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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c

Abstract The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c . This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1 s 3 p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.

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

Detailed modeling of the video signal and optimal readout of charge-coupled devices

This paper provides a practical design methodology to calculate an optimal filter for noise reduction in the readout of charge-coupled devices (CCDs) taking into account the charge transfer and feedthroughs due to capacitive coupling in the CCD. A detailed analysis of the dynamics of the video signal and charge transfer is presented, including the circuital modeling of the output stage of the CCD and the dynamics of the electronics in the video chain before the analog-to-digital (AD) converter. This model is used to compute an optimal filter that minimizes the variance of the pixel noise and uses the samples of the charge transfer, before the charge is fully settled. This is necessary to enhance the performance of previous results that also use optimal filters but do not use the transition samples, while also reducing the pixel readout time, resulting in faster readouts. As a proof of concept for the optimal filter, we present in this paper novel experimental results using a Skipper CCD, which has a floating sense node that allows to measure the charge packet an arbitrary number of times. However, this technique can be applied to any CCD that has a readout system that digitally samples the video signal.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Machine-learning force-field models for dynamical simulations of metallic magnets

We review recent advances in machine-learning (ML) force-field methods for Landau–Lifshitz–Gilbert simulations of itinerant electron magnets, focusing on their scalability and transferability. Built on the principle of locality, a deep neural-network model is developed to efficiently and accurately predict electron-mediated forces governing spin dynamics. Symmetry-aware descriptors constructed through a group-theoretical approach ensure rigorous incorporation of both lattice and spin-rotation symmetries. The framework is demonstrated using the prototypical s-d exchange model widely employed in spintronics. ML-enabled large-scale simulations reveal novel nonequilibrium phenomena, including anomalous coarsening of tetrahedral spin order on the triangular lattice and the freezing of phase-separation dynamics in lightly hole-doped, strong-coupling square-lattice systems. These results establish ML force-field frameworks as scalable, accurate, and versatile tools for modeling nonequilibrium spin dynamics in itinerant magnets.

Artificial neural networks↗
DOE OSTI2026

Nanoarchitectonic Semiconductor–Bio Hybrid Systems with Enhanced Charge Transfer for Hydrogen Peroxide Production

Nanoarchitectonics offers a systematic approach to creating an artificial framework by integrating different multiscale components such as semiconductor lattices and biological substances. However, most nanoarchitectonic abiotic-biotic hybrid systems have intrinsic limitations in imparting nonequilibrium biological features into semiconductor lattices at the nanoscale. Here, in this study, we report a new nanoarchitectonic system integrating bismuth oxychloride (BiOCl) nanosheets with purple membrane (PM) patches. PM is an archaeal subcellular fraction capable of unidirectionally transferring photogenerated charge carriers to its surroundings at the nanoscale independent of archaeal metabolism and retaining this dynamic functionality after isolation from living archaea. Microscopy, spectroscopy, electrochemical, and synchrotron X-ray scattering analyses verify that the nanoarchitectonic hybridization between BiOCl and PM generates a vertical heterostructure, thereby enhancing photogenerated charge-carrier dynamics and enabling the associated photocatalytic capacity. The resulting PM-BiOCl hybrid nanosheets efficiently convert dioxygen into hydrogen peroxide through a two-electron and two-proton transfer process under ambient conditions while simultaneously converting ethylene glycol into value-added chemicals. This study presents a nanoarchitectonic approach that leverages the photogenerated charge-carrier dynamics of the archaeal subcellular fractions to modulate the optoelectronic and catalytic capacity limitations of semiconductors.

catalysis↗
DOE OSTI2022

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗
DOE OSTI2022

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies

Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Forster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with posttranscriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an a-thiophosphorylated variant of rTPT3TP (rTPT3aS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal a-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Using a recirculating anaerobic dynamic membrane bioreactor to treat hydrothermal liquefaction aqueous by-product

