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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Long-Range Allosteric Communication Modulated by Active Site Mn(II) Coordination Drives Catalysis in Xanthobacter autotrophicus Acetone Carboxylase

Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α2β2γ2 heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α2β2γ2 complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme.

Biochemistry & Molecular Biology↗
NASA NTRS1979

A simplified model for glass formation

A simplified model of glass formation based on the formal theory of transformation kinetics is presented, which describes the critical cooling rates implied by the occurrence of glassy or partly crystalline bodies. In addition, an approach based on the nose of the time-temperature-transformation (TTT) curve as an extremum in temperature and time has provided a relatively simple relation between the activation energy for viscous flow in the undercooled region and the temperature of the nose of the TTT curve. Using this relation together with the simplified model, it now seems possible to predict cooling rates using only the liquidus temperature, glass transition temperature, and heat of fusion.

Uhlmann, D. R.↗
NASA NTRS1992

A model for nonlinear collisionless reconnection

The time dependence and scaling of the electric and magnetic field components during the nonlinear phase of reconnection of 'thin' unstable neutral layers (thickness approximately equals electron gyroradius) are investigated. Solutions to model equations show an initial interval of rapid growth and subsequent large-amplitude fluctuations of the trapped magnetic flux and the ion kinetic energy. The fluctuations arise from the transient formation, merging, and dissolution of magnetic islands.

Lovelace, R. V. E.↗
NASA NTRS1976

Bone Formation Rate in Experimental Disuse Osteoporosis in Monkeys

Specific mechanisms underlying weightless and hypodynamic bone loss are obscure. A principal relationship which must be affected is the balance between bone formation and bone resorption rates. In order to better define the influence of those parameters on bone loss, and also to develop measurements in other species as a useful adjunct to human research, studies were undertaken with experimental monkeys. Tests were conducted with a total of 6 adult male monkeys, weighing 10-13 kg, and approximately 10-12 yrs. of age to evaluate specifically bone formation rate during the development of disuse osteoporosis and osteopenia. Three animals were restrained in a semi-recumbent position for six months; three animals served as normal caged controls. Food intake (Purina) was held relatively constant at 200g/day for each animal. Using a Norland Bone Mineral Analyzer, bone mineral losses of 3.5 to 6% were seen in the mid-shaft of the tibia and in the distal radius. Bone loss was confirmed radiographically, with observation of thinning of the proximal tibial cortex and trabeculae in the calcaneus. Bone formation rate was determined using standard Ca-47 kinetics under metabolic balance conditions. After six months of restraint, accretion was 7.2-13.2 mg Ca/kg/day, compared to 3.2-4.1 mg Ca/kg/day in caged controls and 3-8 mg Ca/kg/day in normal adult humans. Fecal and urine calcium was 25-40% higher in restrained animals than in controls. Dietary calcium absorption decreases during restraint, and calcium turnover increases, implying a rise in bone resorption rate concommitant with the observed rise in bone accretion rate. Further studies dealing specifically with bone resorption are underway to define this more fully.

Cann, Christopher↗
NASA NTRS2009

C-12/C-13 Ratio in Ethane on Titan and Implications for Methane's Replenishment

The C-12/C-13 abundance ratio in ethane in the atmosphere of Titan has been measured at 822 cm(sup -1) from high spectral resolution ground-based observations. The value 89(8), coincides with the telluric standard and also agrees with the ratio seen in the outer planets. It is almost identical to the result for ethane on Titan found by the composite infrared spectrometer (CIRS) on Cassini. The C-12/C-13 ratio for ethane is higher than the ratio measured in atmospheric methane by Cassini/Huygens GCMS, 82.3(l), representing an enrichment of C-12 in the ethane that might be explained by a kinetic isotope effect of approximately 1.1 in the formation of methyl radicals. If methane is being continuously resupplied to balance photochemical destruction, then we expect the isotopic composition in the ethane product to equilibrate at close to the same C-12/C-13 ratio as that in the supply. The telluric value of the ratio in ethane then implies that the methane reservoir is primordial.

