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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2022

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune “bond” lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol’s role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA’s conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Altogether, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Measurement-induced criticality in random quantum circuits

We investigate the critical behavior of the entanglement transition induced by projective measurements in (Haar) random unitary quantum circuits. Using a replica approach, we map the calculation of the entanglement entropies in such circuits onto a two-dimensional statistical-mechanics model. In this language, the area- to volume-law entanglement transition can be interpreted as an ordering transition in the statistical-mechanics model. We derive the general scaling properties of the entanglement entropies and mutual information near the transition using conformal invariance. We analyze in detail the limit of infinite on-site Hilbert space dimension in which the statistical-mechanics model maps onto percolation. In particular, we compute the exact value of the universal coefficient of the logarithm of subsystem size in the n th Rényi entropies for n ≥ 1 in this limit using relatively recent results for the conformal field theory describing the critical theory of two-dimensional (2D) percolation, and we discuss how to access the generic transition at finite on-site Hilbert space dimension from this limit, which is in a universality class different from 2D percolation. Here, we also comment on the relation to the entanglement transition in random tensor networks, studied previously in Vasseur et al. [Phys. Rev. B 100, 134203 (2019)].

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

History Matching and Performance Prediction of a Polymer Flood Pilot in Heavy Oil Reservoir on Alaska North Slope

The first-ever polymer flood pilot to enhance heavy oil recovery on Alaska North Slope (ANS) is ongoing. After more than 2.5 years of polymer injection, significant benefit has been observed from the decrease in water cut from 65% to less than 15% in the project producers. The primary objective of this study is to develop a robust history-matched reservoir simulation model capable of predicting future polymer flood performance. In this work, the reservoir simulation model has been developed based on the geological model and available reservoir and fluid data. In particular, four high transmissibility strips were introduced to connect the injector-producer well pairs, simulating short-circuiting flow behavior that can be explained by viscous fingering and reproducing the water cut history. The strip transmissibilities were manually tuned to improve the history matching results during the waterflooding and polymer flooding periods, respectively. It has been found that higher strip transmissibilities match the sharp water cut increase very well in the waterflooding period. Then the strip transmissibilities need to be reduced with time to match the significant water cut reduction. The viscous fingering effect in the reservoir during waterflooding and the restoration of injection conformance during polymer flooding have been effectively represented. Based on the validated simulation model, numerical simulation tests have been conducted to investigate the oil recovery performance under different development strategies, with consideration for sensitivity to polymer parameter uncertainties. The oil recovery factor with polymer flooding can reach about 39% in 30 years, twice as much as forecasted with continued waterflooding. Besides, the updated reservoir model has been successfully employed to forecast polymer utilization, a valuable parameter to evaluate the pilot test’s economic efficiency. All the investigated development strategies indicate polymer utilization lower than 3.5 lbs/bbl in 30 years, which is economically attractive.

Wang, Xindan↗
DOE OSTI2023

Solution Structure and Scaling Laws of Cylindrical and Tapered Bottlebrush Polymers

Bottlebrush polymers are a unique class of macromolecular architectures with a plethora of potential industrial and pharmaceutical applications that critically depend on the bottlebrush shape and dimensions. Here, a systematic series of 12 cylindrical and 12 cone-shaped (tapered) bottlebrush polymers with poly(tert-butyl acrylate) (PtBA) or polystyrene (PS) side chains were synthesized using the sequential addition of macromonomers ring-opening metathesis polymerization (SAM-ROMP) grafting-through method. Small-angle neutron scattering (SANS) studies on dilute solutions of the two types of bottlebrush polymers provided noninvasive characterization of their structural dimensions and chain conformations. Simulated SANS traces, generated using coarse-grained molecular dynamics simulations, reproduced the distinctive features observed in the experimental SANS signals and provided necessary validation for data modeling. The combined analysis of experimental and simulated SANS signals yielded key structural and conformational parameters, including the bottlebrush radius, length, and Kuhn length as well as the excluded volume parameter and the correlation length of the polymer side chains. Importantly, the obtained structural parameters followed well-defined scaling laws as a function of the backbone and side chain degrees of polymerization, as predicted by mean field theories. In conclusion, these findings provide clear experimental and computational evidence of the interdependence of structural and conformational properties in an important class of polymer architectures.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2003

