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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Modulating Enzyme Activity by Altering Protein Dynamics with Solvent

Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ~3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent k hydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased k hydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A Biophysical Perspective on Enzyme Catalysis

According to the article, even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve high catalytic efficiencies remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bring together and properly orient the participants so that the reaction can proceed; therefore, leading to enzymes being viewed as only passive participants in the catalyzed reaction. A growing body of evidence shows that enzymes are not rigid structures but are constantly undergoing a wide range of internal motions and conformational fluctuations. In this Perspective, on the basis of studies from our group, we discuss the emerging biophysical model of enzyme catalysis that provides a detailed understanding of the interconnection among internal protein motions, conformational substates, enzyme mechanisms, and the catalytic efficiency of enzymes. For a number of enzymes, networks of conserved residues that extend from the surface of the enzyme all the way to the active site have been discovered. These networks are hypothesized to serve as pathways of energy transfer that enables thermodynamical coupling of the surrounding solvent with enzyme catalysis and play a role in promoting enzyme function. Additionally, the role of enzyme structure and electrostatic effects has been well acknowledged for quite some time. Collectively, the recent knowledge gained about enzyme mechanisms suggests that the conventional paradigm of enzyme structure encoding function is incomplete and needs to be extended to structure encodes dynamics, and together these enzyme features encode function including catalytic rate acceleration.

Biochemistry & Molecular Biology↗
DOE OSTI2012

Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Finding Our Way in the Dark Proteome

The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. In conclusion, we envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.

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

Heavy-Duty Truck Electrification and the Impacts of Depot Charging on Electricity Distribution Systems

Major technological advancements and recent policy support are improving the outlook for heavy-duty truck electrification in the United States. In particular, short-haul operations (=200 miles (=322 km)) are prevalent and early candidates for plug-in electric vehicles (EVs) given their short, predictable routes and return-to-base applications, which allows vehicles to recharge when off shift at their depots. Although previous studies investigated the impacts of added electrical loads on distribution systems, which included light-duty EVs, the implications for heavy-duty EV charging are underexplored. Here we summarize the causes, costs and lead times of distribution system upgrades anticipated for depot charging. We also developed synthetic depot charging load profiles for heavy-duty trucks from real-world operating schedules, and found that charging requirements are met at common light-duty EV charging rates (=100 kW per vehicle). Finally, we applied depot charging load profiles to 36 distribution real-world substations, which showed that most can accommodate high levels of heavy-duty EV charging without upgrades.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Amorphizing noble metal chalcogenide catalysts at the single-layer limit towards hydrogen production

Rational design of noble metal catalysts with the potential to leverage efficiency is vital for industrial applications. Such an ultimate atom-utilization efficiency can be achieved when all noble metal atoms exclusively contribute to catalysis. In this work, we demonstrate the fabrication of a wafer-size amorphous PtSex film on a SiO 2 substate via a low-temperature amorphization strategy, which offers single-atom-layer Pt catalysts with high atom-utilization efficiency (~26 wt%). This amorphous PtSex (1.2 < x < 1.3) behaves as a fully activated surface, accessible to catalytic reactions, and features a nearly 100% current density relative to a pure Pt surface and reliable production of sustained high-flux hydrogen over a 2 inch wafer as a proof-of-concept. Furthermore, an electrolyser is demonstrated to generate a high current density of 1,000 mA cm –2 . Such an amorphization strategy is potentially extendable to other noble metals, including the Pd, Ir, Os, Rh and Ru elements, demonstrating the universality of single-atom-layer catalysts.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Conversion between triplet pair states is controlled by molecular coupling in pentadithiophene thin films

