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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Metabololipidomic profiling of functional immunoresolvent clusters and eicosanoids in mammalian tissues

Highlights: • New methods for metabololipidomics of specialized proresolving mediators (SPM) and classic eicosanoids. • Illustration from human blood coagulation. • Illustration from solid tumor. • Regulation of SPM biosynthesis by adenosine and adenosine deaminase. Metabolomics enables a systems approach to interrogate the bioactive mediators, their pathways and further metabolites involved in the physiology and pathophysiology of human and animal tissues. New metabololipidomic approaches with mass spectrometry presented in this brief review can now be utilized for the identification and profiling of lipid mediator networks that control inflammation-resolution in human blood and healthy and diseased solid tissues. Coagulation of blood is a protective response that prevents excessive bleeding on injury of blood vessels. Here, we review novel approaches to understand the relationship(s) between coagulation and resolution of inflammation and infection. To determine whether coagulation is involved in host-protective actions by lipid mediators, we used a metabololipidomic-based profiling approach with human whole blood (WB) during coagulation. We identified recently temporal clusters of endogenously produced pro-thrombotic and proinflammatory lipid mediators (eicosanoids), as well as specialized proresolving mediators (SPMs) in this vital process. In addition to the classic eicosanoids (prostaglandins, thromboxanes and leukotrienes), a specific SPM cluster was identified that consists of resolvin E1 (RvE1), RvD1, RvD5, lipoxin B{sub 4}, and maresin 1, each of which present at bioactive concentrations (0.1–1 nM). The removal of adenosine from coagulating blood samples significantly enhances SPM amounts and unleashes the biosynthesis of RvD3, RvD4, and RvD6 evident following rapid snap freezing with centrifugation before extraction and LC-MS-MS. The classic cyclooxygenase inhibitors, celecoxib and indomethacin, that block thromboxanes and prostanoids do not block production of the clot-driven SPM cluster. Unbiased mass cytometry analysis demonstrated that the SPM cluster produced in human blood targets leukocytes at the single-cell level, directly activating extracellular signaling in human neutrophils and monocytes. Human whole blood treated with the components of this SPM cluster enhanced both phagocytosis and killing of Escherichia coli by leukocytes. Thus, we identified a pro-resolving lipid mediator circuit and specific SPM cluster that promotes host defense. This new lipid mediator (LM)-SPM metabololipidomic approach now provides accessible metabolomic profiles in healthy and diseased human tissues, including cancer, for precision and personalized medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

The effects of physical and chemical preprocessing on the flowability of corn stover

Continuous and reliable feeding of biomass is essential for successful biofuel production. However, the challenges associated with biomass solids handling are commonly overlooked. In this study, we examine the effects of preprocessing (particle size reduction, moisture content, chemical additives, etc.) on the flow properties of corn stover. Compressibility, flow properties (interparticle friction, cohesion, unconfined yield stress, etc.), and wall friction were examined for five corn stover samples: ground, milled (dry and wet), acid impregnated, and deacetylated. The ground corn stover was found to be the least compressible and most flowable material. The water and acid impregnated stovers had similar compressibilities. Yet, the wet corn stover was less flowable than the acid impregnated sample, which displayed a flow index equivalent to the dry, milled corn stover. The deacetylated stover, on the other hand, was the most compressible and least flowable examined material. However, all of the tested stover samples had internal friction angles >30°, which could present additional feeding and handling challenges. All of the ''wetted'' materials (water, acid, and deacetylated) displayed reduced flowabilities (excluding the acid impregnated sample), and enhanced compressibilities and wall friction angles, indicating the potential for added handling issues; which was corroborated via theoretical hopper design calculations. All of the ''wetted'' corn stovers require larger theoretical hopper outlet diameters and steeper hopper walls than the examined ''dry'' stovers.

09 BIOMASS FUELS↗
DOE OSTI2021

The RIT1 C-terminus associates with lipid bilayers via charge complementarity

RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. For this study, we used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence

With the advent of faster computer processors and especially graphics processing units (GPUs) over the last few decades, the use of data-intensive machine learning (ML) and artificial intelligence (AI) has increased greatly, and the study of crystal nucleation has been one of the beneficiaries. In this study, we outline how ML and AI have been applied to address four outstanding difficulties of crystal nucleation: how to discover better reaction coordinates (RCs) for describing accurately non-classical nucleation situations; the development of more accurate force fields for describing the nucleation of multiple polymorphs or phases for a single system; more robust identification methods for determining crystal phases and structures; and as a method to yield improved course-grained models for studying nucleation.

