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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Improving modular bootstrap bounds with integrality

We propose methods that efficiently impose integrality — i.e., the condition that the coefficients of characters in the partition function must be integers — into numerical modular bootstrap. We demonstrate the method with a number of examples where it can be used to strengthen modular bootstrap results. First, we show that, with a mild extra assumption, imposing integrality improves the bound on the maximal allowed gap in dimensions of operators in theories with a U(1) c symmetry at c = 3, and reduces it to the value saturated by the SU(4) 1 WZW model point of c = 3 Narain lattices moduli space. Second, we show that our method can be used to eliminate all but a discrete set of points saturating the bound from previous Virasoro modular bootstrap results. Finally, when central charge is close to 1, we can slightly improve the upper bound on the scaling dimension gap.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Role of quadrupole deformation and continuum effects in the “island of inversion” nuclei 28,29,31 F

The peculiar properties of nuclei in the so-called “island of inversion” around Z = 10 and N = 20 are the focus of current nuclear physics research. Recent studies showed that 28 F has a negative-parity ground state and thus lies within the southern shore of the island of inversion, and 29 F presents a halo structure in its ground state, but it is unclear which effects, such as deformation, shell evolution due to tensor forces, or couplings to the continuum, lead to this situation. Here, we investigate the role of quadrupole deformation and continuum effects on the single-particle structure of 28,29,31 F from a relativistic mean-field approach and show how both phenomena can lead to a negative-parity ground state in 28 F and halo structures in 29,31 F. We solve the Dirac equation in the complex-momentum (Berggren) representation for a potential with quadrupole deformation at the first order obtained from relativistic mean-field calculations using the NL3 interaction and calculate the continuum level densities using the Green’s function method. We extract single-particle energies and widths from the continuum level densities to construct the Nilsson diagrams of 28,29,31 F in the continuum and analyze the evolution of both the widths and occupation probabilities of relevant Nilsson orbitals in 28 F and find that some amount of prolate deformation must be present. In addition, we calculate the density distributions for bound Nilsson orbitals near the Fermi surface in 29,31 F and reveal that, for a quadrupole deformation 0.3 ≤ β 2 ≤ 0.45 (prolate), characteristic halo tails appear at large distances. Using the relativistic mean-field approach in the complex-momentum representation with the Green’s function method, we demonstrate that in neutron-rich fluorine isotopes, while in the spherical case the pf shells are already inverted and close to the neutron emission threshold, a small amount of quadrupole deformation can dramatically reduce the gap between positive- and negative-parity states and increase the role of continuum states, ultimately leading to the negative parity in the ground state of 28 F and the halo structures in 29,31 F.

20 ≤ A ≤ 38↗
DOE OSTI2023

Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D

Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRAS G13D , which suggests an exchange between two conformational states in solution. Methyl and 31 P NMR spectra of active KRAS G13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRAS G13D and KRAS G13D -RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRAS G13D , showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

EPR studies of ferredoxin in spinach and cyanobacterial thylakoids related to photosystem I-driven NADP + reduction

