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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

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

Ultrafast conformational dynamics of Rydberg-excited N -methyl piperidine

We have observed the ultrafast conformational dynamics of electronically excited N-methyl piperidine (NMP) using time-resolved Rydberg fingerprint spectroscopy. Optical excitation at various wavelengths ranging from 212 nm to 229 nm leads to the 3s or 3p Rydberg states and induces coherent oscillatory motions with periods of about 700 fs. Furthermore, these coherent motions survive the internal conversion from 3p to 3s but then dephase on a time scale of a few oscillations. Intramolecular vibrational energy redistribution on a picosecond time scale leads to an equilibrium between two conformeric structures that are separated in binding energy by 0.09 eV. Model calculations using the DFT-SIC method are in excellent agreement with the experiments and identify the conformers as the chair and twist structures of NMP. The analysis of the equilibrium parameters at long time delays as a function of excitation wavelength allows for the extraction of thermodynamic parameters for the conformeric transformation. We derive an enthalpy of the chair to twist reaction in the 3s excited state of 62 meV with an entropy of 19.70 J mol –1 K –1 . An activation energy of 276 meV is also obtained with a kinetic model.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Gas phase protonated nicotine is a mixture of pyridine- and pyrrolidine-protonated conformers: implications for its native structure in the nicotinic acetylcholine receptor

The infrared (IR) spectra of gas phase protonated nicotine has been measured in the never-before probed N–H “fingerprint region” (3200–3500 cm -1 ). The protonated molecules generated by an electrospray source are thermalized in the first ion trap with water vapor and He gas at a pre-determined temperature prior to being probed by IR spectroscopy in the second ion trap at 4 K. The IR spectra exhibit two N–H stretching bands which are assigned to the pyridine and pyrrolidine protomers with the aid of high-level electronic structure calculations. This finding is in sharp contrast to previous spectroscopic studies that suggested a single population of the pyridine protomer. The relative populations of the two protomers vary by changing the temperature of the thermalizing trap from 180-300 K. The relative conformer populations at 240 K and 300 K are well reproduced by the theoretical calculations, unequivocally determining that gas phase nicotine is a 3 : 2 mixture of both pyridine and pyrrolidine protomers at room temperature. The thermalizing anhydrous vapor does not result in any population change. It rather demonstrates the catalytic role of water in achieving equilibrium between the two protomers. The combination of IR spectroscopy and electronic structure calculations establish the small energy difference between the pyridine and pyrrolidine protomers in nicotine. Finally, one of the gas phase nicotine pyrrolidine protomers has the closest conformational resemblance among all low-lying energy isomers with the X-ray structure of nicotine in the nicotinic acetylcholine receptor (nAChR).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Deep learning–driven rare-event sampling reveals an Ala7/d-Ala8 conformational hinge governing amphiphilic switching in cyclosporine A

Passive membrane permeability of N-methylated macrocyclic peptides remains poorly understood because high-energy conformational intermediates are rarely sampled by conventional methods. Using the deep learning–driven rare-event sampling framework ES-CRUMPLE, we show that cyclosporine A accesses transient amphiphilic states via a localized conformational hinge at Ala7/d-Ala8, revealing a kinetic design handle that is invisible to population-based analyses.

Lindberg, Edward T [University of Tennessee, Knoxv↗
DOE OSTI2020

Conformation and dynamics of ring polymers under symmetric thin film confinement

Understanding the structure and dynamics of polymers under confinement has been of widespread interest, and one class of polymers that have received comparatively little attention under confinement is that of ring polymers. The properties of non-concatenated ring polymers can also be important in biological fields because ring polymers have been proven to be a good model to study DNA organization in the cell nucleus. From our previous study, linear polymers in a cylindrically confined polymer melt were found to segregate from each other as a result of the strong correlation hole effect that is enhanced by the confining surfaces. By comparison, our subsequent study of linear polymers in confined thin films at similar levels of confinements found only the onset of segregation. Here, we use molecular dynamics simulation to investigate the chain conformations and dynamics of ring polymers under planar (1D) confinement as a function of film thickness. Our results show that conformations of ring polymers are similar to the linear polymers under planar confinement, except that ring polymers are less compressed in the direction normal to the walls. While we find that the correlation hole effect is enhanced under confinement, it is not as pronounced as the linear polymers under 2D confinement. Finally, we show that chain dynamics far above Tg are primarily affected by the friction from walls based on the monomeric friction coefficient we get from the Rouse mode analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Formation and detection of metastable formic acid in a supersonic expansion: High resolution infrared spectroscopy of the jet-cooled cis -HCOOH conformer