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

Effects of neutron irradiation on hydrogen isotope permeation on W-Re

Hydrogen and deuterium permeation behavior for neutron damaged W and W-3 %Re was evaluated using a Plasma Driven Permeation device. For neutron damaged W-3 %Re at 773 K and 1473 K, precipitation of Re and Os was observed by atom probe tomography. Neutron irradiation introduced defect damage throughout the sample and enhanced H and D diffusion toward downstream side. The existence of irradiation damage by neutron irradiation was found to increase hydrogen isotope permeation. Moreover, the existence of Re has suppressed the formation of irradiation defects for hydrogen isotope trapping sites. Further, the recovery of irradiation defects by increasing the irradiation temperature led to the structural changes due to the diffusion of Re and Os, which also affected the hydrogen isotope permeation behavior.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Microstructure evolution of 7050 Al alloy during age-forming

The microstructure evolution of the 7050 Al alloy treated by age-forming was studied using a designed device which can simulate the age-forming process. The grain shape, grain boundary misorientation and grain orientation evolution of 7050 Al alloy during age-forming have been quantitatively characterized by electron backscattering diffraction technique. The results show that age-forming produced abundant low-angle boundaries and elongated grains, which attributed to stress induced dislocation movement and grain boundary migration during the age-forming process. On the other side, the stress along rolling direction caused some unstable orientation grains to rotate towards the Brass and S orientations during the age-forming process. Hence, the intensity of the rolling texture orientation in age-formed samples is enhanced. But this effect decays gradually with increasing aging time, since stress decreases and precipitation hardening occurs during the age-forming process. - Highlights: • Quantitative analysis of grain evolution of 7050 Al alloys during age-forming • Stress induces some grain rotation of 7050 Al alloys during age-forming. • Creep leads to elongate grain of 7050 Al alloys during age-forming. • Obtains a trend on texture evolution during age-forming applied stress.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An ab initio free energy study of the reaction mechanism and rate-limiting steps of CO 2 capture by aqueous glycine

Aqueous amino acids are promising absorbents for direct air capture (DAC) of CO 2 . Herein, we investigate the possibility of kinetic control of CO 2 absorption with aqueous anionic glycine (GLY - ) by employing extensive ab initio molecular dynamics simulations, free energy analysis, and reaction rate theory. We find that first GLY - binds to CO 2 by overcoming a barrier (7.4 kcal/mol) to form a zwitterion intermediate, which then releases a proton by overcoming a similar barrier. Despite the similarity in the barrier, zwitterion formation appears to be the rate-limiting step because it is two orders of magnitude slower (microseconds) than the proton release step. This is predominantly due to stronger nonequilibrium solvent effects for the former that cause many barrier-recrossing events and effectively slow down the reaction rate. Such a detailed fundamental understanding of the amino acid-based CO 2 -absorption mechanism and rates is key to improving the kinetic efficiency of DAC technology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

We report that replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional (2D) replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional (1D) unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a pre-identified “solute”, and a second one via the introduction of flattening torsional free energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of pxylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. Lastly, the tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free energy computations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Bulk Production of Any Ratio 12 C: 13 C Turbostratic Flash Graphene and Its Unusual Spectroscopic Characteristics

As graphene enjoys worldwide research and deployment, the biological impact, geologic degradation, environmental retention, and even some physical phenomena remain less well studied. Bulk production of 13 C-graphene yields a powerful route to study all of these questions. Gram scale synthesis of high quality and high purity turbostratic flash graphene with varying amounts of 13 C-enrichment, from 5% to 99% is reported here. Here, the material is characterized by solid state nuclear magnetic resonance spectroscopy, Raman spectroscopy, infrared (IR) spectroscopy, X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry. Notably, an unusual enhancement in the Raman spectroscopic D’ peak is observed, resulting from the modification in vibrational frequency through isotopic enrichment favoring intravalley phonon scattering modes. While the IR absorbance spectrum of graphene is for the most part silent, we prepare here 13 C-enhanced graphene samples that show a large aromatic 12 C= 13 C stretch that reveals this IR-active mode.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor–acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states. However, due to the lack of polarization, which imparts subtle changes in the charge distribution on atoms, molecular simulations fail to produce accurate average dipole moments. We developed the first polarizable model for a molecular triad to investigate the structural and dynamic properties of a molecular triad in the ground state in an explicit organic solvent, tetrahydrofuran (THF). We performed first-principles electronic structure calculations of the individual components in the triad as well as THF and then fit the partial atomic charges to the electrostatic potential using the i-RESP methodology. We validated these force field parameters by comparing the thermodynamic and dynamic properties obtained from molecular dynamics simulations with those from experiments. We enhanced the sampling of the triad conformations with replica exchange molecular dynamics simulations. We characterized the effects of induced polarization on the structural stability of the triad by analyzing the free energy landscapes constructed with polarizable force fields. Furthermore, by using principal component analysis, we found that the molecular triad conformations adopted a small range of torsional angles with induced polarization. The triad conformation solvated in polar solvent with a polarizable force field qualitatively agrees with that obtained from nuclear magnetic resonance spectroscopy.

