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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗
DOE OSTI2020

Photosynthetic semiconductor biohybrids for solar-driven biocatalysis

Photosynthetic semiconductor biohybrids integrate the best attributes of biological whole-cell catalysts and semiconducting nanomaterials. Enzymatic machinery enveloped in its native cellular environment offers exquisite product selectivity and low substrate activation barriers while semiconducting nanomaterials harvest light energy stably and efficiently. Here, we illustrate the evolution and advances of photosynthetic semiconductor biohybrids focusing on the conversion of CO 2 to value-added chemicals. We begin by considering the potential of this nascent field to meet global energy challenges while comparing it to alternate approaches. This is followed by a discussion of the advantageous coupling of electrotrophic organisms with light-active electrodes for solar-to-chemical conversion. We detail the dynamic investigation of photosensitized microorganisms creating direct light harvesting within unicellular organisms while describing complementary developments in the understanding of charge transfer mechanisms and cytoprotection. Lastly, we focus on trends and improvements needed in photosynthetic semiconductor biohybrids in order to address future challenges and enhance their widespread adoption for the production of solar chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Structural Basis for "Flip-Flop" Action of Human Pyruvate Dehydrogenase

The derivative of vitamin B1, thiamin pyrophosphate is a cofactor of pyruvate dehydrogenase, a component enzyme of the mitochondrial pyruvate dehydrogenase multienzyme complex that plays a major role in directing energy metabolism in the cell. This cofactor is used to cleave the C(sup alpha)-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. In alpha(sub 2)beta(sub 2)-tetrameric human pyruvate dehydrogenase, there are two cofactor binding sites, each of them being a center of independently conducted, although highly coordinated enzymatic reactions. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites can now be understood based on the recently determined crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95A resolution. The structure of pyruvate dehydrogenase was determined using a combination of MAD phasing and molecular replacement followed by rounds of torsion-angles molecular-dynamics simulated-annealing refinement. The final pyruvate dehydrogenase structure included coordinates for all protein amino acids two cofactor molecules, two magnesium and two potassium ions, and 742 water molecules. The structure was refined to R = 0.202 and R(sub free) = 0.244. Our structural analysis of the enzyme folding and domain assembly identified a simple mechanism of this protein motion required for the conduct of catalytic action.

Ciszak, Ewa↗
DOE OSTI2021

CSPlib

This computational singular perturbation library (CSPlib) software is useful for analysis of chemical kinetic systems. The code is used to analyze and describe the dynamical landscape underlying the time evolution of a chemical system. Given a database of state vectors, it allows the analysis of the source term and Jacobian matrix of the chemical system, the identification and decoupling of fast and slow processes, and the analysis of cause-and-effect relationships in the coupled system dynamics. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-2391 O

Najm, HabibN.↗
DOE OSTI2023

Nuclear–Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear–electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. Furthermore, these developments and initial examples provide the foundation for future studies of nuclear–electronic quantum dynamics in complex chemical and biological environments.

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

Pilgrim : A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular. Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm. When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. Finally, this algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Data for: Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events

