Search NASA⌕ Search

SEARCH · Search NASA

Results for “Conformal prediction”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Small-𝑥 behavior in QCD from maximal entanglement and conformal invariance

Recent evidence suggests that, at small Bjorken 𝑥, QCD evolution drives the proton into a state of maximal entanglement. If the evolution kernel is assumed to be conformally invariant—as is the case for the Balitsky-Fadin-Kuraev-Lipatov equation—we can describe it by a conformal field theory. Moreover, the central charge 𝑐 of the corresponding conformal field theory emerges as the key parameter governing the 𝑥 dependence of both the entanglement entropy and the structure function. Here we apply the exact Bethe ansatz methods to the quantum spin chain dual to Lipatov’s high energy effective action to extract the central charge of the theory, and find that 𝑐 = 1. This implies the ∼𝑥 −1/3 small 𝑥 behavior for the structure function—the prediction that can be tested at the forthcoming Electron-Ion Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Conformational diversity of 1-phenylpiperidin-4-one in the gas phase

Conformational preferences of substituted, saturated cyclic ketones may deviate from those of their parent analogues. 1-Phenylpiperidin-4-one was found to exist in several forms differing by not only position (axial or equatorial) of the aryl-substituent but also by a configuration of the piperidine cycle itself: chair-Eq, chair-Ax and twist-Tw. Here, the ratios of the co-existing species contributions in gas phase predicted by various quantum chemical calculations were confirmed by synchronous gas-phase electron diffraction and mass spectrometric experiments carried out for the vapor at 337 K demonstrating a best fit with the B3LYP-D3/cc-pVTZ combination: Eq:Ax:Tw=55(13):22(9):23(10) vs. 40:35:25.

1-phenylpiperidin-4-one↗
DOE OSTI2021

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Component 5: Imaging Protein Conformations, Shapes & Assemblies in Solution & Administration project (Final Scientific/Technical Report, Subcontract No. 6974584)

We set ambitious goals to examine microorganism communities and measure both their chemical input and output as a read out of specific biochemical activity. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in tum modify the environment. By examining how bacteria communities rely on symbiotic metabolic relationships for survival and reproductive success, and how these relationships consequently affect their biochemical capabilities. This was accomplished using state-of-the-art mass spectrometry-based methods, and metabolic fingerprinting approaches with a high degree of chemical specificity and sensitivity. During this period the original effort transitioned and was consolidated into what is now ENIGMA, the efforts on technology development expanded to include more untargeted metabolomics and its application to organisms on a systems level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.

Science & Technology - Other Topics↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Updated systematics of intermediate-energy single-nucleon removal cross sections

The body of experimental measurements of intermediate-energy reactions that remove a single nucleon from a secondary beam of neutron- or proton-rich nuclei continues to grow. These data have been analyzed consistently using an approximate, eikonal-model treatment of the reaction dynamics combined with appropriate shell-model descriptions of the projectile initial state, the bound final states spectrum of the reaction residue, and single-particle removal strengths computed from their wave-function overlaps. Here, the systematics of the ratio R s of the measured inclusive cross section to all bound final states and the calculated cross section to bound shell-model states—in different regions of the nuclear chart and involving both very weakly bound and strongly bound valence nucleons—is important in relating the empirically deduced orbital occupancies to those from the best available shell-model predictions. Importantly, several new higher-energy measurements, for which the sudden-approximation aspect of the dynamical description is placed on an even stronger footing, now supplement the previously analyzed measurements. These additional data sets are discussed. Their R s values are shown to conform to and reinforce the earlier-observed systematics, with no indication that the approximately linear reduction in R s with increasing nucleon separation energy is a consequence of a breakdown of the sudden approximation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks

Abstract Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein–solvent cooperative interactions has not yet been demonstrated. Here we report the design of 14 membrane receptors that catalyse G protein nucleotide exchange through diverse engineered allosteric pathways mediated by cooperative networks of intraprotein, protein–ligand and –solvent molecule interactions. Consistent with predictions, the designed protein activities correlated well with the level of plasticity of the networks at flexible transmembrane helical interfaces. Several designs displayed considerably enhanced thermostability and activity compared with related natural receptors. The most stable and active variant crystallized in an unforeseen signalling-active conformation, in excellent agreement with the design models. The allosteric network topologies of the best designs bear limited similarity to those of natural receptors and reveal an allosteric interaction space larger than previously inferred from natural proteins. The approach should prove useful for engineering proteins with novel complex protein binding, catalytic and signalling activities.

Chemistry↗
DOE OSTI2021

Effect of Graft Molecular Weight and Density on the Mechanical Properties of Polystyrene-Grafted Cellulose Nanocrystal Films

In this work, polymer-grafted nanoparticle (PGN) films were prepared from polystyrene (PS) grafted to rodlike cellulose nanocrystals (MxG-CNC-g-PS) with a controllable grafting density (0.03–0.25 chains/nm 2 ) and molecular weight (5–60 kg/mol). These nanorod-based PGNs are solution- and melt-processible, permitting access to one-component composite films with high nanofiller loadings (with up to 55 wt %). The impact of both grafted polymer density and molecular weight on the mechanical properties of the films was investigated and related to the polymer brush conformation: concentrated polymer brush (CPB), semidilute polymer brush (SDPB), or CPB core with SDPB corona (CPB/SDPB). The rubbery regime storage modulus (above $T_g$) showed 2 orders of magnitude increase, maximizing at a low degree of polymerization (N) and low grafting density (σ). Fracture toughness was maximized in samples with the grafted polymer in the SDPB or CPD/SDPB (higher N and relatively low σ) regime and showed enhancement relative to PS of molecular weight similar to the graft. In line with prior computation predictions, optimizing for both rubbery modulus and fracture toughness in such nanorod-based PGN films requires the polymers in the SDPB regime and CNC loading levels (ca. 50–60 wt %) that are difficult to attain in more traditional two-component CNC composites.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a “brush” surrounding each NF. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Science & Technology - Other Topics↗
DOE OSTI2025

Determining the Conformation of Supported Complexes Using an 17 O TEDOR-like NMR Experiment

Dynamic nuclear polarization surface-enhanced nuclear magnetic resonance (NMR) spectroscopy has enabled the determination of the three-dimensional configuration of surface sites, in particular supported metal complexes of relevance to single-site heterogeneous catalysis. These approaches have chiefly leveraged the application of NMR double-resonance experiments that either reveal the complex conformation via point-to-point intramolecular distances between spin-labeled atoms or the complex-surface orientation via distances between the spins and the surface plane. Either method typically requires expensive isotope labeling and each reports on different structural features. The application of an experiment that simultaneously reveals both types of distances with chemical resolution would be ideal. Here, in this article, we describe an 17 O{ 1 H} pseudo-3D correlation experiment that achieves this goal. Specifically, Si–O–Si and Si–O–M oxygens are well-resolved by 17 O NMR; therefore, distances can be simultaneously measured radially, between Si– 17 O–M and the 1 H’s of the ligands, and vertically to the Si– 17 O–Si linkages of the silica support. We demonstrate the experiment using supported yttrium and zirconium complexes. Good agreement is obtained when comparing the experimental results to theoretical predictions from density functional theory calculations, highlighting the reliability of this relatively simple experiment.

alkyls↗
DOE OSTI2020

Atomistic Insight into Cation Effects on Binding Energies in Cu-Catalyzed Carbon Dioxide Reduction

