with corresponding projections of critical metrics. This paper summarizes the many parts of this comprehensive evaluation and shows how the various parts come together to empower validated conclusions about its process performance. Notably, it is projected that this solvent can operate at a regeneration heat rate of 2.0 GJ per tonne CO 2 for post-combustion capture, and at a total cost of capture of $50.6/tonne CO 2 . Overall, with further process optimization significant reductions in the capture cost are predicted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A comprehensive approach for elucidating the interplay between 4f n +1 and 4f n 5d 1 configurations in Ln 2+ complexes

Lanthanides (Ln) are typically found in the +3 oxidation state. However, in recent decades, their chemistry has been expanded to include the less stable +2 oxidation state across the entire series except promethium (Pm), facilitated by the coordination of ligands such as trimethylsilylcyclopentadienyl, C 5 H 4 SiMe 3 (Cp'). The [LnCp' 3 ] complexes have been the workhorse for the synthesis and theoretical study of the fundamental aspects of divalent lanthanide chemistry, where experimental and computational evidence have suggested the existence of different ground state (GS) configurations, 4f n+1 or 4f n 5d 1 , depending on the specific metal. Standard reduction potentials and 4f n+1 to 4f n 5d 1 promotion energies have been two factors usually considered to rationalize the occurrence of these variable GS configurations, however the driving force behind this phenomenon is still not clear. In this work we present a comprehensive theoretical approach to shed light on this matter using the [LnCp 3 ] - model systems. We begin by calculating 4f n+1 to 4f n 5d 1 promotion energies and successfully correlate them with existing experimental data. Furthermore, we analyze how changes in the GS charge distribution between the Ln ions, LnCp 3 and the reduced [LnCp 3 ] - complexes (Ln = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) correlate with experimental trends in redox potentials and the calculated promotion energies. For this purpose, a comprehensive theoretical work that includes relativistic ligand field density functional theory (LFDFT) and relativistic ab initio wavefunction methods was performed. This study will help the rational design of suitable environments to tune the different GS configurations as well as modulating the spectroscopic properties of new Ln 2+ complexes.

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

Comprehensive study of Al-induced layer-exchange growth for orientation-controlled Si crystals on SiO{sub 2} substrates

Orientation-controlled crystalline Si films on insulating substrates are strongly required to achieve high-performance thin-film devices for next-generation electronics. We have comprehensively investigated the layer-exchange kinetics of Al-induced crystallization (AIC) in stacked structures, i.e., amorphous-Si/Al-oxide/Al/SiO{sub 2}-substrates, as a function of the air-exposure time of Al surfaces (t{sub air}: 0–24 h) to form Al-oxide interface-layers, the thickness of Al and Si layers (d{sub Al,} d{sub Si}: 50–200 nm), the annealing temperature (450–500 °C), and the annealing time (0–50 h). It has been clarified that longer t{sub air} (>60 min) and/or thinner d{sub Al} and d{sub Si} (<50 nm) lead to the (111) oriented growth; in contrast, shorter t{sub air} (<60 min) and/or thicker d{sub Al} and d{sub Si} (>100 nm) lead to the (100) oriented growth. No correlation between the annealing temperature and the crystal orientation is observed. Detailed analysis reveals that the layer-exchange kinetics are dominated by “supply-limited” processing, i.e., diffusion of Si atoms into Al layers through Al-oxide layer. Based on the growth rate dependent Si concentration profiles in Al layers, and the free-energy of Si at Al-oxide/Al or Al/SiO{sub 2} interfaces, a comprehensive model for layer-exchange growth is proposed. This well explains the experimental results of not only Si-AIC but also another material system such as gold-induced crystallization of Ge. In this way, a growth technique achieving the orientation-controlled Si crystals on insulating substrates is established from both technological and scientific points of view.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

NPP financial and regulatory risks-Importance of a balanced and comprehensive nuclear law for a newcomer country considering nuclear power programme