In singlet fission (SF) the initially formed correlated triplet pair state, 1 (TT), may evolve toward independent triplet excitons or higher spin states of the (TT) species. The latter result is often considered undesirable from a light harvesting perspective but may be attractive for quantum information sciences (QIS) applications, as the final exciton pair can be spin-entangled and magnetically active with relatively long room temperature decoherence times. In this study we use ultrafast transient absorption (TA) and time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy to monitor SF and triplet pair evolution in a series of alkyl silyl-functionalized pentadithiophene (PDT) thin films designed with systematically varying pairwise and long-range molecular interactions between PDT chromophores. The lifetime of the (TT) species varies from 40 ns to 1.5 μs, the latter of which is associated with extremely weak intermolecular coupling, sharp optical spectroscopic features, and complex TR-EPR spectra that are composed of a mixture of triplet and quintet-like features. On the other hand, more tightly coupled films produce broader transient optical spectra but simpler TR-EPR spectra consistent with significant population in 5 (TT) 0 . These distinctions are rationalized through the role of exciton diffusion and predictions of TT state mixing with low exchange coupling J versus pure spin substate population with larger J. The connection between population evolution using electronic and spin spectroscopies enables assignments that provide a more detailed picture of triplet pair evolution than previously presented and provides critical guidance for designing molecular QIS systems based on light-induced spin coherence.

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

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Inferring adversarial behaviour in cyber‐physical power systems using a Bayesian attack graph approach

Abstract Highly connected smart power systems are subject to increasing vulnerabilities and adversarial threats. Defenders need to proactively identify and defend new high‐risk access paths of cyber intruders that target grid resilience. However, cyber‐physical risk analysis and defense in power systems often requires making assumptions on adversary behaviour, and these assumptions can be wrong. Thus, this work examines the problem of inferring adversary behaviour in power systems to improve risk‐based defense and detection. To achieve this, a Bayesian approach for inference of the Cyber‐Adversarial Power System (Bayes‐CAPS) is proposed that uses Bayesian networks (BNs) to define and solve the inference problem of adversarial movement in the grid infrastructure towards targets of physical impact. Specifically, BNs are used to compute conditional probabilities to queries, such as the probability of observing an event given a set of alerts. Bayes‐CAPS builds initial Bayesian attack graphs for realistic power system cyber‐physical models. These models are adaptable using collected data from the system under study. Then, Bayes‐CAPS computes the posterior probabilities of the occurrence of a security breach event in power systems. Experiments are conducted that evaluate algorithms based on time complexity, accuracy and impact of evidence for different scales and densities of network. The performance is evaluated and compared for five realistic cyber‐physical power system models of increasing size and complexities ranging from 8 to 300 substations based on computation and accuracy impacts.

Sahu, Abhijeet↗
DOE OSTI2018

ARCADES: analysis of risk from cyberattack against defensive strategies for the power grid

In this study, the authors introduce ARCADES (Analysis of Risk from Cyberattack against DEfensive Strategy), a technique to systematically explore the cybersecurity defence strategies based on contingency rankings in power systems. While cybersecurity defensive standards exist, these approaches are primarily based on expert opinions, rather than systematic studies of risk. ARCADES presents an approach to identify improved cybersecurity defensive strategies based on a graph‐based cyber‐physical security model that is evaluated by resistance‐distance metrics and then prioritised based on contingency analysis studies of the system. This study also proposed a technique that identifies the most critical cybersecurity mechanisms to protect the power grid. Planning and operation: those two applications for cybersecurity on power grid mainly explored in this study. For planning, a systematic method is developed to verify the effectiveness of security strategies and for operation, prioritised the security mechanism for auditing and monitoring purpose. As a case study, they analyse the IEEE‐14 bus, IEEE‐30 bus, and IEEE‐118 bus systems, observe the defensive strategies, and calculate substation criticality ranking by using the authors’ proposed method.