Jennings, Donald E.↗
DOE OSTI2023

Liouvillian dynamics of the open Schwinger model: String breaking and kinetic dissipation in a thermal medium

Understanding the dynamics of bound state formation is one of the fundamental questions in confining quantum field theories such as Quantum Chromodynamics (QCD). One hadronization mechanism that has garnered significant attention is the breaking of a string initially connecting a fermion and an antifermion. Deepening our understanding of real-time string-breaking dynamics with simpler, lower dimensional models like the Schwinger model can improve our understanding of the hadronization process in QCD and other confining systems found in condensed matter and statistical systems. Here in this paper, we consider the string-breaking dynamics within the Schwinger model and investigate its modification inside a thermal medium, treating the Schwinger model as an open quantum system coupled to a thermal environment. Within the regime of weak coupling between the system and environment, the real-time evolution of the system can be described by a Lindblad evolution equation. We analyze the Liouvillian gaps of this Lindblad equation and the time dependence of the system’s von Neumann entropy. We observe that the late-time relaxation rate decreases as the environment correlation length increases. Moreover, when the environment correlation length is infinite, the system exhibits two steady states, one in each of the sectors with definite charge-conjugation-parity (CP) quantum numbers. For parameter regimes where an initial string breaks in vacuum, we observe a delay of the string breaking in the medium, due to kinetic dissipation effects. Conversely, in regimes where an initial string remains intact in vacuum time evolution, we observe string breaking (melting) in the thermal medium. We further discuss how the Liouvillian dynamics of the open Schwinger model can be simulated on quantum computers and provide an estimate of the associated Trotter errors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1989

Monte-Carlo modeling of polar wind photoelectron distributions with anomalous heat flux

In situ measurements above the polar cap by the DE satellites show asymmetric field-aligned electron velocity distributions in the photoelectron energy range 5-60 eV. The formation of these anisotropic distributions is described by a collisional kinetic equation that includes the effects of Coulomb collisions (via a Fokker-Planck operator), those of a parallel electric field, and the magnetic mirror effects of the geomagnetic field. This equation is solved using a Monte Carlo simulation method. The simulation illustrates the formation of the portion of the observed electron distributions originating in the ionosphere and makes it possible to evaluate the significance of the suprathermal electrons at higher altitude. Both observations and calculations indicate that these electrons possess an energy flux which, by its effect on the polar-wind electric field, may influence the dynamics of the polar-wind outflow.

Yasseen, F.↗
NASA NTRS2004

Bone and Calcium Metabolism During Space Flight

Understanding bone loss during space flight is one of the most critical challenges for maintaining astronaut health on space exploration missions. Flight and ground-based studies have been conducted to better understand the nature and mechanisms of weightlessness-induced bone loss, and to identify a means to counteract the loss. Maintenance of bone health requires a balance between bone formation and bone resorption. Early space research identified bone loss as a critical health issue, but could not provide a distinction between the bone formation and breakdown processes. The recent identification of collagen crosslinks as markers of bone resorption has made possible a clear understanding that a decrease in bone resorption is an important effect of space flight, with bone formation being unchanged or only slightly decreased. Calcium regulatory factors have also been studied, in an attempt to understand their role in bone loss. The lack of ultraviolet light exposure and insufficient dietary sources of vitamin D often lead to reduced vitamin D stores on long-duration flights. Serum parathyroid hormone (PTH) concentrations are decreased during flight compared to before flight, although small subject numbers often make this hard to document statistically. As expected, reduced PTH concentrations are accompanied by reduced 1,25-dihydroxyvitamin D concentrations. Calcium kinetic studies during space flight confirm and extend the information gained from biochemical markers of bone metabolism. Calcium kinetic studies demonstrate that bone resorption is increased, bone formation is unchanged or decreased, and dietary calcium absorption is reduced during space flight. Evaluations have also been conducted of countermeasures, including dietary, exercise, and pharmacological treatments. In recent studies, many potential countermeasures show promise at mitigating bone loss in ground-based analogs of weightlessness (e.g., bed rest), but require further ground and flight testing to ensure that the beneficial effects are seen in space flight. As we begin to plan for missions to go back to the Moon, and even off to Mars, many questions are yet to be answered. Maintaining bone is one of the greatest challenges, but with a better understanding of the mechanical processes of bone loss, countermeasures can be designed more efficiently, and the solution (or solutions) may be just over the horizon.