The nature of Nuclear Power Plant (NPP) projects are: long duration (10-15 years for new build), high capital investment, reasonable risks and highly regulated industries to meet national and international requirement on Safety, Security, Safeguards (3S) and Liabilities. It requires long term planning and commitment from siting to final disposal of waste/spent fuel. Potential financial and regulatory risks are common in massive NPP projects and will be magnified in the case of using unproven technology. If the risks are not properly managed, it can lead to high project and operation costs, and, fail to fulfil its objectives to provide compatible electricity prices and. energy security. To ensure successful, the government and investors need to ensure that the NPP project is bankable with low cost of project and funding, have fair treatment and proper risk mitigation, and able to complete on time with no cost overrun. One of the requirements as prerequisite for the development of NPP as stipulated by the International Atomic Energy Agency (IAEA) is the establishment of a Legal and Regulatory Framework. The main objective of nuclear law is to ensure that the activities and projects carried-out in the country are legal and compliant to national and international requirements. The law should also be able to provide fair treatment of risks on its activities that is acceptable to investors. The challenge for a newcomer country is to develop a balanced and comprehensive national nuclear law that meet these objectives while taking into consideration various stakeholders’ interest without compromising on safety, security, safeguard, liability requirements and other international obligations. This paper highlights the nature of NPP projects, its potential and associated financial and regulatory risks, and its major concerns and challenges. It proposes possible risks treatment and mitigation through the formulation of a balanced and comprehensive legislation by clear understanding of various requirements of public, regulators, investors, financial institutions, international community, operator and other important stakeholders. Ambiguities and uncertainties, especially with regards to certain conditions and requirements should be minimised by emulating good practices of experienced nuclear regulators. The imposition of various financial requirements such as funds for decommissioning, radioactive waste management, financial security, nuclear liabilities and licensing fees are necessary, but at the same time the quantum needs to be clearly defined. Concerns on absolute liability of the operators need to be addressed through a creation of necessary and proper nuclear insurance legislations to mitigate operator S nuclear liability obligations and other financial risks. Another major risk to investors is the possibility of public resistance which will not only can hinder the construction but can also stop operation of the nuclear power plant which will contribute to huge losses to investors and countries. This may require a provision in the legislation that provide proper compensation for these situations and at the same time to allow operators to engage in nuclear promotional activities, such as community benefit and public consultation as voluntary initiatives. Through proper planning, research, consultation and execution, the proposed nuclear law shall be able to promote good regulatory practices for public and investors’ confidence and benefit. Early involvement of various stakeholders is essential as a platform for regular communications between regulators and interested parties. Stakeholders’ participation in the NPP programme and law developments will also promote transparency of the projects while upholding the independency of the regulators.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

A comprehensive ARPES study on the type-II Dirac semimetal candidate Ir 1-x Pt x Te 2

The transition metal dichalcogenide Ir 1-x Pt x Te 2 displays both superconductivity and a topological band structure. Using angle-resolved photoemission spectroscopy, we obtain a comprehensive understanding of the three-dimensional electronic structure in the normal state of Ir 1-x Pt x Te 2 for doping levels from x = 0.1 to 0.4, which spans the composition range of a superconducting state to a non-superconducting state. Many features of the electronic structure can be attributed to strong Te–Te interactions between the layers of the layered crystal structure and can be resolved by photon energy dependent measurements. We demonstrate that the type-II Dirac fermions can be successfully tuned via Pt doping, where the Dirac point lies close to the Fermi level for x = 0.1. The band evolution vs doping provides a clearer understanding of the relationship between the superconductivity and electronic structure. In addition, the β band in the superconducting samples locates the system close to a type-II van Hove singularity, where spin triplet paring symmetry has been predicted. Our results provide a comprehensive understanding of the band structure of Ir 1-x Pt x Te 2 , and we discuss the possibilities of the existence of topological superconductivity in this system.