Touhiduzzaman, Md↗
DOE OSTI2019

Method to improve the repeatability of dynamic contact resistance measurement test results for high-voltage circuit breakers

Dynamic contact resistance measurement (DRM) is an effective technique to evaluate the contact condition in substations without dismantling circuit breakers. However, performing DRM tests with unsuitable test parameters will cause low repeatability of the test results, and even lead to the misdiagnosis of contact condition. Performing the DRM tests at high DC injected current can improve the repeatability. This paper studies the mechanism of the DC injected current on the repeatability of the DRM test results, and it also promotes a new determination method of the DC injected current amplitude. The impact of the DC injected current on DRM test results is reviewed. The mechanism of the DC injected current on DRM test results is investigated by analysing the chemical composition of the contact surface, the force exerted on the contacts, and the temperatures of a-spots on the contacts' surface. Results indicate that not the Lorentz force, but the temperature of a-spots is the primary influencing factor. The amplitude of the DC injected current can be determined by calculating the temperatures of the a-spot on the contacts' surface. And this method can also be used for other SF6 circuit breakers.

Cheng, Tingting↗
DOE OSTI2021

Lyapunov stability of smart inverters using linearized distflow approximation

Fast-acting smart inverters that utilize preset operating conditions to determine real and reactive power injection/consumption can create voltage instabilities (over-voltage, voltage oscillations and more) in an electrical distribution network if set-points are not properly configured. In this work, linear distribution power flow equations and droop-based Volt–Var and Volt–Watt control curves are used to analytically derive a stability criterion using Lyapunov analysis that includes the network operating condition. The methodology is generally applicable for control curves that can be represented as Lipschitz functions. The derived Lipschitz constants account for smart inverter hardware limitations for reactive power generation. A local policy is derived from the stability criterion that allows inverters to adapt their control curves by monitoring only local voltage, thus avoiding centralized control or information sharing with other inverters. The criterion is independent of the internal time-delays of smart inverters. Simulation results for inverters with and without the proposed stabilization technique demonstrate how smart inverters can mitigate voltage oscillations locally and mitigate real and reactive power flow disturbances at the substation under multiple scenarios. The study concludes with illustrations of how the control policy can dampen oscillations caused by solar intermittency and cyberattacks.

42 ENGINEERING↗
DOE OSTI2013

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. No , S. Doose, I. Daidone, M. L llmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A.108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. Furthermore, this procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Phosphorescence lifetimes of organic light-emitting diodes from two-component time-dependent density functional theory

“Spin-forbidden” transitions are calculated for an eight-membered set of iridium-containing candidate molecules for organic light-emitting diodes (OLEDs) using two-component time-dependent density functional theory. Phosphorescence lifetimes (obtained from averaging over relevant excitations) are compared to experimental data. Assessment of parameters like non-distorted and distorted geometric structures, density functionals, relativistic Hamiltonians, and basis sets was done by a thorough study for Ir(ppy){sub 3} focussing not only on averaged phosphorescence lifetimes, but also on the agreement of the triplet substate structure with experimental data. The most favorable methods were applied to an eight-membered test set of OLED candidate molecules; Boltzmann-averaged phosphorescence lifetimes were investigated concerning the convergence with the number of excited states and the changes when including solvent effects. Finally, a simple model for sorting out molecules with long averaged phosphorescence lifetimes is developed by visual inspection of computationally easily achievable one-component frontier orbitals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Intersystem-crossing and phosphorescence rates in fac-Ir{sup III}(ppy){sub 3}: A theoretical study involving multi-reference configuration interaction wavefunctions