Photosynthetic light-dependent reactions occur in thylakoid membranes where embedded proteins capture light energy and convert it to chemical energy in the form of ATP and NADPH for use in carbon fixation. One of these integral membrane proteins is Photosystem I (PSI). PSI catalyzes light-driven transmembrane electron transfer from plastocyanin (Pc) to oxidized ferredoxin (Fd). Electrons from reduced Fd are used by the enzyme ferredoxin-NADP + reductase (FNR) for the reduction of NADP + to NADPH. Fd and Pc are both small soluble proteins whereas the larger FNR enzyme is associated with the membrane. To investigate electron shuttling between these diffusible and embedded proteins, thylakoid photoreduction of NADP + was studied. As isolated, both spinach and cyanobacterial thylakoids generate NADPH upon illumination without extraneous addition of Fd. These findings indicate that isolated thylakoids either (i) retain a “pool” of Fd which diffuses between PSI and membrane bound FNR or (ii) that a fraction of PSI is associated with Fd, with the membrane environment facilitating PSI-Fd-FNR interactions which enable multiple turnovers of the complex with a single Fd. To explore the functional association of Fd with PSI in thylakoids, electron paramagnetic resonance (EPR) spectroscopic methodologies were developed to distinguish the signals for the reduced Fe-S clusters of PSI and Fd. Temperature-dependent EPR studies show that the EPR signals of the terminal [4Fe-4S] cluster of PSI can be distinguished from the [2Fe-2S] cluster of Fd at > 30 K. At 50 K, the cw X-band EPR spectra of cyanobacterial and spinach thylakoids reduced with dithionite exhibit EPR signals of a [2Fe-2S] cluster with g-values g x = 2.05, g y = 1.96, and g z = 1.89, confirming that Fd is present in thylakoid preparations capable of NADP + photoreduction. Quantitation of the EPR signals of P 700 + and dithionite reduced Fd reveal that Fd is present at a ratio of ~ 1 Fd per PSI monomer in both spinach and cyanobacterial thylakoids. Light-driven electron transfer from PSI to Fd in thylakoids confirms Fd is functionally associated (< 0.4 Fd/PSI) with the acceptor end of PSI in isolated cyanobacterial thylakoids. Furthermore, these EPR experiments provide a benchmark for future spectroscopic characterization of Fd interactions involved in multistep relay of electrons following PSI charge separation in the context of photosynthetic thylakoid microenvironments.

Electron paramagnetic resonance↗
DOE OSTI2024

A robust spectral element implementation of the $k - τ$ RANS model in Nek5000/NekRS

The $k - ω$ Reynolds Averaged Navier Stokes (RANS) model is one of the industry standard approaches for modeling of turbulent flows. It performs better than the $k - ϵ$ model for low Reynolds number flows and is also more suitable for boundary layers with adverse pressure gradients. Major drawback of the model, however, is that the asymptotic value of $ω$ at the walls is singular, necessitating the use of a contrived “sufficiently” large value for $ω$ as the boundary condition for its transport equation. Here, this invariably leads to the solution being sensitive to near wall grid spacing. While an acceptable solution for low order (finite volume) methods, the excessive near wall gradients lead to persistent numerical stability issues in high order codes. To alleviate the problem, specifically in the context of the high order spectral element code Nek5000, a regularized $k - ω$ approach was formulated in our prior work (Tomboulides et al., 2018). The formulation, however, relies on the use of wall distance and its gradients for modeling the closure terms and can pose problems for simulations in complex geometries. This work presents a novel implementation of the $k - τ$ RANS model in Nek5000, where $τ = 1/ω$, eliminating the need for regularization, owing to the asymptotically bounded behavior of the source terms in the $τ$ transport equation, and also eliminating dependence on wall distance. Robustness and stability of the $k - τ$ model is ensured through implicit treatment of the source terms and their careful numerical implementation and demonstrated through several cases aimed at verification and validation. Studies include both canonical and engineering relevant problems, viz., turbulent channel flow, pipe flow, backward facing step, flow over NACA 0012 airfoil and flow in a T-junction. Results from the $k - τ$ model are shown to be consistent with regularized $k - ω$ model and also with the $k - ω$ SST model in OpenFOAM (for select studies). Comparison with experimental data is also shown, where available, to bolster validation efforts for the $k - τ$ model implementation through prediction of key turbulent quantities of interest.

Nek5000↗
DOE OSTI2020

Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.