Smith, Scott M.↗
DOE OSTI2024

Neural network kinetics for exploring diffusion multiplicity and chemical ordering in compositionally complex materials

Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. The inherent chemical complexity in compositionally complex materials poses challenges for modeling atomic diffusion and the resulting formation of chemically ordered structures. Here, we introduce a neural network kinetics (NNK) scheme that predicts and simulates diffusion-induced chemical and structural evolution in complex concentrated chemical environments. The framework is grounded on efficient on-lattice structure and chemistry representation combined with artificial neural networks, enabling precise prediction of all path-dependent migration barriers and individual atom jumps. To demonstrate the method, we study the temperature-dependent local chemical ordering in a refractory NbMoTa alloy and reveal a critical temperature at which the B2 order reaches a maximum. The atomic jump randomness map exhibits the highest diffusion heterogeneity (multiplicity) in the vicinity of this characteristic temperature, which is closely related to chemical ordering and B2 structure formation. The scalable NNK framework provides a promising new avenue to exploring diffusion-related properties in the vast compositional space within which extraordinary properties are hidden.

36 MATERIALS SCIENCE↗
NASA NTRS1999

Kinetics of template-directed pyrophosphate-linked dideoxyguanylate synthesis as a function of 2-MeImpdG and poly(C) concentration: insights into the mechanism

Aqueous solutions of deoxyguanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpdG, yield primarily deoxyguanosine 5'-monophosphate, 5'dGMP, and pyrophosphate-linked dideoxyguanylate, dG5'ppdG, abbreviated G2p (see Chart 1). The initial rate of G2p formation, d[G2p]/dt in M h-1, determined at 23 degrees C, pH 7.8, 1.0 M NaCl and 0.2 M Mg2+ by timed high-performance liquid chromatography (HPLC) analysis, exhibits a second-order dependence on 2-MeImpdG concentration, [G]o, indicating a bimolecular mechanism of dimerization in the range 0.02 M < or = [G]o < or = 0.09 M. In the presence of polycytidylate, poly(C), G2p synthesis is accelerated and oligodeoxyguanylate products are formed by incorporation of 2-MeImpdG molecules. The kinetics of G2p formation as a function of both monomer and polymer concentration, expressed in C equivalents, were also determined under the above conditions and exhibited a complex behavior. Specifically, at a constant [poly(C)], values of d[G2p]/dt typically increased with [G]o with a parabolic upward curvature. At a constant [G]o, values of d[G2p]/dt increase with [poly(C)], but level off at the higher poly(C) concentrations. As [G]o increases this saturation occurs at a higher poly(C) concentration, a result opposite to expectation for a simple complexation of two reacting monomers with the catalyst prior to reaction. Nevertheless, these results are shown to be quantitatively consistent with a template-directed (TD) mechanism of dimerization where poly(C) acts as the template to bind 2-MeImpdG in a cooperative manner and lead, for the first time, to the formulation of principles that govern template-directed chemistry. Analysis of the kinetic data via a proposed TD cooperative model provides association constants for the affinity between polymer and monomer and the intrinsic reactivity of 2-MeImpdG toward pyrophosphate synthesis. To the best of our knowledge, poly(C)/2-MeImpdG is the first system that could serve as a textbook example of a TD reaction under conditions such that the template is fully saturated by monomers and under conditions that it is not.

NASA Discipline Exobiology↗
DOE OSTI2022

Current challenges in hydrate‐based desalination: Kinetic and thermodynamic perspective