Electrolyte properties in general and electrolyte ions in particular have been shown to have significant effects on the kinetics of electrochemical CO 2 and CO reduction at metal electrodes, but these effects have not yet been fully understood. Here, we investigate the effects of cations at the aqueous electrolyte–Cu(211) interface on adsorbate binding energies and the electrolyte structure using density functional theory (DFT). Charging the interface via explicit Na + has systematic effects on adsorbate–electrolyte interactions and conformations. We describe specific local adsorbate–ion interactions, including direct alkali ion–adsorbate coordination and hydrogen bonding via ion-coordinated water molecules. The relative importance of these specific interactions and purely electrostatic field–adsorbate interactions is investigated by comparing the DFT-calculated ion effects to those predicted by purely electrostatic models of the interface and the adsorbates. We find that the trend in ion effects among different adsorbates at constant surface charge density is well explained by a purely electrostatic interaction model. The binding energy of OCCHO is found to depend strongly on the surface charge density as well as the spatial distribution of ions at constant surface charge density. These effects are also explained by a purely electrostatic local electrostatic field–adsorbate model. This indicates that alkali ion effects can be mainly attributed to purely electrostatic field interactions and that the local field at ion-stabilized active sites can depend significantly on both the overall charge density and on the spatial distribution of ions at constant charge density. This work provides new insight on alkali ion effects on a variety of adsorbates relevant to the CO 2 and CO reduction reactions by describing specific local ion–adsorbate interactions, systematic changes in adsorbate–electrolyte interactions induced by explicit surface charge, and comparisons of the calculated effects on binding energies to simple electrostatic field–adsorbate models to explain trends among various adsorbates and at varying surface charge densities and supercell configurations.

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

Off-Lattice Markov Chain Monte Carlo Simulations of Mechanically Driven Polymers

Here, we develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces by using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed length bonds, with configurations updated through adaptive nonlocal Monte Carlo moves. This proposed method enables precise calculation of a polymer’s response to a wide range of mechanical forces, which traditional on-lattice models cannot achieve. Our approach has shown excellent agreement with theoretical predictions of persistence length and end-to-end distance in quiescent states as well as stretching distances under tension. Moreover, our model eliminates the orientational bias present in on-lattice models, which significantly impacts calculations such as the scattering function, a crucial technique for revealing the polymer conformation.

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

Shear-Induced Conformations of Salt-Free Polyelectrolytes in Semidilute Solutions

Here, we present coarse-grained molecular dynamics simulations of salt-free polyelectrolyte chains in semidilute solutions under simple shear flow, with full hydrodynamic interactions and explicit dipolar solvent. At equilibrium, chain orientation statistics follow a pseudo-Voigt distribution, and the structural correlation length and chain end-to-end vector autocorrelation function exhibit scaling behavior consistent with theoretical predictions for polyelectrolytes. Under shear, chains transition from coiled to stretched states and the end-to-end vector autocorrelation function reveals oscillatory dynamics at high Weissenberg numbers. Analysis of the gyration tensor and shear strain distributions identified three distinct chain populations with directional alignment along and against the shear gradient. Compared with their neutral polymer counterparts, polyelectrolytes exhibit stronger shear thinning and enhanced chain alignment under the same Weissenberg number, which is attributed to electrostatic interactions and shear-induced counterion release. These findings provide molecular insight into the distinct flow response of charged polymers and have implications for tailoring the rheological properties of polyelectrolyte-based materials.

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

Thermal Stability of π-Conjugated n -Ethylene-Glycol-Terminated Quaterthiophene Oligomers: A Computational and Experimental Study

This work represents a joint computational and experimental study on a series of $\textit{n}$-ethylene glycol (PEO$\textit{n}$)-terminated quaterthiophene (4T) oligomers for 1 < $\textit{n}$ < 10 to elucidate their self-assembly behavior into a smectic-like lamellar phase. This study builds on an earlier study for $\textit{n}$ = 4 that showed that our model predictions were consistent with experimental data on the melting behavior and structure of the lamellar phase, with the latter consisting of crystal-like 4T domains and liquid-like PEO4 domains. The present study aims to understand how the length of the terminal PEO$\textit{n}$ chains modulates the disordering temperature of the lamellar phase and hence the relative stability of the ordered structure. In this work, a simplified bilayer model, where the 4T domains are not explicitly described, is put forward to efficiently estimate the disordering effect of the PEO domains with increasing n; this method is first validated by correctly predicting that layers of alkyl (PE)-capped 4T oligomers (for 1 < $\textit{n}$ < 10) stay ordered at room temperature. Both 4T-domain implicit and explicit model simulations reveal that the order-disorder temperature decreases with the length of the PEO capping chains, as the associated increase in conformational entropy drives a tendency toward disorder that overtakes the cohesive energy, keeping the ordered packing of the 4T domains.