This dataset contains data and code associated with the paper Patel et al. "Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events".The coastal terrestrial-aquatic interface (TAI) is a highly dynamic system characterized by strong physical, chemical, and biological gradients. In particular, shifting soil redox conditions and consumption of terminal electron acceptors, due in part to dynamic hydrologic conditions, is a strong driver of carbon availability and transformations across TAIs. However, while redox dynamics are well described, our ability to quantitatively forecast rates of oxic to anoxic shifts in soils with different characteristics and inundation regimes is limited. We integrated field measurements, laboratory incubations, and model simulations to improve mechanistic understanding of oxygen consumption dynamics in coastal soils. Continuous in situ monitoring unexpectedly revealed that flooding caused temporary spikes in subsurface dissolved oxygen followed by rapid consumption in the wetlands. To further investigate these mechanisms in a controlled setting, we performed laboratory incubations using surface and subsurface soils from a TAI gradient (defined here as upland forest to transitional forest to wetland) in Western Lake Erie to measure oxygen consumption rates in TAI soils during flood events. In our experiments, wetland soils reached anoxia the fastest, in ∼ 9 h on average, whereas upland soils turned anoxic in ∼ 18 h. Subsurface upland soils did not turn anoxic even after two weeks of saturation in the lab, and their oxygen consumption patterns suggested carbon and/or nutrient limitation. These results are consistent with in-situ groundwater redox and oxygen measurements in the field, where wetland soils exhibited the highest rates of oxygen consumption along the TAI. Model simulations of oxygen consumption suggested that oxygen consumption had stronger abiotic controls in wetland soils but stronger biotic controls in upland soils, providing a useful framework for future incubation experiments. Microbial activity is a strong driver of oxygen consumption in TAI soils, although it is constrained by the availability of dissolved carbon in subsurface soils.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/COMPASS-DOE/cmps-time_to_anoxia (DOI: 10.5281/zenodo.10815374).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Revealing the nature of electron correlation in transition metal complexes with symmetry breaking and chemical intuition

Here, in this work, we provide a nuanced view of electron correlation in the context of transition metal complexes, reconciling computational characterization via spin and spatial symmetry breaking in single-reference methods with qualitative concepts from ligand-field and molecular orbital theories. These insights provide the tools to reliably diagnose the multi-reference character, and our analysis reveals that while strong (i.e., static) correlation can be found in linear molecules (e.g., diatomics) and weakly bound and antiferromagnetically coupled (monometal-noninnocent ligand or multi-metal) complexes, it is rarely found in the ground-states of mono-transition-metal complexes. This leads to a picture of static correlation that is no more complex for transition metals than it is, e.g., for organic biradicaloids. In contrast, the ability of organometallic species to form more complex interactions, involving both ligand-to-metal σ-donation and metal-to-ligand π-backdonation, places a larger burden on a theory's treatment of dynamic correlation. We hypothesize that chemical bonds in which inter-electron pair correlation is non-negligible cannot be adequately described by theories using MP2 correlation energies and indeed find large errors vs experiment for carbonyl-dissociation energies from double-hybrid density functionals. A theory's description of dynamic correlation (and to a less important extent, delocalization error), which affects relative spin-state energetics and thus spin symmetry breaking, is found to govern the efficacy of its use to diagnose static correlation.

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

Generalized quantum master equations can improve the accuracy of semiclassical predictions of multitime correlation functions

Multitime quantum correlation functions are central objects in physical science, offering a direct link between the experimental observables and the dynamics of an underlying model. While experiments such as 2D spectroscopy and quantum control can now measure such quantities, the accurate simulation of such responses remains computationally expensive and sometimes impossible, depending on the system’s complexity. A natural tool to employ is the generalized quantum master equation (GQME), which can offer computational savings by extending reference dynamics at a comparatively trivial cost. However, dynamical methods that can tackle chemical systems with atomistic resolution, such as those in the semiclassical hierarchy, often suffer from poor accuracy, limiting the credence one might lend to their results. By combining work on the accuracy-boosting formulation of semiclassical memory kernels with recent work on the multitime GQME, here we show for the first time that one can exploit a multitime semiclassical GQME to dramatically improve both the accuracy of coarse mean-field Ehrenfest dynamics and obtain orders of magnitude efficiency gains.

Chemistry↗
NASA NTRS2003

Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of tightly connected domains. The dynamic exchange of those tautomers, in turns, is required during the reactions of pyruvate decarboxylation and reductive acetylation of lipoamide. Thus the shuttle-like motion of the domains is coordinated with the reactions of decarboxylation and acetylation, which are carried out in each of the cofactor sites resulting in a flip-flop action of the enzyme. The structure-derived mechanism of action of human pyruvate dehydrogenase may be likely common for other TPP-dependent enzymes.