Iron catalyst chemistry in modeling a high-pressure carbon monoxide nanotube reactor

The high-pressure carbon monoxide (HiPco) technique for producing single-wall carbon nanotubes (SWNTs) is analyzed with the use of a chemical reaction model coupled with flow properties calculated along streamlines, calculated by the FLUENT code for pure carbon monoxide. Cold iron pentacarbonyl, diluted in CO at about 30 atmospheres, is injected into a conical mixing zone, where hot CO is also introduced via three jets at 30 degrees with respect to the axis. Hot CO decomposes the Fe(CO)5 to release atomic Fe. Then iron nucleates and forms clusters that catalyze the formation of SWNTs by a disproportionation reaction (Boudouard) of CO on Fe-containing clusters. Alternative nucleation rates are estimated from the theory of hard sphere collision dynamics with an activation energy barrier. The rate coefficient for carbon nanotube growth is estimated from activation energies in the literature. The calculated growth was found be about an order of magnitude greater than measured, regardless of the nucleation rate. A study of cluster formation in an incubation zone prior to injection into the reactor shows that direct dimer formation from Fe atoms is not as important as formation via an exchange reaction of Fe with CO in FeCO.

Evaluation Studies↗
DOE OSTI2025

The HTAP_v3.2 emission mosaic: merging regional and global monthly emissions (2000–2020) to support air quality modelling and policies

This study, performed under the umbrella of the Task Force on Hemispheric Transport of Air Pollution (TF-HTAP), responds to the need of the global and regional atmospheric modelling community of having a mosaic emission inventory of air pollutants that conforms to specific requirements: global coverage, long time series, spatially distributed emissions with high time resolution, and a high sectoral resolution. The mosaic approach of integrating official regional emission inventories based on locally reported data, with a global inventory based on a globally consistent methodology, allows modellers to perform simulations of a high scientific quality while also ensuring that the results remain relevant to policymakers. HTAP_v3.2, an ad-hoc global mosaic of anthropogenic inventories, is an update to the HTAP_v3 global mosaic inventory and has been developed by integrating official inventories over specific areas (North America, Europe, Asia including China, Japan and Korea) with the independent Emissions Database for Global Atmospheric Research (EDGAR) inventory for the remaining world regions. The results are spatially and temporally distributed emissions of SO 2 , NO x , CO, NMVOC, NH 3 , PM 10 , PM 2.5 , Black Carbon (BC), and Organic Carbon (OC), with a spatial resolution of 0.1 × 0.1° and time intervals of months and years covering the period 2000–2020 (https://doi.org/10.5281/zenodo.17086684, Crippa, 2025, https://edgar.jrc.ec.europa.eu/dataset_htap_v32, last access: 27 October 2025). The emissions are further disaggregated to 16 anthropogenic emitting sectors. This paper describes the methodology applied to develop such an emission mosaic, reports on source allocation, differences among existing inventories, and best practices for the mosaic compilation. One of the key strengths of the HTAP_v3.2 emission mosaic is its temporal coverage, enabling the analysis of emission trends over the past two decades. The development of a global emission mosaic over such long time series represents a unique product for global air quality modelling and for better-informed policy making, reflecting the community effort expended by the TF-HTAP to disentangle the complexity of transboundary transport of air pollution.