Hydrothermal liquefaction (HTL) has the potential to improve resource recovery at water resource recovery facilities (WRRF), but the production of a high-strength aqueous by-product (HTL-aq) is hampering HTL implementation. The formation of biofilms in anaerobic digestion have been shown to be useful when degrading recalcitrant compounds present in HTL-aq due to the promotion of direct interspecies electron transfer (DIET) and increase in the microbial activity of syntrophic and methanogenic populations. The Recirculating Anaerobic Dynamic Membrane Bioreactor (RAnDMBr) was able to degrade 65% of the chemical oxygen demand (COD) at 1.5 ± 0.2 g COD LR −1 day −1 and 5.6 ± 2.3 days producing 0.19 ± 0.02 LCH4 gCOD fed −1 . However, adding a solution rich in nutrients on a daily basis was necessary. The system presented microbial populations able to degrade aromatic compounds (i.e., Anaerolinaceae) to perform DIET and syntrophy (i.e., Syntrophus) and methanogens (i.e., Methanobacterium and Methanosarcina) with the biofilm having a higher relative abundance of methanogens than the suspended biomass. Increasing the organic loading rate to 2 g COD LR −1 day −1 caused inhibition in the system by accumulation of volatile fatty acids, probably due to an increase in phenol, N-heterocyclic and aromatic compounds. Overall, this research shows that the RAnDMBr can be used to treat HTL-aq in WRRF without inhibition at OLRs of 1.5 ± 0.2 g COD LR −1 day −1 or lower, making HTL-aq treatment more feasible. Future research should focus co-digestion of HTL-aq with a co-substrate rich in nutrients and on fouling mitigation strategies that will allow to increase the recirculation ratio to promote advective substrate transport through the biofilm.

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

Chemical bond reorganization in intramolecular proton transfer revealed by ultrafast X-ray photoelectron spectroscopy

Time-resolved X-ray photoelectron spectroscopy (TR-XPS) is used in a simulation study to monitor the excited state intramolecular proton transfer between oxygen and nitrogen atoms in 2-(iminomethyl)phenol. Real-time monitoring of the chemical bond breaking and forming processes is obtained through the time evolution of excited-state chemical shifts. By employing individual atomic probes of the proton donor and acceptor atoms, we predict distinct signals with opposite chemical shifts of the donor and acceptor groups during proton transfer. Details of the ultrafast bond breaking and forming dynamics are revealed by extending the classical electron spectroscopy chemical analysis to real time. Through a comparison with simulated time-resolved photoelectron spectroscopy at the valence level, the distinct advantage of TR-XPS is demonstrated thanks to its atom specificity.

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

Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Here, using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H 3 O + ) that was formed within 140 femtoseconds through a direct oxygen-oxygen bond contraction and proton transfer, followed by the radical-cation pair dissociation and the subsequent structural relaxation of water within 250 femtoseconds. These measurements provide direct evidence of capturing this metastable radical-cation complex before separation, thereby improving our fundamental understanding of elementary reaction dynamics in ionized liquid water.

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

Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation

Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.

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

Numerical analysis of coalescence-induced bubble departure for enhanced boiling heat transfer

Boiling heat transfer plays a crucial role in a wide range of applications, such as power generation, refrigeration, electronics cooling, and pharmaceutics. Among the various factors that influence boiling heat transfer, the dynamics of vapor bubble nucleation, growth, and departure from the heated surface stand out as particularly important. An emerging phenomenon that can promote the departure of bubbles smaller than the Fritz diameter is coalescence-induced departure. If the dynamics of this process are fully understood, then surfaces can be engineered to promote faster bubble departure and substantially increase the performance of boiling heat transfer. Further, this work expands on published results by presenting a detailed numerical analysis of bubble coalescence and departure for a range of initial bubble diameters and size ratios between coalescing bubbles. Analysis of the results is focused on explaining how the release of surface energy and bubble surface dynamics lead to bubble departure, as well as fundamentally distinguishing capillary–inertial jumping and buoyant–inertial departure mechanisms across different bubble sizes and size ratios. The results show that both the initial sizes of the coalescing bubbles and the ratio between their sizes can determine whether the merged bubble will leave the surface through capillary–inertial jumping or buoyant departure. Below a certain bubble size, the release of surface energy by the merger is not sufficient to propel the merged bubble from the surface.