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

Chlorocobaltate-Enabled Selective Separation of CoCl 2 from Mixed Chloride and Nitrate Salts of Mn, Co, and Ni

Described here is the effect of anionic metalates─chlorocobaltate and nitratocobaltate─on the heat-driven separation of the critical element cobalt from potentially competing transition metal salts. Resins bearing the hexadentate glycolamide receptor L (PS-L) exhibit sorption capacities, Q = 1.33 mmol/g for CoCl 2 and Q = 0.66 mmol/g for Co(NO 3 ) 2 , as inferred from sorption isotherm studies. This trend runs counter to the typical Hofmeister series for anion selectivity. Ion chromatographic analysis of a mixed CoCl 2 /Co(NO 3 ) 2 solution revealed an increase in chloride content from 55 mol % to 90 mol % after a single thermally driven catch-and-release cycle. This chloride-selective behavior was recapitulated in a mixed-metal cation, mixed-anion system containing the chloride and nitrate salts of Mn(II), Co(II), and Ni(II) at near-equimolar concentrations. PS-L also displayed enhanced selectivity for Co using this mixed stock solution as observed by ICP-OES. In contrast, for a nitrate-only solution containing Mn(II), Co(II), and Ni(II), PS-L showed increased affinity for Mn, with its proportion rising from 36.6 mol % to 58.1% after a single catch-and-release cycle. Density functional theory calculations support the suggestion that the enhanced uptake of Co(II) in chloride-rich media arises from the high thermodynamic stability of [CoCl 4 ] 2– , which facilitates its outer-sphere coordination to cationic resin-bound cobalt species. Single crystal X-ray crystallographic analyzes of L•MCl 2 (M = Mn, Co, Ni) and L•M(NO 3 ) 2 (M = Mn, Co) confirmed metal complexation by L in the solid state and the concomitant formation of metalate counteranions. Here, the present study highlights a relatively simple approach for separating cobalt from its transition metal congeners.

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

How μ-opioid receptor recognizes fentanyl

Abstract Roughly half of the drug overdose-related deaths in the United States are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, X-ray crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like opioids remains lacking. Exploiting the X-ray structure of BU72-bound mOR and several molecular simulation techniques, we elucidated the detailed binding mechanism of fentanyl. Surprisingly, in addition to the salt-bridge binding mode common to morphinan opiates, fentanyl can move deeper and form a stable hydrogen bond with the conserved His297 6.52 , which has been suggested to modulate mOR’s ligand affinity and pH dependence by previous mutagenesis experiments. Intriguingly, this secondary binding mode is only accessible when His297 6.52 adopts a neutral HID tautomer. Alternative binding modes may represent a general mechanism in G protein-coupled receptor-ligand recognition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Asynchronous quadratic control for constrained hidden markov jump linear systems with incomplete MTPM and MOCPM

Abstract This paper investigates the quadratic optimal control problem for constrained Markov jump linear systems with incomplete mode transition probability matrix (MTPM). Considering original system mode is not accessible, observed mode is utilized for asynchronous controller design where mode observation conditional probability matrix (MOCPM), which characterizes the emission between original modes and observed modes is assumed to be partially known. An LMI optimization problem is formulated for such constrained hidden Markov jump linear systems with incomplete MTPM and MOCPM. Based on this, a feasible state-feedback controller can be designed with the application of free-connection weighting matrix method. The desired controller, dependent on observed mode, is an asynchronous one which can minimize the upper bound of quadratic cost and satisfy restrictions on system states and control variables. Furthermore, clustering observation where observed modes recast into several clusters, is explored for simplifying the computational complexity. Numerical examples are provided to illustrate the validity.

Zhu, Jin↗
DOE OSTI2021

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A

Staphylococcus aureus causes reiterative and chronic persistent infections. This can be explained by the formidable ability of this pathogen to escape immune surveillance mechanisms. Cells of S. aureus display the abundant staphylococcal protein A (SpA). SpA binds to immunoglobulin (Ig) molecules and coats the bacterial surface to prevent phagocytic uptake. SpA also binds and cross-links variable heavy 3 (V H 3) idiotype (IgM) B cell receptors, promoting B cell expansion and the secretion of nonspecific V H 3-IgM via a mechanism requiring CD4 + T cell help. SpA binding to antibodies is mediated by the N-terminal Ig-binding domains (IgBDs). The so-called region X, uncharacterized LysM domain, and C-terminal LPXTG sorting signal for peptidoglycan attachment complete the linear structure of the protein. Here, we report that both the LysM domain and the LPXTG motif sorting signal are required for the B cell superantigen activity of SpA in a mouse model of infection. SpA molecules purified from staphylococcal cultures are sufficient to exert B cell superantigen activity and promote immunoglobulin secretion as long as they carry intact LysM and LPXTG motif domains with bound peptidoglycan fragments. The LysM domain binds the glycan chains of peptidoglycan fragments, whereas the LPXTG motif is covalently linked to wall peptides lacking glycan. These findings emphasize the complexity of SpA interactions with B cell receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multilevel Techniques for Compression and Reduction of Scientific Data---The Unstructured Case