Abstract Water scarcity is becoming a severe problem worldwide due to inadequate freshwater resources and swift population growth. Seawater desalination is one of the vital approaches to meet the demand for freshwater. However, energy and associated costs with conventional seawater desalination techniques are incentivizing non‐conventional water desalination processes. Water desalination using gas hydrates formation is one of the emerging non‐conventional processes. In this perspective article, recent advances in hydrate‐based seawater desalination (HBSD) have been critically analyzed to outline a future path towards a clean and efficient hydrate‐based desalination process. It provides a detailed comparison of various processes developed over decades, and measured desalination efficiencies with their process details. Moreover, the current challenges, limitations, and future perspectives of hydrate‐based desalination are also discussed. The study also recapitulates the thermodynamics and kinetics aspects of the hydrate‐based desalination process. In addition, various factors controlling the desalination efficiencies, such as control of the separation of hydrate crystals, salt deposition on hydrate particles, and hydrate morphology, were thoroughly investigated with their proposed process designs. The kinetics of hydrate formation is also assessed, with the possibility of a zero‐induction regime and its consequent impact on hydrate morphology. The current capabilities of the thermodynamics models (Gibbs energy minimization + electrolyte equation of state) were discussed using various commercially available software. Additionally, the role of hydrate promotors is also discussed, which can reduce the higher cost associated with the hydrate‐based desalination process.

Khan, Muhammad Naveed↗
DOE OSTI2023

Decoding Zeolite Crystallization and Stage III in Nuclear Waste Glasses by Coupled Modeling and Experiments

Under specific conditions of pH and temperature, nuclear waste immobilization borosilicate glasses may exhibit a sudden acceleration in their corrosion kinetics (stage III)—a behavior that has been associated with the formation of zeolite crystals. Such accelerated dissolution may compromise the integrity of nuclear wasteforms placed in geological depositories. However, thus far, none of the available models is able to predict the thermodynamic propensity and kinetics of zeolite precipitation as a function of the solution conditions due to (i) a lack of fundamental knowledge regarding the nucleation & growth mechanisms of zeolitic phases, (ii) uncertainty regarding the compositions (types) of zeolites that may form and the rate-limiting step in their precipitation as a function of the solution conditions, and (iii) the complexities that arise due to the vast parametric space (i.e., solution chemistry, temperature, number of secondary phases, etc.) that encompass these systems under conditions of environmental exposure. To resolve these challenges, this project aimed to unambiguously identify the thermodynamic propensity for zeolite precipitation and the kinetics thereof as a function of the solution conditions (composition, pH, and temperature). To achieve this goal: 1) We identified the solution conditions and zeolite phases relevant to nuclear glass dissolution. 2) We performed a series of ab initio molecular dynamics (AIMD) simulations to compute the thermodynamic properties of a group of characteristic zeolites that features a large range of compositions, various hydration levels, a wide range of framework structures, and partial atomic site occupancies. 3) We released a first-of-a-kind self-consistent thermodynamic database that can be used to assess the kinetics and the stability fields of zeolitic phases within a Gibbs energy minimization (GEM) framework. 4) We developed a robust geochemical modeling method allowing us to predict the stability of secondary phases (including zeolites, calcium–silicate–hydrate gels, and clays) upon the dissolution of nuclear waste immobilization glasses. 5) We introduced a model that predicts the dissolution kinetics of a series of borosilicate nuclear waste immobilization glasses in terms of the topology of their atomic network. 6) We investigated the roles of the solution composition on the crystallization kinetics of phillipsite zeolites and tobermorite silicate hydrates. Via PNNL’s collaboration and engagement, this project directly supports DOE’s nuclear waste immobilization activities by offering a technical, science-based foundation that will (i) facilitate predictions of the long-term corrosion rates and extents of existing nuclear waste immobilization glasses to help ensure safe and successful vitrification operations, (ii) inform the development of advanced glass formulations with enhanced durability, and, (iii) enable cost-savings that result from making more decisive and hence less conservative predictions while offering higher levels of nuclear waste embedment in smaller, more compact glass volumes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Experimental and computational study of phase space dynamics in strongly coupled plasmas with steep density gradients

Understanding how plasmas thermalize when density gradients are steep remains a fundamental challenge in plasma physics, with direct implications for fusion experiments and astrophysical phenomena. Standard hydrodynamic models break down in these regimes, and kinetic theories make predictions that have never been directly tested. Here, we present the first detailed phase-space measurements of a strongly coupled plasma as it evolves from sharp density gradients to thermal equilibrium. Using laser-induced fluorescence imaging of an ultracold calcium plasma, we track the complete ion distribution function f(x,v,t). We discover that commonly used kinetic models (Bhatnagar–Gross–Krook and Lenard–Bernstein) overpredict thermalization rates, even while correctly capturing the initial counterstreaming plasma formation. Our measurements reveal that the initial ion acceleration response scales linearly with electron temperature, and that the simulations underpredict the initial ion response. In our geometry we demonstrate the formation of well-controlled counterpropagating plasma beams. This experimental platform enables precision tests of kinetic theories and opens new possibilities for studying plasma stopping power and flow-induced instabilities in strongly coupled systems.