36 MATERIALS SCIENCE↗
DOE OSTI2015

A comprehensive archival search for counterparts to ultra-compact high-velocity clouds: Five Local Volume dwarf galaxies

We report five Local Volume dwarf galaxies (two of which are presented here for the first time) uncovered during a comprehensive archival search for optical counterparts to ultra-compact high-velocity clouds (UCHVCs). The UCHVC population of HI clouds are thought to be candidate gas-rich, low-mass halos at the edge of the Local Group and beyond, but no comprehensive search for stellar counterparts to these systems has been presented. Careful visual inspection of all publicly available optical and ultraviolet imaging at the position of the UCHVCs revealed six blue, diffuse counterparts with a morphology consistent with a faint dwarf galaxy beyond the Local Group. Optical spectroscopy of all six candidate dwarf counterparts show that five have an Hα-derived velocity consistent with the coincident HI cloud, confirming their association; the sixth diffuse counterpart is likely a background object. The size and luminosity of the UCHVC dwarfs is consistent with other known Local Volume dwarf irregular galaxies. The gas fraction (M{sub HI}/M{sub star}) of the five dwarfs are generally consistent with that of dwarf irregular galaxies in the Local Volume, although ALFALFA-Dw1 (associated with ALFALFA UCHVC HVC274.68+74.70–123) has a very high M{sub HI}/M{sub star} ∼ 40. Despite the heterogenous nature of our search, we demonstrate that the current dwarf companions to UCHVCs are at the edge of detectability due to their low surface brightness, and that deeper searches are likely to find more stellar systems. If more sensitive searches do not reveal further stellar counterparts to UCHVCs, then the dearth of such systems around the Local Group may be in conflict with ΛCDM simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

CD −24°17504 REVISITED: A NEW COMPREHENSIVE ELEMENT ABUNDANCE ANALYSIS

With [Fe/H] ∼ −3.3, CD −24°17504 is a canonical metal-poor main-sequence turn-off star. Though it has appeared in numerous literature studies, the most comprehensive abundance analysis for the star based on high-resolution, high signal-to-noise ratio (S/N) spectra is nearly 15 years old. We present a new detailed abundance analysis for 21 elements based on combined archival Keck-HIRES and Very Large Telescope-UVES spectra of the star that is higher in both spectral resolution and S/N than previous data. Our results are very similar to those of an earlier comprehensive study of the star, but we present for the first time a carbon abundance from the CH G-band feature as well as improved upper limits for neutron-capture species such as Y, Ba, and Eu. In particular, we find that CD −24°17504 has [Fe/H] = −3.41, [C/Fe] = +1.10, [Sr/H] = −4.68, and [Ba/H] ≤ −4.46, making it a carbon-enhanced metal-poor star with neutron-capture element abundances among the lowest measured in Milky Way halo stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

SIMULATION OF ASTRONOMICAL IMAGES FROM OPTICAL SURVEY TELESCOPES USING A COMPREHENSIVE PHOTON MONTE CARLO APPROACH

We present a comprehensive methodology for the simulation of astronomical images from optical survey telescopes. We use a photon Monte Carlo approach to construct images by sampling photons from models of astronomical source populations, and then simulating those photons through the system as they interact with the atmosphere, telescope, and camera. We demonstrate that all physical effects for optical light that determine the shapes, locations, and brightnesses of individual stars and galaxies can be accurately represented in this formalism. By using large scale grid computing, modern processors, and an efficient implementation that can produce 400,000 photons s{sup −1}, we demonstrate that even very large optical surveys can be now be simulated. We demonstrate that we are able to (1) construct kilometer scale phase screens necessary for wide-field telescopes, (2) reproduce atmospheric point-spread function moments using a fast novel hybrid geometric/Fourier technique for non-diffraction limited telescopes, (3) accurately reproduce the expected spot diagrams for complex aspheric optical designs, and (4) recover system effective area predicted from analytic photometry integrals. This new code, the Photon Simulator (PhoSim), is publicly available. We have implemented the Large Synoptic Survey Telescope design, and it can be extended to other telescopes. We expect that because of the comprehensive physics implemented in PhoSim, it will be used by the community to plan future observations, interpret detailed existing observations, and quantify systematics related to various astronomical measurements. Future development and validation by comparisons with real data will continue to improve the fidelity and usability of the code.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task

ABSTRACT Motivation Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model’s performance. Results We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets—BioASQ-7b, BioASQ-8b and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets. Availability and implementation BioADAPT-MRC is freely available as an open-source project at https://github.com/mmahbub/BioADAPT-MRC. Supplementary information Supplementary data are available at Bioinformatics online.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Comprehensive High Throughput One‐Pot Analysis of Glycoproteins through Tool for Rapid Analysis of Glycopeptide by Permethylation (TRAP) Method.

