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Results for “conformers”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Processable High Electron Mobility {pi}-Copolymers via Mesoscale Backbone Conformational Ordering

The synthesis and experimental/theoretical characterization of a new series of electron-transporting copolymers based on the naphthalene bis(4,8-diamino-1,5-dicarboxyl)amide (NBA) building block are reported. Comonomers are designed to test the emergent effects of manipulating backbone torsional characteristics, and density functional theory (DFT) analysis reveals the key role of backbone conformation in optimizing electronic delocalization and transport. The NBA copolymer conformational and electronic properties are characterized using a broad array of molecular/macromolecular, thermal, optical, electrochemical, and charge transport techniques. All NBA copolymers exhibit strongly aggregated morphologies with significant nanoscale order. Copolymer charge transport properties are investigated in thin-film transistors and exhibit excellent electron mobilities ranging from 0.4 to 4.5 cm(2) V-1 s(-1). Importantly, the electron transport efficiency correlates with the film mesoscale order, which emerges from comonomer-dependent backbone planarity and extension. These results illuminate the key NBA building block structure-morphology-bulk property design relationships essential for processable, electronics-applicable high-performance polymeric semiconductors.

n‐↗
DOE OSTI2023

Hidden conformal symmetry from the lattice

We analyze newly expanded and refined data from lattice studies of an SU(3) gauge theory with eight Dirac fermions in the fundamental representation. We focus on the light composite states emerging from these studies, consisting of a set of pseudoscalars and a single light scalar. We first consider the view that this theory is just outside the conformal window. In this case, the pseudoscalars arise from spontaneous breaking of chiral symmetry. Identifying the scalar in this case as an approximate dilaton, we fit the lattice data to a dilaton effective field theory, finding that it yields a good fit even at lowest order. For comparison, we then consider the possibility that the theory is inside the conformal window. The fermion mass provides a deformation, triggering confinement. We employ simple scaling laws to fit the lattice data, and find that it is of lesser quality.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Measuring Relative Energies of Ligand Binding Conformations on Nanocluster Surfaces with Temperature-Dependent FTIR Spectroscopy

We present a method to measure relative energies between binding conformations of carboxylate ligands on InP magic-sized clusters in solution. Using Markov chain Monte Carlo global fitting analysis on temperature-dependent vibrational spectra of cluster-bound ligands, we observe significantly different relative energies between various bidentate and monodentate binding motifs. Relative to the monodentate motif, the chelating conformation is 0.7 ± 0.3 kcal/mol more stable and the syn–syn bridging conformation is 1.1 ± 0.5 kcal/mol more stable, but the syn–anti bridging conformation exhibits no significant difference. Our results demonstrate that the relative energy between monodentate-bound carboxylates and unbound carboxylic acids is 4.52 ± 0.05 kcal/mol, or 1582 ± 19 cm –1 , nearly identical to the carboxylate asymmetric stretching frequency. Here, we suggest that the ligand vibrational energy may play a key role in ligand dissociation by compensating for energy differences between bound and dissociated ligand states. This approach gives important experimental insights into ligand binding and can inform future nanocrystal surface engineering.

Conformation↗
DOE OSTI2020

A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl–/H+ transport cycle

Among coupled exchangers, CLCs uniquely catalyze the exchange of oppositely charged ions (Cl– for H+). Transport-cycle models to describe and explain this unusual mechanism have been proposed based on known CLC structures. While the proposed models harmonize with many experimental findings, gaps and inconsistencies in our understanding have remained. One limitation has been that global conformational change – which occurs in all conventional transporter mechanisms – has not been observed in any high-resolution structure. Here, we describe the 2.6 Å structure of a CLC mutant designed to mimic the fully H+-loaded transporter. This structure reveals a global conformational change to improve accessibility for the Cl– substrate from the extracellular side and new conformations for two key glutamate residues. Together with DEER measurements, MD simulations, and functional studies, this new structure provides evidence for a unified model of H+/Cl– transport that reconciles existing data on all CLC-type proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ~90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.

KRAS↗
DOE OSTI2022

PMC$_\infty$: Infinite-Order Scale-Setting method using the Principle of Maximum Conformality and preserving the Intrinsic Conformality

We show results for Thrust and C-parameter in e^+ e^- e + e − annihilation to 3 jets obtained using the recently developed new method for eliminating the scale ambiguity and the scheme dependence in pQCD namely the Infinite-Order Scale-Setting method using the Principle of Maximum Conformality (PMC _\infty ∞ ). This method preserves an important underlying property of gauge theories: intrinsic Conformality (iCF). It leads to a remarkably efficient method to eliminate the conventional renormalization scale ambiguity at any order in pQCD. A comparison with Conventional Scale Setting method (CSS) is also shown.

