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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
NASA NTRS1997

Quantum Chemistry Study of Cycloaddition Pathways for the Reaction of o-Benzyne with Fullerenes and Carbon Nanotubes

Functionalization of fullerenes via the [2+2] cycloaddition reaction with o-benzyne has been demonstrated in the laboratory. In contrast, [2+4) cycloaddition products are formed when benzyne reacts with planar polycyclic aromatic hydrocarbons. Using density functional theory (DFT) calculations with Becke's hybrid functional and small contracted gaussian basis sets, we are able to reproduce these product preferences. The objective of this work is to explore the functionalization of carbon nanotubes. We have studied o-benzyne cycloaddition products with a [14,0] single-walled nanotube. We find both the [2+2] and [2+4] adducts to be stable, with the latter product being somewhat favored.

Jaffe, Richard↗
DOE OSTI2023

Assessing mechanisms for microbial taxa and community dynamics using process models

Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Precision e + e − hemisphere masses in the dijet region with power corrections

We derive high-precision results for the e + e − heavy jet mass (HJM) dσ/dρ and dihemisphere mass (DHM) d 2 σ/(ds 1 ds 2 ) distributions, for s 1 ~ s 2 , in the dijet region. New results include: i) the N 3 LL resummation for HJM of large logarithms ln n (ρ) at small ρ including the exact two-loop non-global hemisphere soft function, the 4-loop cusp anomalous dimension and the 3-loop hard and jet functions, ii) N 3 LL results for DHM with resummation of logarithms ln(s 1,2 /Q 2 ) when there is no large separation between s 1 and s 2 , iii) profile functions for HJM to give results simultaneously valid in the peak and tail regions, iv) a complete two-dimensional basis of non-perturbative functions which can be used for double differential observables, that are needed for both HJM and DHM in the peak region, and v) an implementation of renormalon subtractions for large-angle soft radiation to $\mathcal{O}$ (α$^{3}_{s}$) together with a resummation of the additional large ln(Qρ/Λ QCD ) logarithms. Here Q is the e + e − center-of-mass energy. Our resummation results are combined with known fixed-order $\mathcal{O}$ (α$^{3}_{s}$) results and we discuss the convergence and remaining perturbative uncertainty in the cross section. We also prove that, at order 1/Q, the first moment of the HJM distribution involves an additional non-perturbative parameter compared to the power correction that shifts the tail of the spectrum (where 1 ≫ ρ ≫ Λ QCD /Q). This differs from thrust where a single non-perturbative parameter at order 1/Q describes both the first moment and the tail, and it disfavors models of power corrections employing a single non-perturbative parameter, such as the low-scale effective coupling model. In this paper we focus only on the dijet region, not the far-tail distribution for ρ ≳ 0.2 beyond which the trijet factorization and resummation become important.

Factorization↗
DOE OSTI2019

Electronic and Vibrational Properties of LiBO{sub 2} Crystals

On the basis of the density functional theory using the CRYSTAL code, electronic and vibrational properties of lithium metaborate in the monoclinic and tetragonal phases are studied. The band spectra, elastic moduli, long-wave vibrational frequencies at the point Г, dynamic charges, and acoustic velocities are calculated for both phases. The influence of structural features and short-range order in trigonal BO{sub 3}- and tetragonal BO{sub 4}- groups on the significant difference in physical properties in the low-temperature and high-temperature phases of LiBO{sub 2} crystal is established.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Large-scale calculations of atomic level and transition properties in the aluminum isoelectronic sequence from Ti X through Kr XXIV, Xe XLII, and W LXII