Dominiak, Paulina↗
DOE OSTI2025

Multiscale Nuclear-Electronic Orbital Quantum Dynamics in Complex Environments

Many renewable energy conversion processes rely on the movement of protons as well as electrons through either electrocatalysis or photoexcitation. The simulation of such processes requires a quantum mechanical description of coupled nuclear-electronic dynamics in a solvent or heterogeneous chemical environment. The overall objective of this project is the development of theoretical and computational capabilities for simulating nuclear-electronic quantum dynamics in complex environments and the creation of high-performance, open-source software. This multiscale framework will enable simulations of the real-time dynamics of nonequilibrium excited state proton-coupled electron transfer, quantum decoherence, vibronic energy transfer, and ultrafast radiolysis, as well as their associated time-resolved multidimensional spectroscopies. An important outcome of this project will be a sustainable, reusable, and interoperable open-source software ecosystem. This software will be designed for emerging exascale and future national leadership computers. Another key outcome will be a multiscale quantum dynamics method and software enabling simulations of nonequilibrium nuclear-electronic quantum dynamics in complex environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial en- zymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld’s ability to work with diverse partners, we solved its crystal structure. We observed the canonical fla- vodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize part- ner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein– protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3- 19 F-Tyr in place of Tyr has only a modest effect on Rp9Fld’s redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19 F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We pro- pose that the loops surrounding the flavin adopt altered con- formations upon binding to partners and may even participate actively in electron transfer.

19F NMR↗
DOE OSTI2022

Evidence for Dissociation and Ionization in Shock Compressed Nitrogen to 800 GPa

Triple bonding in the nitrogen molecule (N 2 ) is among the strongest chemical bonds with a dissociation enthalpy of 9.8 eV/molecule. Nitrogen is therefore an excellent test bed for theoretical and numerical methods aimed at understanding how bonding evolves under the influence of the extreme pressures and temperatures of the warm dense matter regime. Here, we report laser-driven shock experiments on fluid molecular nitrogen up to 800 GPa and 4.0 g/cm 3 . Line-imaging velocimetry measurements and impedance matching method with a quartz reference yield shock equation of state data of initially precompressed nitrogen. Comparison with numerical simulations using path integral Monte Carlo and density functional theory molecular dynamics reveals clear signatures of chemical dissociation and the onset of L-shell ionization. Furthermore, combining data along multiple shock Hugoniot curves starting from densities between 0.76 and 1.29 g/cm 3 , our study documents how pressure and density affect these changes in chemical bonding and provides benchmarks for future theoretical developments in this regime, with applications for planetary interior modeling, high energy density science, and inertial confinement fusion research.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nonadiabatic couplings from a variational excited state method based on constrained DFT

Excited Costrained Density Functional Theory (XCDFT) is a variational excited state method that extends ground state DFT to the computation of low-lying excited states. It borrows much of the machinery of Constrained DFT (CDFT) with a crucial difference: the constraint imposes a population of one electron in the Hilbert space spanned by the virtuals of a reference ground state. Here, we present theory and implementation for evaluating nonadiabatic coupling vectors (NACVs) between the first excited state computed with XCDFT and the ground state. Our NACVs are computed analytically using density functional perturbation theory with a formalism that is general enough that could be applied to CDFT diabatic states. We showcase the new method with pilot NACV calculations for the conical intersection in H 3 , the avoided crossing in selenoacrolein, and the NACV magnitudes in azobenzene. Despite complications from the nonorthogonality of the wavefunctions, XCDFT’s energy surfaces and NACVs reproduce benchmark values and respect known sum rules within a reasonable degree. This shows that XCDFT is a viable method for nonadiabatic dynamics simulations.