High-resolution direct absorption infrared spectra of metastable cis-formic acid (HCOOH) trapped in a cis-well resonance behind a 15 kcal/mol barrier are reported for the first time, with the energetically unstable conformer produced in a supersonic slit plasma expansion of trans-formic acid/H 2 mixtures. We present a detailed high-resolution rovibrational analysis for cis-formic acid species in the OH stretch (ν 1 ) fundamental, providing first precision vibrational band origin, rotational constants, and term values, which in conjunction with ab initio calculations at the couple-cluster with single, double, and perturbative triple [CCSD(T)]/ANOn (n = 0, 1, 2) level support the experimental assignments and establish critical points on the potential energy surface for internal rotor trans-to-cis isomerization. Relative intensities for a- and b-type transitions observed in the spectra permit the transition dipole moment components to be determined in the body fixed frame and prove to be in good agreement with ab initio CCSD(T) theoretical estimates but in poor agreement with simple bond-dipole predictions. As a result, the observed signal dependence on H 2 in the discharge suggests the presence of a novel H atom radical chemical mechanism for strongly endothermic “up-hill” internal rotor isomerization between trans- and cis-formic acid conformers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Axial vs equatorial: Capturing the intramolecular charge transfer state geometry in conformational polymorphic crystals of a donor–bridge–acceptor dyad in nanosecond-time-scale

Two conformational polymorphs of a donor–bridge–acceptor (D-B-A) dyad, p-(CH 3 ) 2 N-C 6 H 4 -(CH 2 ) 2 -(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH 3 ) 2 N-C 6 H 4 /DMA is connected through a bridging group (B), –CH 2 –CH 2 –, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ~3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ~7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C–N–(CH 3 ) 2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Nodavirus RNA replication crown architecture reveals proto-crown precursor and viral protein A conformational switching

Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric “crown” at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryoelectron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multidomain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a “proto-crown” precursor that assembles prior to RNA template recruitment, RNA synthesis, and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 Å resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding “legs.” The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and nonsymmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility, and evolutionary plasticity and insights into (+)RNA virus replication and control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism

Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental access. This shortcoming is evident with Escherichia coli dihydrofolate reductase (DHFR), a model system for the role of protein dynamics in catalysis, for which it is unknown how the enzyme regulates the different active site environments required to facilitate proton and hydride transfer. Here, we describe ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments to map the conformational dynamics of the Michaelis complex of DHFR. We resolve coupled global and local motions and find that these motions are engaged by the protonated substrate to promote efficient catalysis. This result suggests a fundamental design principle for multistep enzymes in which pre-existing dynamics enable intermediates to drive rapid electrostatic reorganization to facilitate subsequent chemical steps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism

Removing glutamate from the synaptic cleft is vital for proper function of the brain. Excitatory amino acid transporters mediate this process by uptaking the neurotransmitter from the synaptic cleft back to the cell after its release. The archaeal homolog, Glt Ph , an aspartate transporter fromPyrococcus horikoshii, presents the best structurally characterized model for this family of transporters. In order to transport, Glt Ph undergoes elevator-like conformational changes between inward-facing (IF) and outward-facing (OF) states. Here, we characterize, at an atomic level, the OF⇌IF transition of Glt Ph in differentapo/bound states using a combination of ensemble-based enhanced sampling techniques, employing more than two thousand of coupled simulation replicas of membrane-embedded Glt Ph . The resulting free-energy profiles portray the transition ofapo/bound states as a complex four-stage process, while sodium binding alone locks the structure in one of its states. Along the transition, the transport domain (TD) disengages from the scaffold domain (SD), allowing it to move as a piston sliding vertically with respect to the membrane during the elevator-like motion of TD. Lipid interactions with residues comprising the SD–TD interface directly influence the large-scale conformational changes and, consequently, the energetics of transport. Structural intermediates formed during the transition leak water molecules and may correlate to the uncoupled Cl − ion conductance observed experimentally in both prokaryotic and mammalian glutamate transporters. Mechanistic insights obtained from our study provide a structural framework for better development of therapeutic for neurological disorders.

Science & Technology - Other Topics↗
DOE OSTI2025

Nucleotide- and metalloid-driven conformational changes in the arsenite efflux ATPase ArsA

Arsenite (As III ) is toxic to all organisms due to its ability to tightly bind exposed thiols within cells. An important As III resistance mechanism in prokaryotes involves proteins encoded by thearsoperon. A central component of thearsoperon in many bacteria is the cytoplasmic ATPase, ArsA, which orchestrates a series of nucleotide-dependent handoffs, starting with the capture of As III by the ArsD metallochaperone and culminating in its removal from the cell by the ArsB efflux pump. Although the mechanism of ArsA has been widely studied, the molecular details of how nucleotide hydrolysis modulates these events remain unclear. ArsA is an archetypal member of the intradimeric Walker A (IWA) family of ATPases, implicated in a diversity of complex biological functions. Conformational changes typical of IWA ATPases have been postulated to drive these molecular events but have not been demonstrated. We report cryogenic electron microscopy (cryo-EM) structures of ArsA in MgADP-bound and MgATP-boundopenstates, as well as a distinctclosedMgATP-bound state liganded to As III . X-ray absorption spectroscopy (XAS) confirmed three-coordinate binding of As III to the conserved cysteines at the metalloid-binding site of the closed state. Coupled with biochemical characterization, our cryo-EM structures reveal key conformational changes in the ArsA catalytic cycle consistent with other IWA ATPases and provide the structural basis for allosteric activation of nucleotide hydrolysis by As III . This work establishes how the nucleotide state of ArsA transiently creates a high-affinity binding site that can sequester metalloid within the cell, followed by a nucleotide-driven handoff to ArsB for efflux.