Large-scale self-consistent multiconfiguration Dirac–Hartree–Fock subsequent relativistic configuration interaction (RCI) calculations are reported for 360 states belonging to the 30 configurations 3s{sup 2}{3l,4l,5l}, 3p{sup 2}{3d,4l}, 3s{3p"2,3d"2}, 3s{3p3d,3p4l,3p5s,3d4l"′}, 3p3d{sup 2}, 3p{sup 3} and 3d{sup 3} with l=0,1,…,n−1 and l{sup ′}=0,1,2 in 17 systems of the aluminum-like isoelectronic sequence: Ti X through Kr XXIV, Xe XLII, and W LXII. Effects from electron correlation are taken into account by means of large expansions in terms of a basis of configuration state functions (CSF) and calculated energy levels are compared with existing theoretical calculations and the NIST Atomic Spectra database. Radiative E1, E2, M1 and M2 transition rates and associated lifetimes of energy levels are presented in online tables. The uncertainties of the calculated energies are very small, on average between 0.02% and 0.05%, which aid new line identifications in laboratory and astronomical spectra and also make it possible to find and rule out misidentifications. The uncertainties of the E1 transition probabilities, based on the agreement between values in the length and velocity gauges, are estimated to be of the order 0.5% for the strong transitions and 25% for the weaker intercombination transitions. The M1 transition values are not sensitive to electron correlation and are believed to be accurate to well within 1%.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2012

Generally Contracted Valence-Core/Valence Basis Sets for Use with Relativistic Effective Core Potentials and Spin-Orbit Coupling Operators

A procedure for structuring generally contracted valence-core/valence basis sets of Gaussian-type functions for use with relativistic effective core potentials (gcv-c/v-RECP basis sets) is presented. Large valence basis sets are enhanced using a compact basis set derived for outer core electrons in the presence of small-core RECPs. When core electrons are represented by relativistic effective core potentials (RECPs), and appropriate levels of theory, these basis sets are shown to provide accurate representations of atomic and molecular valence and outer-core electrons. Core/valence polarization and correlation effects can be calculated using these basis sets through standard methods for treating electron correlation. Calculations of energies and spectra for Ru, Os, Ir, In and Cs are reported. Spectroscopic constants for RuO2+, OsO2+, Cs2 and InH are calculated and compared with experiment.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2011

Substrate-Induced Conformational Changes Occur in All Cleaved Forms of Caspase-6

Caspase-6 is an apoptotic cysteine protease that also governs disease progression in Huntington's and Alzheimer's diseases. Caspase-6 is of great interest as a target for treatment of these neurodegenerative diseases; however, the molecular basis of caspase-6 function and regulation remains poorly understood. In the recently reported structure of caspase-6, the 60's and 130's helices at the base of the substrate-binding groove extend upward, in a conformation entirely different from that of any other caspase. Presently, the central question about caspase-6 structure and function is whether the extended conformation is the catalytically competent conformation or whether the extended helices must undergo a large conformational rearrangement in order to bind substrate. We have generated a series of caspase-6 cleavage variants, including a novel constitutively two-chain form, and determined crystal structures of caspase-6 with and without the intersubunit linker. This series allows evaluation of the role of the prodomain and intersubunit linker on caspase-6 structure and function before and after substrate binding. Caspase-6 is inherently more stable than closely related caspases. Cleaved caspase-6 with both the prodomain and the linker present is the most stable, indicating that these two regions act in concert to increase stability, but maintain the extended conformation in the unliganded state. Moreover, these data suggest that caspase-6 undergoes a significant conformational change upon substrate binding, adopting a structure that is more like canonical caspases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Application of Koopman operator for model-based control of fracture propagation and proppant transport in hydraulic fracturing operation

This work explores the application of the recently developed Koopman operator approach for model identification and feedback control of a hydraulic fracturing process. Controlling fracture propagation and proppant transport with precision is a challenge due in large part to the difficulty of constructing approximate models that accurately capture the characteristic moving boundary and highly-coupled dynamics exhibited by the process. Koopman operator theory is particularly attractive here as it offers a way to explicitly construct linear representations for even highly nonlinear dynamics. The method is data-driven and relies on lifting the states to an infinite-dimensional space of functions called observables where the dynamics are governed by a linear Koopman operator. Here this work considers two problems: (a) fracture geometry control, and (b) proppant concentration control. In both cases, an approximate linear model of the corresponding dynamics is constructed and used to design a model predictive controller (MPC). The manuscript shows that in the case of highly nonlinear dynamics, as observed in the proppant concentration, use of canonical functions in the observable basis fails. In such cases, a priori system knowledge can be leveraged to choose the required basis. The numerical experiments demonstrate that the Koopman linear model shows excellent agreement with the real system and successfully achieves the desired target values maximizing the oil and gas productivity. Additionally, due to its linear structure, the Koopman models allow convex MPC formulations that avoid any issues associated with nonlinear optimization.