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

Optimizing the Smoothness and Thickness Uniformity of Thin-Film Parylene-N Vapor-Deposited Coatings for Inertial Confinement Fusion Experiments

Polymer coatings with submicrometer smoothness and constant thickness are a required component in a variety of inertial confinement fusion experiments. Smoothness is important for minimizing Rayleigh-Taylor-driven hydrodynamic instabilities, and uniform thickness is important for uniform shock propagation and shell convergence, both of which are critical phenomena that affect the experiment. The preferred polymer coating method is to vapor deposit the parylene-N polymer because it provides nominally smooth conformal coatings. As the coating thickness exceeds 5 µm, however, dome-shaped nodular growth defects develop and the thickness will vary by up to 17% over a distance of 3 cm. This study presents a deterministic method for achieving uniform film thicknesses with ±2% variability over 3 cm and a predictive method to control the thickness to within 5% of the desired value. A coating smoothness of ∼50 nm rms, measured over 40 000 µm 2 , was achieved by adding additional surfaces near the substrates. This additional area improved the thickness uniformity, an effect that is attributed to the low sticking coefficient of the parylene monomer.

chemical vapor deposition (CVD)↗
DOE OSTI2023

Inhibition of Extracellular Enzyme Activity by Reactive Oxygen Species upon Oxygenation of Reduced Iron-Bearing Minerals

The dual roles of minerals in inhibiting and prolonging extracellular enzyme activity in soils and sediments are governed by enzyme adsorption to mineral surface. Oxigenation of mineral-bound Fe(II) generates reactive oxygen species (ROS), yet it is unknown whether and how this process alters the activity and functional lifespan of extracellular enzymes. Here, the effect of mineral-bound Fe(II) oxidation on the hydrolytic activity of a cellulose-degrading enzyme ß-glucosidase (BG) was studied using two pre-reduced Fe-bearing clay minerals (nontronite and montmorillonite) and one pre-reduced iron oxide (magnetite) at pH 5 and 7. Under anoxic condition, BG adsorption to mineral surface decreased its activity but prolonged its lifespan. Under oxic condition, ROS was produced, with the amount of •OH, the most abundant ROS, being positively correlated with the extent of structural Fe(II) oxidation in reduced minerals. •OH decreased BG activity and shortened its lifespan via conformational change and structural decomposition of BG. These results suggest that under oxic condition the ROS-induced inhibitory role of Fe(II)-bearing minerals outweighed their adsorption-induced protective role in controlling enzyme activity. These results disclose a previously unknown mechanism of extracellular enzyme inactivation, which have pivotal implications for predicting the active enzyme pool in redox-oscillating environments.

58 GEOSCIENCES↗
DOE OSTI2025

STEPs-SOL, a Peptoid Force Field Parameterization to Include Solvent Effects

As peptoids (N-substituted glycines) continue to gain popularity as a class of biomimetic polymers, the importance and demand for accurate force fields in molecular simulations also grow. Building on the vacuum-optimized Systematic and Extensible Force Field for Peptoids (STEPs) force field, here we present STEPs-SOL, a novel peptoid force field parametrization that effectively incorporates solvent effects to enhance the accuracy of peptoid simulations. The development of STEPs-SOL is based on the need for precise electrostatic modeling achieved through solvent-specific partial charge optimization. Here, our systematic approach significantly improves agreement with experimental measurements, reducing the mean absolute error in cis/trans ratio predictions (ΔG c/t ) by an average of 38% across multiple peptoid residues and solvent environments. This improved parametrization addresses computational challenges associated with nonbonded energies while maintaining a workflow that relies on high-level quantum mechanical data rather than depending solely on limited experimental equilibrium properties. By evaluating the effects of conformational bias in restrained electrostatic potential (RESP) charge generation and examining their impact on peptoid conformations in various solvents, we enhance our understanding of peptoid structural dynamics while providing a more accurate modeling framework.

force field↗