Glycoproteins plays key roles in various cellular functions such as protein folding, protein targeting, receptor function, cell–cell recognition, protein stability, signaling, and other cellular functions. Currently a comprehensive and universal tool for the automated analysis of glycopeptides through their tandem mass spectrometry and data processing is a tedious process. We recently developed a method, Tool for Rapid Analysis of glycopeptide by Permethylation (TRAP), that simplifies glycoprotein analysis by integrating glycan sequencing and glycopeptide analysis in a single experiment. We employed this approach for the detailed analysis of glycosidic linkages, composition, glycan sequencing, glycosylation site mapping and sequencing of peptide moiety of glycopeptides of glycoproteins from both prokaryotes and eukaryotes. Here we are presenting an easy to use, robust, suitable for large as well as small sample sets and also cost‐effective glycoprotein analysis tool through TRAP approach. A permethylation protocol which can be automated and suitable for reliable permethylation of glycopeptides from the protease digest of glycoproteins was developed. Initial studies on glycopeptides from a model glycoprotein bovine RNAse B indicates that improved sensitivity and throughput of permethylation reactions can be achieved in conducting the reaction in microscale. This approach would enable convenient, rapid, and reliable high‐throughput screening of protein glycosylation and can be employed as a cost‐effective kit for glycosylated biomarker discoveries. In order to improvise the comprehensive glycosylation analysis and throughput, we have also developed an LC‐MS/MS platform for the analysis of glycopeptides processed through TRAP. We have conducted the analysis of standard glycoproteins such as bovine RNase B, human transferrin, and bovine fetuin and our preliminary results indicate that TRAP hyphened with LC‐MS/MS enables characterization of isomers of each glycoform at each glycosylation sites of complex glycoprotein mixtures. Support or Funding Information This research was supported by the National Institutes of Health (NIH) funded research, Grant R21GM122633; resource for biomedical glycomics, Grant P41GM103490; instrument grant, Grant S10OD018530; and U.S. Department of Energy grant, Grant DE‐SC0015662, to the Complex Carbohydrate Research Center. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Shajahan, Asif↗
DOE OSTI2015

A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes

A comprehensive and up-to-date review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes is reported. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. The uptake of the method is such that it is experiencing what can only be described as explosive growth. This timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. A model of how crystallization comes about mechanistically is presented for a more rational approach to crystallization. The possible involvement of the lamellar and inverted hexagonal phases in crystallogenesis and the application of the method to water-soluble, monotopic and lipid-anchored proteins are addressed. How to set up trials manually and automatically with a robot is introduced with reference to open-access online videos that provide a practical guide to all aspects of the method. These range from protein reconstitution to crystal harvesting from the hosting mesophase, which is noted for its viscosity and stickiness. The sponge phase, as an alternative medium in which to perform crystallization, is described. The compatibility of the method with additive lipids, detergents, precipitant-screen components and materials carried along with the protein such as denaturants and reducing agents is considered. The powerful host and additive lipid-screening strategies are described along with how samples that have low protein concentration and cell-free expressed protein can be used. Assaying the protein reconstituted in the bilayer of the cubic phase for function is an important element of quality control and is detailed. Host lipid design for crystallization at low temperatures and for large proteins and complexes is outlined. Experimental phasing by heavy-atom derivatization, soaking or co-crystallization is routine and the approaches that have been implemented to date are described. An overview and a breakdown by family and function of the close to 200 published structures that have been obtained using in meso-grown crystals are given. Recommendations for conducting the screening process to give a more productive outcome are summarized. The fact that the in meso method also works with soluble proteins should not be overlooked. Recent applications of the method for in situ serial crystallography at X-ray free-electron lasers and synchrotrons are described. The review ends with a view to the future and to the bright prospects for the method, which continues to contribute to our understanding of the molecular mechanisms of some of nature’s most valued proteinaceous robots.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