42 ENGINEERING↗
DOE OSTI2024

Elucidating Photoinduced Processes of Photosystem I Via Multidimensional Electronic and Vibrational Spectroscopies

This project was motivated by an overarching goal to elucidate the mechanism of energy and electron transfer that governs the efficient charge separation in photosystem I (PSI) complexes. PSI is a natural light harvesting complex that drives oxygenic photosynthesis in plants, algae, and cyanobacteria. It uses ~300 tightly packed chlorophylls (Chls) to absorb photons, transfer the excitation energy to the reaction center (RC), and generate a charge separated state with near unity quantum efficiency (QE). A better understanding of the mechanism of energy transfer and charge separation in PSI is required for understanding the high QE of natural light harvesting complexes, and it could lead to the further development of artificial photosynthetic systems for solar energy conversion and modification of light harvesting complexes to improve crop yields. We applied two-dimensional optical spectroscopies to different cyanobacterial photosystem I complexes, including PSI complexes that contain Chl f molecules, to map energy transfer pathways and gain insight into the efficient light harvesting of PSI. We used two-dimensional electronic spectroscopies (2DES) to map energy transfer in Chl a and Chl f containing PSI complexes. To investigate the Chl f PSI complexes, we modified our spectrometer to probe the lower energy states associated with Chl f molecules. We interpreted the 2DES spectra through global analysis procedures to generate maps of energy transfer. We also constructed a two-dimensional electronic vibrational (2DEV) spectrometer that will be used to investigate charge transfer transitions and dynamics within PSI complexes. Measurements were performed on model systems to establish general data analysis procedures for interpreting 2D spectra and gain insight into protein cofactor interactions.

14 SOLAR ENERGY↗
DOE OSTI2021

Ultrafast time-resolved x-ray absorption spectroscopy of ionized urea and its dimer through ab initio nonadiabatic dynamics

Investigating the early dynamics of chemical systems following ionization is essential for our understanding of radiation damage. However, experimental as well as theoretical investigations are very challenging due to the complex nature of these processes. Time-resolved x-ray absorption spectroscopy on a femtosecond timescale, in combination with appropriate simulations, is able to provide crucial insights into the ultrafast processes that occur upon ionization due to its element-specific probing nature. In this theoretical study, we investigate the ultrafast dynamics of valence-ionized states of urea and its dimer employing Tully's fewest switches surface hopping approach using Koopmans' theorem to describe the ionized system. We demonstrate that following valence ionization through a pump pulse, the time-resolved x-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges reveal rich insights into the dynamics. Excited states of the ionized system give rise to time-delayed blueshifts in the x-ray absorption spectra as a result of electronic relaxation dynamics through nonadiabatic transitions. Moreover, our statistical analysis reveals specific structural dynamics in the molecule that induce time-dependent changes in the spectra. For the urea monomer, we elucidate the possibility to trace effects of specific molecular vibrations in the time-resolved x-ray absorption spectra. For the urea dimer, where ionization triggers a proton transfer reaction, we show how the x-ray absorption spectra can reveal specific details on the progress of proton transfer.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Coherent Control over Nuclear Hyperpolarization Using an Optically Initializable Chromophore-Radical System