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

Design of high polarization low switching barrier hybrid improper ferroelectric perovskite oxide superlattices

Hybrid improper ferroelectricity is a useful tool to design ABO 3 /A'BO 3 polar superlattices from non polar building blocks. In this study, we have designed high polarization-low switching barrier hybrid improper ferroelectric superlattices with efficient polarization, and polarization-magnetization switching properties above room temperature, using density functional theory and ab initio molecular dynamics simulations. Superlattices with a chemical formula of (AAlO 3 ) m /(A'AlO 3 ) n , where m/n = 1/1, 1/3, 3/1, 1/5 and 5/1, A, A' = Lanthanide and Y cations are considered to outline the design principles behind polarization switching and (LaFeO 3 ) 3 /(CeFeO 3 ) 1 is investigated for polarization-magnetization switching. We find that the unconventional switching paths via out-of-phase rotation Q R- (a 0 a 0 c - ) and tilt precession QTP always yield lower switching barrier compared to those via in-phase rotation Q R+ (a 0 a 0 c + ) and tilt QT (a - a - c 0 ) of BO 6 octahedra. Results from ab initio molecular dynamics simulations estimate the temperature at which the lowest energy barrier can be overcome. Furthermore, it is possible to tune the polarization switching barrier by tuning the tolerance factor, A,A' cation radius mismatch and super lattice periodicity. For switching via Q R- , the switching barrier varies exponentially with rotation angle, indicating how high switching barrier is expected for systems, away from cubic symmetry. We provide a recipe to overcome such a bottleneck by tuning superlattice periodicity. Finally, we have proposed the multiferroic device application concept through a proposed polarization-temperature hysteresis loop and magnetization switching.

36 MATERIALS SCIENCE↗
NASA NTRS2002

Chemistry-Climate Interactions in the Goddard Institute for Space Studies General Circulation Model: New Insights into Modeling the Pre-Industrial Atmosphere - 2

We investigate the chemical (hydroxyl and ozone) and dynamical response to changing from present day to pre-industrial conditions in the Goddard Institute for Space Studies General Circulation Model (GISS GMC). We identify three main improvements not included by many other works. Firstly, our model includes interactive cloud calculations. Secondly we reduce sulfate aerosol which impacts NOx partitioning hence Ox distributions. Thirdly we reduce sea surface temperatures and increase ocean ice coverage which impact water vapor and ground albedo respectively. Changing the ocean data (hence water vapor and ozone) produces a potentially important feedback between the Hadley circulation and convective cloud cover. Our present day run (run 1, control run) global mean OH value was 9.8 x 10(exp 5) molecules/cc. For our best estimate of pre-industrial conditions run (run 2) which featured modified chemical emissions, sulfate aerosol and sea surface temperatures/ocean ice, this value changed to 10.2 x 10(exp 5) molecules/cc. Reducing only the chemical emissions to pre-industrial levels in run 1 (run 3) resulted in this value increasing to 10.6 x 10(exp 5) molecules/cc. Reducing the sulfate in run 3 to pre-industrial levels (run 4) resulted in a small increase in global mean OH (10.7 x 10(exp 5) molecules/cc). Changing the ocean data in run 4 to pre-industrial levels (run 5) led to a reduction in this value to 10.3 x 10(exp 5) molecules/cc. Mean tropospheric ozone burdens were 262, 181, 180, 180, and 182 Tg for runs 1-5 respectively.

Grenfell, J. Lee↗
DOE OSTI2025

Assessment of ESM Readiness Level for Exascale HPC

Advancement of Earth System Models (ESMs) is becoming increasingly challenging due to a confluence of factors including increasing model complexity – to more fully represent the earth system, increasing spatial resolution - to achieve higher accuracy by resolving fine-scale dynamical to physical, biological, and chemical processes and their interaction, increasing ensemble size - to more accurately represent predictive uncertainty, and increased computing requirements – to enable more accurate and timely weather predictions and climate projections for societal benefit. The belief by many that computing will take care of itself is no longer valid given the disruptive changes in HPC that are driving up the cost of computing, increasing the difficulty of using emerging HPC effectively, and exposing limits in parallelism, portability and scalability of the ESM applications themselves.

54 ENVIRONMENTAL SCIENCES↗