Previous work on multilevel techniques for compression and reduction of scientific data is extended to the case of data given on unstructured meshes in two and three dimensions. The centerpiece of the work is a decomposition algorithm which is shown to be optimal, in terms of both storage and operational complexity, applicable to unstructured grids in both two and three dimensions, and which implicitly gives a Riesz basis that can be exploited to reduce the data while maintaining rigorous bounds on the loss incurred. The flexibility of the approach is illustrated by applications to potential flow around an airfoil and the effect of compression on quantities of interest relevant to airfoil design; compression of computational simulation of a nonlinear reaction-diffusion system with special attention given to the problem of time series reduction; and, data from a simulation of magnetically confined plasma in a fusion reactor reduced so as to preserve the electric field computed from the data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Comparing Sensor Fusion and Multimodal Chemometric Models for Monitoring U(VI) in Complex Environments Representative of Irradiated Nuclear Fuel

Optical sensors and chemometric models were leveraged for the quantification of uranium(VI) (0–100 μg mL –1 ), europium (0–150 μg mL –1 ), samarium (0–250 μg mL –1 ), praseodymium (0–350 μg mL –1 ), neodymium (0–1000 μg mL –1 ), and HNO 3 (2–4 M) with varying corrosion product (iron, nickel, and chromium) levels using laser fluorescence, Raman scattering, and ultraviolet–visible–near-infrared absorption spectra. In this paper, an efficient approach to developing and evaluating tens of thousands of partial least-squares regression (PLSR) models, built from fused optical spectra or multimodal acquisitions, is discussed. Each PLSR model was optimized with unique preprocessing combinations, and features were selected using genetic algorithm filters. The 7-factor D-optimal design training set contained just 55 samples to minimize the number of samples. The performance of PLSR models was evaluated by using an automated latent variable selection script. PLS1 regression models tailored to each species outperformed a global PLS2 model. PLS1 models built using fused spectra data and a multimodal (i.e., analyzed separately) approach yielded similar information, resulting in percent root-mean-square error of prediction values of 0.9–5.7% for the seven factors. Further, the optical techniques and data processing strategies established in this study allow for the direct analysis of numerous species without measuring luminescence lifetimes or relying on a standard addition approach, making it optimal for near-real-time, in situ measurements. Nuclear reactor modeling helped bound training set conditions and identified elemental ratios of lanthanide fission products to characterize the burnup of irradiated nuclear fuel. Leveraging fluorescence, spectrophotometry, experimental design, and chemometrics can enable the remote quantification and characterization of complex systems with numerous species, monitor system performance, help identify the source of materials, and enable rapid high-throughput experiments in a variety of industrial processes and fundamental studies.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Extreme-scale stochastic optimization and simulation via learning-enhanced decomposition and parallelization (Final Technical Report)