Chromophore radicals (CR) are emerging as important components for molecular quantum information science (QIS), especially in the context of quantum sensing. Here, we demonstrate that the optically hyperpolarized electrons in a 1,6,7,12-tetrakis(4-tert-butylphenoxy)-perylene-3,4,9,10-bis(dicarboximide) (tpPDI) covalently linked to a partially deuterated 1,3-bis(diphenylene)-d 16 -2-phenylallyl radical (BDPA-d 16 ) can be coherently manipulated via pulsed dynamic nuclear polarization (DNP) methods to transfer polarization to nuclear spins and back. Under light illumination at 85 K, electron hyperpolarization in BDPA is enhanced 2.1- to 2.4-fold over thermal polarization and lasts for more than 100 ms. By applying nuclear orientation via electron spin-locking (NOVEL) DNP, this optically amplified electron hyperpolarization was successfully transferred to a 1 H nuclear spin within the CR system and efficiently returned to the electron spin for readout via reverse-NOVEL. The NOVEL transfer efficiency of 65% amounts to a 688-fold nuclear spin hyperpolarization of the target nuclear spin, considering the 2.1-fold electron spin hyperpolarization. This reversible coherent manipulation of hyperpolarization transfer highlights the utility of CR systems to initialize and read out nuclear spin states in a disordered matrix at moderate cryogenic temperatures. Coupled with CRs’ environmental compatibility, tunability, and precise state initialization, these results highlight the promising role of nuclear spins in CRs for QIS applications, including quantum sensing and memory.

charge transfer↗
DOE OSTI2021

Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, e pre – , which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence e pre – states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. As a result, solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.

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

NOCI-F Electronic Couplings in Assemblies of Indolonaphthyridine Molecules: From Dimers to the Full Stack

Key electronic processes related to molecular excitonic states of finite stacks of indolonaphthyridine molecules are analyzed via the non-orthogonal configuration interaction with fragments (NOCI-F) method. Indolonaphthyridine is an organic chromophore that can undergo several electronic photoexcitation-related intermolecular processes, such as exciton and electron transfer. The structures studied here are noncrystalline arrangements built as either ordered stacks of indolonaphthyridine or stacks extracted from molecular dynamics simulations including thermal disorder. Taking dimers or trimers from either model, we performed CASSCF and NOCI-F calculations to quantify the intermolecular electronic couplings governing singlet fission, excited singlet and triplet diffusion, and hole and electron diffusion processes. Also, comparing the results for the different models, we studied the effect of structural disorder and distortion on these couplings. Finally, we present a newly developed, advanced postanalysis tool. It takes the NOCI-F data as input to carry out a multifragment full Hamiltonian procedure that involves the complete stack, providing physical information not available from the dimer/trimer models, hence giving access to additional insight into the material’s properties.

coupling reactions↗
DOE OSTI2020

Long-distance coherence of Majorana wires

Theoretically, a pair of Majorana bound states in a topological superconductor forms a single fermionic level even at large separations, implying that the parity information is stored nonlocally. The nonlocality leads to a long-distance coherence for electrons tunneling through a Coulomb-blockaded Majorana wire, an effect that can be observed, e.g., in an interferometer. Here, we examine theoretically the coherent electron transfer, taking into account that tunneling implies the long-distance transfer of charge, which is carried by one-dimensional plasmons. In this work, we show that the charge dynamics does not affect the coherence of the electron tunneling process in a topological superconductor consisting of a semiconductor wire proximitized by a single bulk superconductor. The coherence may be strongly suppressed, however, if the topological superconductivity derives from a semiconductor wire proximitized by a granular superconductor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Pore-Selective Fullerene Loading in a Porphyrin-Based Metal–Organic Framework Controls Photoinduced Charge-Transfer Dynamics

Building porous donor−acceptor networks based on host−guest interactions in metal organic frameworks (MOFs) provides unique opportunities for tuning charge separation in highly tailorable materials. Here we focus on installing electron-rich porphyrins and electron-deficient fullerene derivatives in the PCN-222 MOF using a solvent assisted ligand insertion (SALI) method. The fullerene is primarily bound in the large pore, where it is subject to distinct dielectric environments through dimethylformamide (DMF) and 1,4-dioxane solvent exchange. Following photoexcitation, sub-picosecond charge transfer involving initial exciplex population is observed, with different charge recombination pathways and lifetimes depending on solvent polarity through modulation of charge-transfer state energies. While the 1,4-dioxane environment yields charge recombination within 1 ns via local fullerene and porphyrin triplet state population, DMF results in charge recombination directly to the ground state on much longer time scales, including some lifetime components in the microsecond range. Fullerene loading influences these kinetics, and the potential for charge delocalization due to fullerene aggregation within the pores is evaluated by using molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