Guizzardi, Diego [European Commission, Ispra (Ital↗
NASA NTRS1999

Nucleic acid duplexes incorporating a dissociable covalent base pair

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

Non-NASA Center↗
DOE OSTI2022

Noise effects on Padé approximants and conformal maps

Here, we analyze the properties of Padé and conformal map approximants for functions with branch points, in the situation where the expansion coefficients are only known with finite precision or are subject to noise. We prove that there is a universal scaling relation between the strength of the noise and the expansion order at which Padé or the conformal map breaks down. We illustrate this behavior with some physically relevant model test functions and with two non-trivial physical examples where the relevant Riemann surface has complicated structure.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

X-57 “Maxwell” High-Lift Propeller Testing and Model Development

NASA’s X-57 “Maxwell” distributed electric propulsion flight demonstrator has a high-lift system that includes 12 fixed-pitch high-lift propellers located upstream of the wing leading edge for lift augmentation at low speeds. These high-lift propellers are not required at higher speeds and are folded conformally along the nacelles to reduce drag when not in operation. Aircraft performance models and flight simulations incorporate propeller performance to predict thrust, moments, and power consumption and propeller model accuracy is important in identifying safe operating regimes for this aircraft. Current high-lift propeller performance models have been verified and calibrated against numerous computational fluid dynamics analyses under a variety of flight conditions. We performed a series of full-scale wind tunnel tests at the NASA Langley Research Center Low Speed Aeroacoustic Wind Tunnel to further validate these models, to identify any adverse operating conditions for these propellers, and to assess the accuracy of the facility’s new Propeller Test Stand. The results indicate that the models accurately predicted performance and that the right-handed propeller showed lower torque and thrust for a given propeller speed compared to the left-handed version. Acoustic data support these measurements, showing higher tonal noise for the left versus right propeller. We suspect this is due to slight differences in the material properties between the early production (right) and more recent (left) blade sets leading to greater detwisting in the right-handed blades under load. Both propellers demonstrated very stable operation throughout the test including during deployment, stowing, and windmilling. Furthermore, high-speed imagery of the spinning propeller indicated no blade oscillations or instabilities for any test case. We also leveraged these images to analyze the effects of propeller loading on blade detwisting and tip position. Unfortunately, the thrust measurements varied significantly during the test due to cross-loading of the Propeller Test Stand load cell, though trends in the thrust data were still observable. The torque measurement, however, remained very precise for all test points and was used for performance comparisons. As a result of this test, we validated and improved the X-57 high-lift propeller performance models, obtained detailed propeller acoustic data and high-speed imagery, observed the propeller operating safely during a variety of dynamic events, and identified two potentially adverse, low-propeller-speed conditions which will be avoided during normal aircraft operation.

X-57↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
NASA NTRS2002

Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the submicromolar range was developed. Copyright 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 517-526, 2002.

Evaluation Studies↗
NASA NTRS1978

An exact derivation of contact resistance to planar devices

A mixed boundary-value problem is formulated for an imperfect rectangular contact to a semiconducting sheet (layer). An exact model for derivation of contact resistance is developed and its solution by conformal mapping and eigenfunction expansion is presented. The expression for contact resistance is similar to that for a perfect (lossless) contact but includes an additional term containing the lowest-order coefficient in the infinite series expansion of the complex potential function. The calculated contact resistances are compared with those obtained from three approximate models: lossless contact, transmission line, and extended transmission line models. The extended transmission line model appears to be a very satisfactory approximation provided the ratio of contact length to sheet thickness is no less than 0.5.

Schuldt, S. B.↗
DOE OSTI2020

Replica wormhole and information retrieval in the SYK model coupled to Majorana chains

Motivated by recent studies of the information paradox in (1+1)-D anti-de Sitter spacetime with a bath described by a (1+1)-D conformal field theory, we study the dynamics of second Ŕenyi entropy of the Sachdev-Ye-Kitaev (SYK) model (χ) coupled to a Majorana chain bath (ψ). The system is prepared in the thermofield double (TFD) state and then evolved by HL + HR. For small system-bath coupling, we find that the second Rényi entropy $S^(2)_{χL,χR}$ of the SYK model undergoes a first order transition during the evolution. In the sense of holographic duality, the long-time solution corresponds to a “replica wormhole”. The transition time corresponds to the Page time of a black hole coupled to a thermal bath. We further study the information scrambling and retrieval by introducing a classical control bit, which controls whether or not we add a perturbation in the SYK system. The mutual information between the bath and the control bit shows a positive jump at the Page time, indicating that the entanglement wedge of the bath includes an island in the holographic bulk.