We have employed combined density functional theory and multi-reference configuration interaction methods including spin–orbit coupling (SOC) effects to investigate the photophysics of the green phosphorescent emitter fac-tris-(2-phenylpyridine)iridium (fac-Ir(ppy){sub 3}). A critical evaluation of our quantum chemical approaches shows that a perturbational treatment of SOC is the method of choice for computing the UV/Vis spectrum of this heavy transition metal complex while multi-reference spin–orbit configuration interaction is preferable for calculating the phosphorescence rates. The particular choice of the spin–orbit interaction operator is found to be of minor importance. Intersystem crossing (ISC) rates have been determined by Fourier transformation of the time correlation function of the transition including Dushinsky rotations. In the electronic ground state, fac-Ir(ppy){sub 3} is C{sub 3} symmetric. The calculated UV/Vis spectrum is in excellent agreement with experiment. The effect of SOC is particularly pronounced for the metal-to-ligand charge transfer (MLCT) band in the visible region of the absorption spectrum which does not only extend its spectral onset towards longer wavelengths but also experiences a blue shift of its maximum. Pseudo-Jahn-Teller interaction leads to asymmetric coordinate displacements in the lowest MLCT states. Substantial electronic SOC and a small energy gap make ISC an ultrafast process in fac-Ir(ppy){sub 3}. For the S{sub 1}↝T{sub 1} non-radiative transition, we compute a rate constant of k{sub ISC} = 6.9 × 10{sup 12} s{sup −1} which exceeds the rate constant of radiative decay to the electronic ground state by more than six orders of magnitude, in agreement with the experimental observation of a subpicosecond ISC process and a triplet quantum yield close to unity. As a consequence of the geometric distortion in the T{sub 1} state, the T{sub 1} → S{sub 0} transition densities are localized on one of the phenylpyridyl moieties. In our best quantum chemical model, we obtain phosphorescence decay times of 264 μs, 13 μs, and 0.9 μs, respectively, for the T{sub 1,I}, T{sub 1,II}, and T{sub 1,III} fine-structure levels in dichloromethane (DCM) solution. In addition to reproducing the correct orders of magnitude for the individual phosphorescence emission probabilities, our theoretical study gives insight into the underlying mechanisms. In terms of intensity borrowing from spin-allowed transitions, the low emission probability of the T{sub 1,I} substate is caused by the mutual cancellation of contributions from several singlet states to the total transition dipole moment. Their contributions do not cancel but add up in case of the much faster T{sub 1,III} → S{sub 0} emission while the T{sub 1,II} → S{sub 0} emission is dominated by intensity borrowing from a single spin-allowed process, i.e., the S{sub 2} → S{sub 0} transition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

An analytical method based on a three-time correlation function and the corresponding two-dimensional (2D) lifetime spectrum is developed to elucidate the time-dependent couplings between the multi-timescale (i.e., hierarchical) conformational dynamics in heterogeneous systems such as proteins. In analogy with 2D NMR, IR, electronic, and fluorescence spectroscopies, the waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra can provide a quantitative description of the dynamical correlations between the conformational motions with different lifetimes. The present method is applied to intrinsic conformational changes of substrate-free adenylate kinase (AKE) using long-time coarse-grained molecular dynamics simulations. It is found that the hierarchical conformational dynamics arise from the intra-domain structural transitions among conformational substates of AKE by analyzing the one-time correlation functions and one-dimensional lifetime spectra for the donor-acceptor distances corresponding to single-molecule Förster resonance energy transfer experiments with the use of the principal component analysis. In addition, the complicated waiting-time dependence of the off-diagonal peaks in the 2D lifetime spectra for the donor-acceptor distances is attributed to the fact that the time evolution of the couplings between the conformational dynamics depends upon both the spatial and temporal characters of the system. The present method is expected to shed light on the biological relationship among the structure, dynamics, and function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

The allosteric switching mechanism in bacteriophage MS2

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A temporally and spatially resolved electron density diagnostic method for the edge plasma based on Stark broadening

An electron density diagnostic (≥10{sup 10} cm{sup −3}) capable of high temporal (ms) and spatial (mm) resolution is currently under development at Oak Ridge National Laboratory. The diagnostic is based on measuring the Stark broadened, Doppler-free spectral line profile of the n = 6–2 hydrogen Balmer series transition. The profile is then fit to a fully quantum mechanical model including the appropriate electric and magnetic field operators. The quasi-static approach used to calculate the Doppler-free spectral line profile is outlined here and the results from the model are presented for H-δ spectra for electron densities of 10{sup 10}–10{sup 13} cm{sup −3}. The profile shows complex behavior due to the interaction between the magnetic substates of the atom.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