Di Giustino, Leonardo↗
NASA NTRS1986

Conforming versus non-conforming boundary elements in three-dimensional elastostatics

A critical comparison of two basic formulations in three-dimensional elastostatics, using conforming and nonconforming boundary elements, is presented. The basic structure of the boundary element method is developed. The peculiarities that both types of boundary elements present in relation to the numerical implementation are discussed. Through selected examples, key issues such as the computational advantages and disadvantages of both formulations, mesh discretization and accuracy questions, and optimal location of the collocation nodes in the case of nonconforming elements are addressed. It is shown that conforming elements are able to produce more accurate results than nonconforming ones, with substantial economy in the final size of the system equations.

Manolis, G. D.↗
DOE OSTI2021

The Pollica perspective on the (super)-conformal world

This manuscript samples a series of recent results in the quest for a systematic understanding of the space of conformal field theories, with a particular focus on theories with extended supersymmetry. The large majority of results reported here were presented during the second Pollica summer workshop which took place from June 3–21 2019 and focused on mathematical and geometric tools for superconformal field theories. Furthermore, this manuscript represents in many ways a partial summary of the workshop.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site

Abstract ADARs (adenosine deaminases acting on RNA) can be directed to sites in the transcriptome by complementary guide strands allowing for the correction of disease-causing mutations at the RNA level. However, ADARs show bias against editing adenosines with a guanosine 5′ nearest neighbor (5′-GA sites), limiting the scope of this approach. Earlier studies suggested this effect arises from a clash in the RNA minor groove involving the 2-amino group of the guanosine adjacent to an editing site. Here we show that nucleosides capable of pairing with guanosine in a syn conformation enhance editing for 5′-GA sites. We describe the crystal structure of a fragment of human ADAR2 bound to RNA bearing a G:G pair adjacent to an editing site. The two guanosines form a Gsyn:Ganti pair solving the steric problem by flipping the 2-amino group of the guanosine adjacent to the editing site into the major groove. Also, duplexes with 2′-deoxyadenosine and 3-deaza-2′-deoxyadenosine displayed increased editing efficiency, suggesting the formation of a Gsyn:AH+anti pair. This was supported by X-ray crystallography of an ADAR complex with RNA bearing a G:3-deaza dA pair. This study shows how non-Watson–Crick pairing in duplex RNA can facilitate ADAR editing enabling the design of next generation guide strands for therapeutic RNA editing.

Doherty, Erin E.↗
DOE OSTI2024

Non-conformity Scores for High-Quality Uncertainty Quantification from Conformal Prediction

High-quality uncertainty quantification (UQ) is a critical component of enabling trust in deep learning (DL) models and is especially important if DL models are to be deployed in high-consequence applications. Conformal prediction (CP) methods represent an emerging nonparametric approach for producing UQ that is easily interpretable and, under weak assumptions, provides a guarantee regarding UQ quality. This report describes the research outputs of an Exploratory Express Laboratory Directed Research and Development (LDRD) project at Sandia National Laboratories. This project focused on how best to implement CP methods for DL models. This report introduces new methodology for obtaining high-quality UQ from DL models using CP methods, describes a novel system of assessing UQ quality, and provides experimental results that demonstrate the quality of the new methodology and utility of the UQ quality assessment system. Avenues for future research and discussion of potential impacts at Sandia and in the wider research community are also given.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1988

Conformation-dependent recognition of a protein by T-lymphocytes: apomyoglobin-specific T-cell clone recognizes conformational changes between apomyoglobin and myoglobin

A T-cell clone specific to apomyoglobin was generated. It was prepared from a T-cell culture obtained by in vitro driving of lymph node cells with apomyoglobin from SJL mice that have been primed in vivo with apomyoglobin. In proliferative assays, the T-cell clone responded to apomyoglobin but did not recognize native myoglobin or any of the synthetic peptides corresponding to the six T sites of myoglobin. The demonstration that a T-cell clone can be isolated, whose specificity is directed entirely to apomyoglobin and not to its counterpart myoglobin, with an identical amino acid composition, indicates the importance of the three-dimensional structure in the presentation of the protein to T cells.

Apoproteins/immunology↗