42 ENGINEERING↗
DOE OSTI2021

Resistive AC-Coupled Silicon Detectors: principles of operation and first results from a combined analysis of beam test and laser data

This paper presents the principles of operation of Resistive AC-Coupled Silicon Detectors (RSDs) and measurements of the temporal and spatial resolutions using a combined analysis of laser and beam test data. RSDs are a new type of n-in-p silicon sensor based on the Low-Gain Avalanche Diode (LGAD) technology, where the n+ implant has been designed to be resistive, and the read-out is obtained via AC-coupling. The truly innovative feature of RSD is that the signal generated by an impinging particle is shared isotropically among multiple read-out pads without the need for floating electrodes or an external magnetic field. Careful tuning of the coupling oxide thickness and the n+ doping profile is at the basis of the successful functioning of this device. Several RSD matrices with different pad width-pitch geometries have been extensively tested with a laser setup in the Laboratory for Innovative Silicon Sensors in Torino, while a smaller set of devices have been tested at the Fermilab Test Beam Facility with a 120 GeV/c proton beam. The measured spatial resolution ranges between 2.5μm for 70–100 pad-pitch geometry and 17μm with 200–500 matrices, a factor of 10 better than what is achievable in binary read-out (bin size/12). Beam test data show a temporal resolution of ~40ps for 200 μm pitch devices, in line with the best performances of LGAD sensors at the same gain.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Alkylation of monomeric, dimeric, and polymeric lignin models through carbon-hydrogen activation using Ru-catalyzed Murai reaction

In this study, we have assessed directed carbon-hydrogen activation (CHA) for alkylation of monomeric, dimeric, and polymeric lignin models using Murai's catalyst [RuH 2 (CO)(PPh 3 ) 3 ]. Based on related work from our laboratory showing that isolated organosolv lignin bears benzylic directing groups ideal for CHA reactions, this approach could offer new methodology for the valorization of biorefinery lignin. Monomeric and dimeric models bearing a keto group at the benzylic position undergo Ru-catalyzed alkylation in good to excellent yield. Similarly, models bearing a benzylic OH group also undergo alkylation via a tandem oxidation/alkylation process enabled by the Ru catalyst. Polymeric models show low levels of functionalization as a result of the poor solubility of the starting polymer. With unsymmetrical models, functionalization occurs first at the least sterically hindered ortho-site, but a subsequent alkylation, leading to disubstituted products can occur at the more sterically hindered site, leading to hexasubstituted arenes. The reaction shows sensitivity to free phenolic OH groups, which appears to reduce the yield in some reactions, and is also a contributing factor to the low yields observed with polymeric lignin models. Finally, combining CHA methodology with lignin isolation technology able to introduce appropriate directing groups for catalytic functionalization will form the basis for improved conversion of lignin to high value chemical products.

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

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

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

Copper-Based Catalysts Confined in Carbon Nanocage Reactors for Condensed Ester Hydrogenation: Tuning Copper Species by Confined SiO 2 and Methanol Resistance

Hydrogenation of aliphatic esters to natural alcohols is an important strategy for the efficient utilization of biomass-derived oils. The synthesis of highly active copper (Cu)-based catalysts is a challenge for condensed-phase ester hydrogenation due to the difficulties in controlling active sites and catalyst deactivation. In this work, a copper-based catalyst confined in a carbon nanocage reactor was successfully designed and prepared. The copper catalyst with 56 wt % SiO 2 exhibited the best performance because of the optimum proportion of Cu + and Cu 0 sites and high dispersion. The interaction between SiO 2 and Cu particles contributes to the formation of Cu + species, which is the key site for the adsorption of carbonyl groups. Meanwhile, the confinement effect of the carbon nanocages effectively inhibited the agglomeration of the copper particles. The catalysts exhibited not only excellent thermal stability but also superior methanol resistance in comparison with the Cu/SiO 2 catalyst. On the basis of the density functional theory (DFT) calculations results, methanol resistance should be attributed to the fewer hydroxyl groups on the catalyst surface, which increase the activation barrier for the dissociation of silica, allowing the stable holding of the copper species in the methanol solvent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Crystal Structure of the Central Coiled-Coil Domain from Human Liprin-[beta]2