Stochastic optimization and simulation models ubiquitously arise in designing and operating complex service/engineering systems. They can be extreme in scale due to high-dimensional data and decisions, and can also involve decisions made sequentially in response to newly revealed data, both causing significant computational challenge. The objective of this research is to explore a unified framework that integrates machine learning with discrete optimization and risk-averse modeling, to improve the efficiency of decomposition paradigms for stochastic optimization and simulations at extreme scale. The models we consider represent a broad class of complex decision-making problems, where 0-1 or continuous decisions are made before and/or after knowing multiple sources of uncertainties that could be correlated. We will employ machine learning methods to dynamically decide and prioritize computational procedures, including cut generation, branching, and bounding of the optimal objective. Furthermore, the research will shed new lights on the traditional decomposition algorithms for extreme-scale computing. Deliverables of the research include new modeling and computational methods for advancing the state-of-the-art research in optimization and simulation, bringing many relevant risk-averse, data-driven optimization problems in practice within the range of tractability. Examples include distributed computing server scheduling and sensor deployment for monitoring critical infrastructures. Success in this effort will enable progress in solving multiple extreme-scale problems in the complex system design and operations arising from DoE missions in energy, environment, and national security.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

M + (M=Ca, Ba) Cations Bound to Molecular Cavities: A New Strategy for Incorporating Molecular Quantum States into Quantum Information

This project pursued a novel strategy for incorporating multiple qubits per ion into ion-trap based quantum computing (ITQC) involving Ca + and Ba + . By forming molecular complexes of these cations with molecular-scale cages, we hypothesized that molecular energy levels could be incorporated into quantum computing while retaining key properties of the atomic ions intact. We experimented with a variety of molecular cages and found that Na + , K + , Rb + , Ca 2+ , Sr 2+ , and Ba 2+ could be captured and brought into the gas phase efficiently by imbedding them inside [2.2.2]-benzocryptand. IR and UV spectra of these cage complexes are sensitive to the size and charge state of the ion, reporting on the structures and binding properties of the cage complexes. UV photofragmentation of the Ba 2+ -Acetate -1 -BzCrypt complex produces Ba + -BzCrypt, the complex targeted for exploration in the original hypothesis. Follow-on funding is needed to pursue the spectroscopy of this complex as a target for ITQC.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites

Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA 2 “green” (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA 2 into preformed host–guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA 2 was found to be similar to those reported earlier at the same DNA site for BLMB 2 , the intercalated bithiazole of BLMB 2 is “flipped” 180° relative to DNA-bound BLMA 2 . Further, this finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modulating the Electron Affinity of Small Bipyridyl Molecules on Single Gold Nanoparticles for Plasmon-Driven Electron Transfer

Developing controlled platforms for plasmon-driven chemistry is of great importance in catalytic reactions at the nanoscale. We report anion radical formation for five bipyridyl complexes of varying degrees of electron affinity utilizing optically fo-cused intraband (594 nm) and interband (532 nm) pump excitation of single gold nanoparticles. The surface-enhanced Raman scattering (SERS) of anion radicals for the five non-resonant adsorbed molecules 2,2’-bipyridine (22BPY), 4,4’-bipyridine (44BPY), trans-1,2-bis(4-pyridyl)ethylene (BPE), 1,2-bis(4-pyridyl)acetylene (BPA), and 1,2-bis(4-pyridyl)ethane (BPEt) were detected using localized surface-plasmon resonance (LSPR) excitation with 785 nm. The electron affinity of the five bipyridyl complexes were determined using electrochemistry. Molecules with low electron affinity experienced high-er instances of radical anion formation under a plasmon-coupled intraband electron transfer excitation (594 nm) whereas molecules with high electron affinity showed a preference for anion radical formation under direct interband electron trans-fer excitation (532 nm). The lowest unoccupied molecular orbital (LUMO) energy levels for low electron affinity surface-bound molecules (22BPY, BPEt) are on average ~0.43 eV higher for high electron affinity surface-bound molecules (BPA, BPE, 44BPY) as calculated using time-dependent density functional theory, elucidating the importance of plasmon coupling to energy levels that facilitate charge transfer pathways. We also show the ability to ‘activate’ high vs low electron affinity single nanoparticles with the choice of pump excitation wavelength. The findings show the complex interplay between molecular electron affinity, orbital overlap with the density of states of the plasmonic metal, and excitation energetics of the pump laser wavelength. Potential applications of this work include enhanced control over molecular scale catalysis, biosensor design, and solar energy capture.

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

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