Science & Technology - Other Topics↗
DOE OSTI2024

Integrating chromosome conformation and DNA repair in a computational framework to assess cell radiosensitivity

Objective. The arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows for in silico investigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure. Approach. In this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results. Main results. We found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario. Significance. This framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Impact of transforming to conformal Fermi coordinates on quasisingle field non-Gaussianity

In general relativity, predictions for observable quantities can be expressed in a coordinate independent way. Nonetheless it may be inconvenient to do so. Using a particular frame may be the easiest way to connect theoretical predictions to measurable quantities. For the cosmological curvature bispectrum such frame is described by the conformal Fermi coordinates. In single field inflation it was shown that going to this frame cancels the squeezed limit of the density perturbation bispectrum calculated in global coordinates. Furthermore, we explore this issue in quasisingle field inflation when the curvaton mass and the curvaton-inflaton mixing are small. In this case, the contribution to the bispectrum from the coordinate transformation to conformal Fermi coordinates is of the same order as that from the inflaton-curvaton interaction term but does not cancel it.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Conformal correlators on the Lorentzian torus

The general form of a 2D conformal field theory (CFT) correlator on a Euclidean Riemann surface, Lorentzian plane or Lorentzian cylinder is well known. This paper describes the general form of 2- and 3-point CFT correlators on the Lorentzian torus LT 2 which arises as the conformal boundary of the group manifold SL ( 2 , R ) ≃ AdS 3 / Z . We consider only generic points, thereby omitting an analysis of contact terms, which already exhibits a surprisingly rich structure. The results are relevant to celestial holography, for which the LT 2 at the boundary of Klein space is the home of the putative celestial CFT. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Exact evaluation of large-charge correlation functions in nonrelativistic conformal field theory

The large-charge master field which generates all n -point correlation functions with an insertion of large charge Q in nonrelativistic conformal field theory is obtained. This field is used to compute Schrödinger-invariant n -point correlation functions of large-charge operators via a direct evaluation of the path integral. Conformal dimensions are found to agree with calculations based on the state-operator correspondence. The master field solution exhibits an emergent harmonic trap whose frequency is a function of the Euclidean time. The large-charge effective action with operator insertions describes a droplet of superfluid matter whose spatial size scales with the time separation of sources. The solution is used to compute Schrödinger symmetry breaking corrections in the large-charge effective field theory (EFT) due to a finite scattering length in the fundamental theory of fermions near unitarity. The scaling of these effects in the large-charge power counting scheme is established, and the size of the effects is quantified using input from quantum Monte Carlo simulations of the near-unitary gas, as well as from the large- N expansion at large charge. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Impossible symmetries and conformal gravity

We explore the physics of relativistic gapless phases defined by a mixed anomaly between two generalized conserved currents. The gapless modes can be understood as Goldstone modes arising from the nonlinear realization of (generically higher-form) symmetries arising from these currents. In some cases, the anomaly cannot be reproduced by any local and unitary theory, indicating that the corresponding symmetries are impossible, in the sense that they cannot appear in a Lorentzian physical system. We give a general construction and illustrate it with several examples. Most notably, we study conformal gravity from this perspective, describing the higher-form symmetries of the linear theory and showing how it can be understood in terms of anomalies. Along the way we clarify some aspects of electric-magnetic duality in linear conformal gravity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Precision Reconstruction of Rational Conformal Field Theory from Exact Fixed-Point Tensor Network

The novel concept of entanglement renormalization and its corresponding tensor network renormalization technique have been highly successful in developing a controlled real-space renormalization group (RG) scheme. Numerically approximate fixed-point (FP) tensors are widely used to extract the conformal data of the underlying conformal field theory (CFT) describing critical phenomena. In this paper, we present an explicit analytical construction of the FP tensor for 2D rational CFT. We define it as a correlation function between the “boundary-changing operators” (BCO) on triangles. Our construction fully captures all the real-space RG conditions. We also provide concrete examples, such as Ising, Yang-Lee, and tricritical Ising models, to compute the scaling dimensions explicitly based on the corresponding FP tensor. The BCO descendants turn out to be an optimal basis such that truncation in bond dimensions naturally produces comparable accuracies with the leading existing FP algorithms. Interestingly, our construction of FP tensors is closely related to a strange correlator, where the holographic picture naturally emerges. Our results also open a new door toward understanding CFT in higher dimensions. Published by the American Physical Society 2025

Cheng, Gong (ORCID:0009000891587404)↗
DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