Starovoytov, Oleg N.↗
DOE OSTI2013

Plastic deformation and sintering of alumina under high pressure

Plastic deformation of alumina (Al{sub 2}O{sub 3}) under high pressure was investigated by observing the shape changes of spherical particles, and the near fully dense transparent bulks were prepared at around 5.5 GPa and 900 °C. Through analyzing the deformation features, densities, and residual micro-strain of the Al{sub 2}O{sub 3} compacts prepared under high pressures and temperatures (2.0–5.5 GPa and 600–1200 °C), the effects of plastic deformation on the sintering behavior of alumina have been demonstrated. Under compression, the microscopic deviatoric stress caused by grain-to-grain contact could initiate the plastic deformation of individual particles, eliminate pores of the polycrystalline samples, and enhance the local atomic diffusion at the grain boundaries, thus produced transparent alumina bulks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Effect of sulfur doping on thermoelectric properties of tin selenide – A first principles study

In this work we present the thermoelectric properties of tin selenide (SnSe) and sulfur doped tin selenide(SnSe{sub (1-x)}S{sub x}, x= 0.125 and 0.25) obtained using first principles calculations. We investigated the electronic band structure using the FP-LAPW method within the sphere of the density functional theory. Thermoelectric properties were calculated using BOLTZTRAP code using the constant relaxation time approximation at three different temperatures 300, 600 and 800 K. Seebeck coefficient (S) was found to decrease with increasing temperature, electrical conductivity (σ/τ) was almost constant in the entire temperature range and thermal conductivity (κ/τ) increased with increasing temperature for all samples. Sulfur doped samples showed enhanced seebeck coefficient, decreased thermal conductivity and decreased electrical conductivity at all temperatures. At 300 K, S increased from 1500 µV/K(SnSe) to 1720μV/K(SnSe{sub 0.75}S{sub 0.25}), thermal conductivity decreased from 5 × 10{sup 15} W/mKs(SnSe) to 3 × 10{sup 15} W/mKs(SnSe{sub 0.75}S{sub 0.25}), electrical conductivity decreased from 7 × 10{sup 20}/Ωms(SnSe) to 5 × 10{sup 20} /Ωms(SnSe{sub 0.75}S{sub 0.25}). These calculations show that sulfur doped tin selenide exhibit better thermoelectric properties than undoped tin selenide.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

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

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Significance A major challenge in biology is characterizing the structural flexibility of intrinsically disordered proteins (IDPs). Ensemble-averaged experimental data do not provide the underlying protein structures. Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. We report that enhancing the sampling of the simulations can generate an ensemble of IDP structures in quantitative agreement with scattering and NMR, without the need for biasing the simulation or reweighting the results. The demonstration of established simulation technology that produces accurate physical models of flexible biosystems may pave the way to relating conformational flexibility to biological function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

GLOBULAR CLUSTER POPULATIONS: FIRST RESULTS FROM S{sup 4}G EARLY-TYPE GALAXIES

Using 3.6 μm images of 97 early-type galaxies, we develop and verify methodology to measure globular cluster populations from the S{sup 4}G survey images. We find that (1) the ratio, T {sub N}, of the number of clusters, N {sub CL}, to parent galaxy stellar mass, M {sub *}, rises weakly with M {sub *} for early-type galaxies with M {sub *} > 10{sup 10} M {sub ☉} when we calculate galaxy masses using a universal stellar initial mass function (IMF) but that the dependence of T {sub N} on M {sub *} is removed entirely once we correct for the recently uncovered systematic variation of IMF with M {sub *}; and (2) for M {sub *} < 10{sup 10} M {sub ☉}, there is no trend between N {sub CL} and M {sub *}, the scatter in T {sub N} is significantly larger (approaching two orders of magnitude), and there is evidence to support a previous, independent suggestion of two families of galaxies. The behavior of N {sub CL} in the lower-mass systems is more difficult to measure because these systems are inherently cluster-poor, but our results may add to previous evidence that large variations in cluster formation and destruction efficiencies are to be found among low-mass galaxies. The average fraction of stellar mass in clusters is ∼0.0014 for M {sub *} > 10{sup 10} M {sub ☉} and can be as large as ∼0.02 for less massive galaxies. These are the first results from the S{sup 4}G sample of galaxies and will be enhanced by the sample of early-type galaxies now being added to S{sup 4}G and complemented by the study of later-type galaxies within S{sup 4}G.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