SEARCH · Search NASA
Results for “structural dynamics”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Understanding Interfacial Block Copolymer Structure and Dynamics
Here, block copolymer (BCP) structure and dynamics were studied using small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and molecular dynamics (MD) simulations to obtain a fundamental understanding of the impact of an interfacial block on chain dynamics. A glassy block acted as the interface, and the dynamics of a rubbery block was studied. The rubbery block was protonated near the interface in one sample and near the chain end in another sample to observe the interfacial effect on the rubbery polymer. Analysis of the structure and dynamics revealed that the interfacial rubbery block was confined in layered morphologies and exhibited much slower dynamics than the chain-end rubbery block that was dispersed in the rubbery matrix. The interfacial rubbery block showed weaker dynamical relaxation than that at the chain end, and it also had critically important length scale dependence. Dynamical slowing was only observed at length scales significantly larger than the characteristic segmental length, and the disparity between interfacial and chain-end dynamics increased with increasing length.
Electronic structure and dynamics analysis of the Cu-Ag binary alloy by a tight-binding parametrization
Not provided.
In Situ/Operando Probing of Dynamic Phase Structures of Alumina‐Supported Ultrasmall Copper‐Gold Alloy Nanoparticles Under Reaction Conditions
Abstract The ability to control phase structures and surface sites of ultrasmall alloy nanoparticles under reaction conditions is essential for preparing catalysts by design. This is, however, challenging due to limited understanding of the atomic‐scale phases and their correlation with the ensemble‐averaged structures and activities of catalysts during catalytic reactions. We reveal here a dynamic structural stability of alumina‐supported ultrasmall and equiatomic copper‐gold alloy nanoparticles under reaction conditions as a model system in the in situ/operando study. In situ atomic‐scale morphological tracking under oxygen reveals temperature‐dependent dynamic crystalline‐amorphous dual‐phase structures, showing dynamic stability over an elevated temperature range. This atomic‐scale dynamic phase stability coincides with a “conversion plateau” observed for carbon monoxide oxidation on the catalyst. It is substantiated by the stable lattice ordering/disordering structures and surface sites with oscillatory characteristics shown by operando ensemble‐average structural tracking of the catalyst during the oxidation reaction. The understanding of the atomic‐scale dynamic phase structures in correlation with the ensemble‐average dynamic ordering/disordering phase structures and surface sites provides fresh insights into the unique synergy of the supported alloy nanoparticles. This understanding has implications for the design and structural tuning of active and stable ultrasmall alloy catalysts under elevated temperatures.
Structure and dymanics of uranyl (VI) and plutonyl (VI) cations in ionic liquid / water mixtures via molecular dynamics simulations
Explore the source record for details and available documents.
Insights into the structure and dynamics of K + ions at the muscovite–water interface from machine learning potential simulations
The surfaces of many minerals are covered by naturally occurring cations that become partially hydrated and can be replaced by hydronium or other cations when the surface is exposed to water or an aqueous solution. These ion exchange processes are relevant to various chemical and transport phenomena, yet elucidating their microscopic details is challenging for both experiments and simulations. Here, in this work, we make a first step in this direction by investigating the behavior of the native K + ions at the interface between neat water and the muscovite mica (001) surface with ab-initio -based machine learning molecular dynamics and enhanced sampling simulations. Our results show that the desorption of the surface K + ions in pure ion-free water has a significant free energy barrier irrespective of their local surface arrangement. In contrast, facile K + diffusion between mica’s ditrigonal cavities characterized by different Al/Si orderings is observed. This behavior suggests that the K + ions may favor a dynamic disordered surface arrangement rather than complete desorption when exposed to deionized water.
Stellar orbital studies in normal spiral galaxies. II. Restrictions on structural and dynamical parameters on spiral arms
Making use of a set of detailed potential models for normal spiral galaxies, we analyze disk stellar-orbital dynamics as the structural and dynamical parameters of spiral arms (mass, pattern speed, and pitch angle) are gradually modified. With this comprehensive study of ordered and chaotic behavior, we constructed an assemblage of orbitally supported galactic models and plausible parameters for orbitally self-consistent spiral arm models. We find that to maintain orbital support for the spiral arms, the spiral arm mass, M{sub sp}, must decrease with the increase of the pitch angle, i. If i is smaller than ∼10{sup ∘}, M{sub sp} can be as large as ∼7%, ∼6%, or ∼5% of the disk mass, for Sa, Sb, and Sc galaxies, respectively. If i increases up to ∼25{sup ∘}, the maximum M{sub sp} is ∼1% of the disk mass, independent of morphological type, in this case. For values larger than these limits, spiral arms would likely act as transient features. Regarding the limits posed by extreme chaotic behavior, we find a strong restriction on the maximum plausible values of spiral arm parameters on disk galaxies beyond which chaotic behavior becomes pervasive. We find that for i smaller than ∼20{sup ∘}, ∼25{sup ∘}, or ∼30{sup ∘}, for Sa, Sb, and Sc galaxies, respectively, M{sub sp} can go up to ∼10%, of the mass of the disk. If the corresponding i is around ∼40{sup ∘}, ∼45{sup ∘}, ∼50{sup ∘}, M{sub sp} is ∼1%, ∼2%, ∼3% of the mass of the disk. Beyond these values, chaos dominates phase space, destroying the main periodic orbits and the neighboring quasiperiodic orbits.
Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions
The aim of this paper is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. Finally, this study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.
The carboxylation status of osteocalcin has important consequences for its structure and dynamics
The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch
Abstract not provided
Structure and dynamics of aqueous solution of uranyl ions
The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.
From bulk to surface: Structure and dynamics of amorphous alumina from deep potential molecular dynamics
Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains challenging. We employ Deep Potential (DP) molecular dynamics to generate large-scale, ab initio -quality models of amorphous Al 2 O 3 bulk glasses and melt-quenched free surfaces, enabling a quantitative analysis of both structure and relaxation dynamics with statistical confidence inaccessible to direct ab initio simulation. The trained DP model reproduces experimental liquid and glass structure, captures the cooling-rate dependence of the bulk glass transition, and corrects systematic biases in the polyhedral populations predicted by widely used classical force fields. At the free surface, mass density recovers to bulk values over ~10 Å, while local coordination requires a slightly wider subsurface region to fully converge. The outermost layer is oxygen-enriched, exhibits altered polyhedral connectivity with contracted Al–O bonds, and hosts a broad population of under-coordinated motifs (notably AlO 3 and OAl 2 ) whose abundances are governed by glass stability. These under-coordinated surface motifs exhibit distinct vibrational signatures and occur as locally paired Lewis acid and Brønsted base sites consistent with bond-valence compensation, yet remain spatially dispersed rather than aggregating into extended clusters. Despite this pronounced structural heterogeneity, surface relaxation and the glass-transition temperature remain comparable to their bulk counterparts, suggesting that the disordered surface is kinetically stable once formed. Together, these results establish a molecular-level picture of amorphous alumina surfaces and demonstrate the capability of machine-learned potentials to resolve structure–property relationships in disordered oxide interfaces.
Universal progression of structure and dynamics in colloidal nanocrystal gels during salt-accelerated aging
Controlling the structure and function of colloidal gels requires a detailed understanding of how the various components govern network formation and aging. In particular, molecular additives like salts are widely used to tune interparticle interactions, yet their influence on gelation pathways in complex systems such as colloidal nanocrystal gels remains inadequately understood. Here, we investigate how noncoordinating salts modulate the evolution of gels formed using chemically linked tin-doped indium oxide nanocrystals. Through combined structural, dynamic, and kinetic analyses, we demonstrate that increasing salt concentration accelerates gelation. When rescaled by salt-dependent characteristic times, the evolution collapses onto universal trajectories, revealing a time-salt superposition principle. The universality extends across length scales, suggesting a consistent salt-dependent mechanism that controls both local structuring and macroscopic network formation. This observed salt modulation of structure and dynamics provides a predictive basis for controlling the kinetics of nonequilibrium nanocrystal gel assembly, enhancing the rational design of functional nanomaterials with tunable properties.
Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity
We perform molecular dynamics simulations to observe the structure and dynamics of water using different water models (TIP3P, TIP4P, TIP5P) at ambient conditions, constrained by planar walls, which are either modeled by smooth potentials or regular atomic lattices, imitating the honeycomb-structure of graphene. We implement walls of different hydroaffinity, different lattice constant, and different types of interaction with the water molecules. We find that in the hydrophobic regime the smooth wall generally represents a good abstraction of the atomically rough walls, while in the hydrophilic regime there are noticeable differences in structure and dynamics between all stages of wall roughness. For a small lattice constant however the smooth and the atomically rough wall still share a number of structural and dynamical similarities. Out of the three water models, TIP5P water shows the largest degree of tetrahedral ordering and is often the one that is least perturbed by the presence of the wall.
Probing potential energy landscapes via electron-beam-induced single atom dynamics
Structure, bonding, and chemical dynamics of reactions at surfaces and interfaces, and therefore most material properties are intrinsically tied to the energetic landscape in which each atom resides. Here, we demonstrate that a moving atom under electron beam excitation can be used to probe the energy landscape along (confined) step edges, providing information about atomic-scale potentials. In conclusion, the techniques for experimentally exploring atomic potentials holds promise for predictive atom-by-atom fabrication using electron beams.