Bergeson, Scott (ORCID:0000000231249226)↗
NASA NTRS2003

Kinetic Fractionation of Stable Isotopes in Carbonates on Mars: Terrestrial Analogs

An ancient Martian hydrosphere consisting of an alkali-rich ocean would likely produce solid carbonate minerals through the processes of evaporation and/or freezing. We postulate that both (or either) of these kinetically-driven processes would produce carbonate minerals whose stable isotopic compositions are highly fractionated (enriched) with respect to the source carbon. Various scenarios have been proposed for carbonate formation on Mars, including high temperature formation, hydrothermal alteration, precipitation from evaporating brines, and cryogenic formation. 13C and 18O -fractionated carbonates have previously been shown to form kinetically under some of these conditions, ie.: 1) alteration by hydrothermal processes, 2) low temperature precipitation (sedimentary) from evaporating bicarbonate (brine) solutions, and 3) precipitation during the process of cryogenic freezing of bicarbonate-rich fluids. Here we examine several terrestrial field settings within the context of kinetically controlled carbonate precipitation where stable isotope enrichments have been observed.

Socki, Richard A.↗
DOE OSTI2021

Potential Dependent Mn Oxidation and Its Role in Passivation of Ni 38 Fe 20 Cr 22 Mn 10 Co 10 Multi-Principal Element Alloy Using Multi-Element Resolved Atomic Emission Spectroelectrochemistry

The identity of passivating oxides on multi-principal element alloys is of great interest as their optimization offers the potential for exceptional corrosion resistance in aqueous solutions over a broad range of potential and pH. This study focuses on a non-equiatomic Ni 38 Fe 20 Cr 22 Mn 10 Co 10 solid solution alloy and tracks the fate of each alloying element during linear sweep voltammetry, low and intermediate potential holds in the passive potential domain as well as during open circuit relaxation after anodic polarization in slightly acidified Cl − solution. Ni dissolves at all potentials investigated in this work, Fe and Co are incorporated into oxides or hydroxides in low concentrations whilst Cr and Mn are enriched at passive potentials. At low passivating potentials, Mn(II) dissolves and is incorporated in minor amounts in oxides containing large concentrations of Cr(III). Considerable enrichment in Mn(II)-species occurs relative to Cr(III) in the oxide at 0.1 V vs SCE. Electrochemical impedance spectroscopy suggests the presence of layered oxides with marginal passivation at high Mn(II) levels. The formation of these oxides depends on a combination of thermodynamic and kinetic factors as well as the sequence of passivation.

Han, Junsoo (ORCID:0000000192952954)↗
DOE OSTI2025

Mechanistic Insights into Acetate Selectivity on Intermetallic CuPd(110) in CO Reduction

Experimental studies demonstrate that CuPd(110) uniquely favors acetate formation during CO reduction (CORR), contrasting with the preference for ethylene on Cu surfaces. To elucidate this selectivity, we employed explicit solvation density functional theory (DFT) calculations to investigate the reaction mechanism from both thermodynamic and kinetic angles. Here, our findings reveal that on CuPd(110), the acetate-pathway intermediate H 2 CCO is thermodynamically favored at experimental conditions, while CHCHO─a precursor to ethylene─is preferred on Cu(111). Beyond thermodynamics, we find that H 2 CCO is kinetically accessible under the experimental conditions on CuPd(110), aiding acetate formation. Electron density difference analyses further corroborate distinct protonation preferences supporting this mechanism. We propose a thermodynamic screening parameter based on the Gibbs free energy, G H 2 CCO < G CHCHO , as a guide for designing Cu-based catalysts with enhanced acetate selectivity. These results offer critical mechanistic insights into the CORR product distribution and a rational framework for future catalyst design.

Acetate↗