1/N Expansion↗
DOE OSTI2021

On rational points in CFT moduli spaces

Motivated by the search for rational points in moduli spaces of two-dimensional conformal field theories, we investigate how points with enhanced symmetry algebras are distributed there. We first study the bosonic sigma-model with S 1 target space in detail and uncover hitherto unknown features. We find for instance that the vanishing of the twist gap, though true for the S 1 example, does not automatically follow from enhanced symmetry points being dense in the moduli space. We then explore the supersymmetric sigma-model on K3 by perturbing away from the torus orbifold locus. Though we do not reach a definite conclusion on the distribution of enhanced symmetry points in the K3 moduli space, we make several observations on how chiral currents can emerge and disappear under conformal perturbation theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Comments on the quantum field theory of the Coulomb gas formalism

The holomorphic Coulomb gas formalism, as developed by Feigin-Fuchs, Dotsenko-Fateev and Felder, is a set of rules for computing minimal model observables using free field techniques. We attempt to derive and clarify these rules using standard techniques of quantum field theory. We begin with a careful examination of the timelike linear dilaton. Although the background charge of the model breaks the scalar field’s continuous shift symmetry, the exponential of the action remains invariant under a discrete shift because the background charge is imaginary. Gauging this symmetry makes the dilaton compact and introduces winding modes into the spectrum. One of these winding operators corresponds to the anti-holomorphic completion of the BRST current first introduced by Felder, and the full left/right cohomology of this BRST charge isolates the irreducible representations of the Virasoro algebra within the degenerate Fock space of the linear dilaton. The “supertrace” in the BRST complex reproduces the minimal model partition function and exhibits delicate cancellations between states with both momentum and winding. The model at the radius $R=\sqrt{pp^{\prime }}$ has two marginal operators corresponding to the Dotsenko-Fateev “screening charges”. Deforming by them, we obtain a model that might be called a “BRST quotiented compact timelike Liouville theory”. The Hamiltonian of the zero-mode quantum mechanics of this model is not Hermitian, but it is PT -symmetric and exactly solvable. Its eigenfunctions have support on an infinite number of plane waves, suggesting an infinite reduction in the number of independent states in the full quantum field theory. Applying conformal perturbation theory to the exponential interactions reproduces the Coulomb gas calculations of minimal model correlation functions. In contrast to spacelike Liouville, these “resonance correlators” are finite because the zero mode is compact. We comment on subtleties regarding the reflection operator identification, as well as naive violations of truncation in correlators with multiple reflection operators inserted. This work is part of an attempt to understand the relationship between the JT model of two dimen- sional gravity and the worldsheet description of the (2 , p ) minimal string as suggested by Seiberg and Stanford.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

The quantum p -spin glass model: a user manual for holographers

We study a large-N bosonic quantum mechanical sigma-model with a spherical target space subject to disordered interactions, more colloquially known as the p-spin spherical model. Replica symmetry is broken at low temperatures and for sufficiently weak quantum fluctuations, which drives the system into a spin glass (SG) phase. The first half of this paper is dedicated to a discussion of this model's thermodynamics, with particular emphasis on the marginally stable SG. This phase exhibits an emergent conformal symmetry in the strong coupling regime, which dictates its thermodynamic properties. It is associated with an extensive number of nearby states in the free energy landscape. We discuss in detail an elegant approximate solution to the SG equations, which interpolates between the conformal regime and an ultraviolet-complete short distance solution. In the second half of this paper we explore the real-time dynamics of the model and uncover quantum chaos as measured by out-of-time-order four-point functions, both numerically and analytically. We find exponential Lyapunov growth, which intricately depends on the model's couplings and becomes strongest in the quantum critical regime. We emphasize that the SG phase also exhibits quantum chaos, albeit with parametrically smaller Lyapunov exponent than in the replica symmetric phase. An analytical calculation in the marginal SG phase suggests that this Lyapunov exponent vanishes in a particular infinite coupling limit. Finally, we comment on the potential meaning of these observations from the perspective of holography.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