Liprins are a conserved family of scaffolding proteins important for the proper regulation and development of neuronal synapses. Humans have four liprin-{alpha}s and two liprin-{beta}s which all contain long coiled-coil domains followed by three tandem SAM domains. Complex interactions between the coiled-coil and SAM domains are thought to create liprin scaffolds, but the structural and biochemical properties of these domains remain largely uncharacterized. In this study we find that the human liprin-{beta}2 coiled-coil forms an extended dimer. Several protease-resistant subdomains within the liprin-{beta}1 and liprin-{beta}2 coiled-coils were also identified. A 2.0 {angstrom} crystal structure of the central, protease-resistant core of the liprin-{beta}2 coiled-coil reveals a parallel helix orientation. These studies represent an initial step toward determining the overall architecture of liprin scaffolds and understanding the molecular basis for their synaptic functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Optical Absorption and Band Gap Reduction in (Fe 1– x Cr x ) 2 O 3 Solid Solutions: A First-Principles Study

We provide a detailed theoretical analysis of the character of optical transitions and band gap reduction in (Fe1-xCrx)2O3 solid solutions using extensive periodic model and embedded cluster calculations. Optical absorption bands for x = 0.0, 0.5, and 1.0 are assigned on the basis of timedependent density functional theory (TDDFT) calculations. A band-gap reduction of as much as 0.7 eV with respect to that of pure α-Fe2O3 is found. This result can be attributed to predominantly two effects: (i) the higher valence band edge for x ≈ 0.5, as compared to those in pure α-Fe2O3 and α-Cr2O3, and, (ii) the appearance of Cr α Fe d–d transitions in the solid solutions. Broadening of the valence band due to hybridization of the O 2p states with Fe and Cr 3d states also contributes to band gap reduction.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Ebola virus VP30 and nucleoprotein interactions modulate viral RNA synthesis

Ebola virus (EBOV) is an enveloped negative-sense RNA virus that causes sporadic outbreaks with high case fatality rates. Ebola viral protein 30 (eVP30) plays a critical role in EBOV transcription initiation at the nucleoprotein (eNP) gene, with additional roles in the replication cycle such as viral assembly. However, the mechanistic basis for how eVP30 functions during the virus replication cycle is currently unclear. Here we define a key interaction between eVP30 and a peptide derived from eNP that is important to facilitate interactions leading to the recognition of the RNA template. We present crystal structures of the eVP30 C-terminus in complex with this eNP peptide. Functional analyses of the eVP30–eNP interface identify residues that are critical for viral RNA synthesis. Altogether, these results support a model where the eVP30–eNP interaction plays a critical role in transcription initiation and provides a novel target for the development of antiviral therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The cluster decomposition of the configurational energy of multicomponent alloys

Abstract The cluster expansion method (CEM) is a widely used lattice-based technique in the study of multicomponent alloys. Despite its prevalent use, a clear understanding of expansion terms is lacking. We present a modern mathematical formalism of the CEM and introduce thecluster decomposition—a unique and basis-independent decomposition for functions of the atomic configuration in a crystal. We identify the cluster decomposition as an invariant ANOVA decomposition; and demonstrate how functional analysis of variance and sensitivity analysis can be used to interpret interactions among species. Furthermore, we show how the mathematical structure of the cluster decomposition enables numerical evaluation that scales with the number of clusters and is independent of the number of species. Overall, our work enables rigorous interpretations of interactions among species, provides opportunities to explore parameter estimation beyond linear regression, introduces a numerical efficient implementation, and enables analysis of cluster expansions based on established mathematical and statistical principles.

Chemistry↗