Electronic Structure, Phonon Dynamical Properties, and CO 2 Capture Capability of Na 2 - x M x Zr O 3 ( M = Li ,K): Density-Functional Calculations and Experimental Validations
The electronic structural and phonon properties of Na 2-α M α ZrO 3 (M ¼ Li,K, α = ¼ 0.0,0.5,1.0,1.5,2.0) are investigated by first-principles density-functional theory and phonon dynamics. The thermodynamic properties of CO 2 absorption and desorption in these materials are also analyzed. With increasing doping level α, the binding energies of Na 2-α Li α ZrO 3 are increased while the binding energies of Na 2-α K α ZrO 3 are decreased to destabilize the structures. The calculated band structures and density of states also show that, at the same doping level, the doping sites play a significant role in the electronic properties. The phonon dispersion results show that few soft modes are found in several doped configurations, which indicates that these structures are less stable than other configurations with different doping levels. From the calculated relationships among the chemical-potential change, the CO 2 pressure, and the temperature of the CO 2 capture reactions by Na 2-α M α ZrO 3 , and from thermogravimetric-analysis experimental measurements, the Li- and K-doped mixtures Na 2-α M α ZrO 3 have lower turnover temperatures (T t ) and higher CO 2 capture capacities, compared to pure Na 2 ZrO 3 . The Li-doped systems have a larger T t decrease than the K-doped systems. When increasing the Li-doping level α, the T t of the corresponding mixture Na 2-α Li α ZrO 3 decreases further to a low-temperature range. However, in the case of K-doped systems Na 2-α K α ZrO 3 , although doping K into Na 2 ZrO 3 initially shifts its T t to lower temperatures, further increases of the K-doping level α causes T t to increase. Therefore, doping Li into Na 2 ZrO 3 has a larger influence on its CO 2 capture performance than the K-doped Na 2 ZrO 3 . Compared with pure solidsM 2 ZrO 3 , after doping with other elements, these doped systems’ CO 2 capture performances are improved.
Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study
Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Here in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.
Dynamics of Organophosphate‐Induced Structural Changes in Acetylcholinesterase Revealed by Time‐Resolved Small‐Angle X‐Ray Scattering and Inelastic Neutron Scattering
Organophosphates (OPs), the active compounds in nerve agents and insecticides such as paraoxon (POX), exert their toxic effects by irreversibly inhibiting acetylcholinesterase (AChE). Currently available antidotes for OP toxicity can reactivate AChE, but reactivation rates are slow which can lead to irreversible nervous system damage or death. We hypothesize that better antidotes with accelerated reactivation rates can be developed by understanding the structural dynamics of OP‐AChE conjugates. Previous steady‐state small‐angle X‐ray scattering (SAXS) experiments showed that POX and certain other OPs induce quaternary structural changes in human AChE (hAChE) that were reversible by oxime antidotes. To characterize the dynamics of these OP‐induced structural changes we have used time‐resolved SAXS (TR‐SAXS) and inelastic neutron scattering (INS). Stopped‐flow TR‐SAXS experiments were performed at BL‐4 at the Stanford Synchrotron Radiation Lightsource by mixing a molar excess of POX (500 μM) with hAChE (50 μM). Scattering data were collected every 20 msec during the first 1000 msec after mixing. Changes in the solution structure of hAChE during this period occurred with k obs = 0.13(±0.01) s −1 . This rate of structural change is comparable to the rate of hAChE inactivation observed using biochemical assays. INS data were collected at the Cold Neutron Chopper Spectrometer at the Spallation Neutron Source at Oakridge National Laboratory using 100 mg samples of hAChE and POX‐hAChE that were lyophilized and rehydrated in D 2 O. INS data collected at 120 K (to prevent translational motions) were used to compare the vibrational density states of native and POX‐conjugated hAChE. The POX‐conjugated hAChE exhibited an increased number of vibrational states, particularly those associated with regional motions such as loop dynamics, whereas global collective motions remained unchanged. Molecular dynamics simulations were used to simulate the vibrational spectra and identify the region(s) in hAChE that contributed to the differences in the INS experimental data. In aggregate, these studies provide experimental evidence for OP conjugate‐induced changes in hAChE dynamics that has to be considered in the design of antidotes for OP poisoning that have improved efficacy and patient outcomes. Support or Funding Information This work was supported by the CounterACT Program, National Institutes of Health Office of the Director, Grant 1U01NS083451 from NINDS, and by grants to SSRL and ORNL from the U.S. Department of Energy, and the National Institutes of Health. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .