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Results for “dynamic structural analysis”

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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Ultrafast photodissociation dynamics and nonadiabatic coupling between excited electronic states of methanol probed by time-resolved photoelectron spectroscopy

The electronic and nuclear dynamics in methanol, following 156 nm photoexcitation, are investigated by combining a detailed analysis of time-resolved photoelectron spectroscopy experiments with electronic structure calculations. The photoexcitation pump pulse is followed by a delayed 260 nm photoionization probe pulse to produce photoelectrons that are analyzed by velocity map imaging. The yields of mass-resolved ions, measured with similar experimental conditions, are found to exhibit the same time-dependence as specific photoelectron spectral features. Energy-resolved signal onset and decay times are extracted from the measured photoelectron spectra to achieve high temporal resolution, beyond the 20 fs pump and probe pulse durations. When combined with ab initio calculations of selected cuts through the excited state potential energy surfaces, this information allows the dynamics of the transient excited molecule, which exhibits multiple nuclear and electronic degrees of freedom, to be tracked on its intrinsic few-femtosecond time scale. Within 15 fs of photoexcitation, we observe nuclear motion on the initially bound photoexcited 2 1 A" (S 2 ) electronic state, through a conical intersection with the 1 1 A' (S3) state, which reveals paths to photodissociation following C–O stretch and C–O–H angle opening.

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

Magnetism and finite-temperature effects in UZr 2 : A density functional theory analysis

The structure and the thermophysical properties of d-UZr 2 are investigated using 0 K density functional theory and ab initio molecular dynamics (AIMD). Modeling the true paramagnetic state of this intermetallic compound has been challenging using first-principles calculations. For the first time, we find that the generalized gradient approximation method without applying an on-site Coulomb interaction term (Hubbard U) can result in a ground state that is antiferromagnetic (AFM). We believe that this weak AFM ground state is the closest to the real paramagnetic state. We found that structure optimization at finite temperatures using AIMD is necessary to achieve this ground state instead of the non-magnetic and ferromagnetic states previously reported in the literature. Our findings indicate that applying the Hubbard U on uranium f-orbitals in this metallic system is unnecessary and not recommended, as it leads to a large overestimation of the volume and introduces an unphysical strong spin polarization. Finally, our approach results in atomic volume, thermal expansion, and heat capacities that have strong agreement with experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin

Several class-A G protein-coupled receptor (GPCR) proteins act as constitutive phospholipid scramblases catalyzing the transbilayer translocation of >10,000 phospholipids per second when reconstituted into synthetic vesicles. To address the molecular mechanism by which these proteins facilitate rapid lipid scrambling, we carried out large-scale ensemble atomistic molecular dynamics simulations of the opsin GPCR. We report here that, in the process of scrambling, lipid head groups traverse a dynamically revealed hydrophilic pathway in the region between transmembrane helices 6 and 7 of the protein while their hydrophobic tails remain in the bilayer environment. We present quantitative kinetic models of the translocation process based on Markov State Model analysis. As key residues on the lipid translocation pathway are conserved within the class-A GPCR family, our results illuminate unique aspects of GPCR structure and dynamics while providing a rigorous basis for the design of variants of these proteins with defined scramblase activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advanced Interactive 3D Visualization Tool for Customizable Analyses of Tomography Datasets in Material Science

Current methods for visualizing and analyzing 3D tomography datasets in materials science often lack the interactivity and depth required for detailed structural insights. This limitation restricts a researchers' ability to accurately interpret complex data, which is critical for advancing material innovations and understanding structural properties. To address this issue, we have developed a novel, web-based interactive 3D visualization and analysis tool from the Trame framework that offers customizable features to enhance data interpretability. The tool allows users to adjust parameters such as visible range, slice planes, data rotation, and layering, providing a more detailed and dynamic view of complex structures. Its user-friendly web interface increases the accessibility and ease of use for both novice and experienced researchers, to visualize large volumetric datasets. The tool supports a diverse range of data formats, making it versatile for various research applications. Unique capabilities include real-time data manipulation, automated feature detection, context-sensitive feedback, and real-time volume calculations and distributions per sliced region or layer, alongside the ability to quickly generate high-quality screenshots and videos for presentations and reports. These advancements offer a comprehensive solution for enhanced 3D data exploration, significantly improving the analysis process and communication of results in materials science.

36 - MATERIALS SCIENCE↗
DOE OSTI2022

Tracking structural solvent reorganization and recombination dynamics following e – photoabstraction from aqueous I – with femtosecond x-ray spectroscopy and scattering

Here we present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I–(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L 1 -edge of the generated nascent iodine atoms (I 0 ) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I 0 :e–) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H 2 O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I–) to an expanded cavity around I 0 with a more random orientation of the H 2 O molecules in a broadened first solvation shell.

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

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D. In this paper, we use the individual-particle electron tomography method and reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~6-14 nm resolution. The statistical analyses of these conformations lead to understanding the 3D structural dynamics of Bennett linkage mechanisms. Moreover, our effort provides experimental verification of a theoretical kinematics model of DNA origami, which can be used as feedback to improve the design and control of motion via optimized DNA sequences and routing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Development and Clustering of Rate-Oriented Load Metrics for Customer Price-Plan Analysis

One of the few methods electric utilities can use to motivate and change customer energy consumption is through retail rate structures. Utilities are increasingly moving toward more dynamic rate plans to encourage energy conservation, utilization of onsite renewable generation, peak demand reduction and flattening of demand profiles. This paper creates a set of rate-oriented load metrics that are the determinants of customers' bills under four unique rate plans. These metrics are not only indicative of which rate structure can provide customer bill reductions based on their load profile characteristics, but also convey useful information about load consumption behavior. With these metrics, utilities can analyze their customers and identify classes that are rewarded under each rate plan. This can help inform utilities whether the customers rewarded under each rate plans are meeting their original objectives. To develop these customer classes, we calculate these rate-oriented load metrics for each customer and perform k-means clustering. The analysis is conducted on a set of 300 customer profiles, examining four different rate plans, different numbers of clusters, customer bills and cluster load profile characteristics.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

A semi-coupled aero-servo-hydro numerical model for floating vertical axis wind turbines operating on TLPs

Floating vertical axis wind turbines (VAWTs) have many advantages over floating horizontal axis wind turbines (HAWTs) at large scales in deep water; however, there are several key challenges to overcome as well. One of the challenges is accurate prediction of the dynamic motion and loads performance of a floating VAWT. Here, a new semi-coupled aero-servo-hydro method is developed to assess dynamic responses of a floating VAWT by modeling the system as a 7-degree-of-freedom (7-DOF) model: the supporting platform is considered as a 6-DOF rigid body; the rotation of the rotor is considered as the 7th DOF. Aerodynamic, hydrodynamic, and mooring loads and control of the rotor speed are fully considered. This model can predict performance of floating VAWTs with reasonable fidelity according to validation with OrcaFlex through static and dynamic responses of a floating VAWT with Darrieus rotor operating on a new tension-leg platform (TLP). Being a reduced complexity model, the 7-DOF model can be efficiently applied to assess performance of the newly designed floating VAWT. This model is used to examine the relative contributions of aerodynamic and wave loads imparted to the floating system and the benefits of a three-bladed VAWT over a two-bladed VAWT through dynamic and fatigue analysis.

17 WIND ENERGY↗
DOE OSTI2023

Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser

We apply ultrashort x-ray laser pulses to track optically excited structural dynamics of [Ir 2 (dimen) 4 ] 2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered x-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir 2 (dimen) 4 ] 2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir 2 (dimen) 4 ] 2+ with a larger Ir–Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. In conclusion, the proposed x-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.

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

Generation of High Frequency Response in a Dynamically Loaded, Nonlinear Soil Column

Detailed guidance on linear seismic analysis of soil columns is provided in “Seismic Analysis of Safety-Related Nuclear Structures and Commentary (ASCE 4, 1998),” which is currently under revision. A new Appendix in ASCE 4-2014 (draft) is being added to provide guidance for nonlinear time domain analysis which includes evaluation of soil columns. When performing linear analysis, a given soil column is typically evaluated with a linear, viscous damped constitutive model. When submitted to a sine wave motion, this constitutive model produces a smooth hysteresis loop. For nonlinear analysis, the soil column can be modelled with an appropriate nonlinear hysteretic soil model. For the model in this paper, the stiffness and energy absorption result from a defined post yielding shear stress versus shear strain curve. This curve is input with tabular data points. When submitted to a sine wave motion, this constitutive model produces a hysteresis loop that looks similar in shape to the input tabular data points on the sides with discontinuous, pointed ends. This paper compares linear and nonlinear soil column results. The results show that the nonlinear analysis produces additional high frequency response. The paper provides additional study to establish what portion of the high frequency response is due to numerical noise associated with the tabular input curve and what portion is accurately caused by the pointed ends of the hysteresis loop. Finally, the paper shows how the results are changed when a significant structural mass is added to the top of the soil column.

nonlinear↗
DOE OSTI2020

High-pressure annealing driven nanocrystal formation in Zr 50 Cu 40 Al 10 metallic glass and strength increase

Pressure-induced structural changes in metallic glasses have been of great interest as they are expected to open new ways to synthesize novel materials with unexpected properties. Here, we investigated the effect of simultaneous high-pressure and high-temperature treatment on the structure and properties of a Zr 50 Cu 40 Al 10 metallic glass by in situ X-ray structure measurement and property analysis of the final material. We found the unusual formation of Cu-rich nanocrystals at high pressure and temperature, accompanied by significant strength and hardness enhancement. Based on reverse Monte Carlo modeling and molecular dynamics simulations, the structure of the metallic glass changed to a densely packed, chemically uniform configuration with high short-range and medium-range ordering at high pressure and temperature. These results show that high-pressure annealing processes provide a new way to improve and control properties without changing their composition.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Rotation profile flattening and toroidal flow shear reversal due to the coupling of magnetic islands in tokamaks

The electromagnetic coupling of helical modes, even those having different toroidal mode numbers, modifies the distribution of toroidal angular momentum in tokamak discharges. This can have deleterious effects on other transport channels as well as on magnetohydrodynamic (MHD) stability and disruptivity. At low levels of externally injected momentum, the coupling of core-localized modes initiates a chain of events, whereby flattening of the core rotation profile inside successive rational surfaces leads to the onset of a large m/n = 2/1 tearing mode and locked-mode disruption. With increased torque from neutral beam injection, neoclassical tearing modes in the core may phase-lock to each other without locking to external fields or structures that are stationary in the laboratory frame. The dynamic processes observed in these cases are in general agreement with theory, and detailed diagnosis allows for momentum transport analysis to be performed, revealing a significant torque density that peaks near the 2/1 rational surface. However, as the coupled rational surfaces are brought closer together by reducing q{sub 95}, additional momentum transport in excess of that required to attain a phase-locked state is sometimes observed. Rather than maintaining zero differential rotation (as is predicted to be dynamically stable by single-fluid, resistive MHD theory), these discharges develop hollow toroidal plasma fluid rotation profiles with reversed plasma flow shear in the region between the m/n = 3/2 and 2/1 islands. The additional forces expressed in this state are not readily accounted for, and therefore, analysis of these data highlights the impact of mode coupling on torque balance and the challenges associated with predicting the rotation dynamics of a fusion reactor—a key issue for ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Case studies of the time-dependent potential energy surface for dynamics in cavities

Here, the exact time-dependent potential energy surface driving the nuclear dynamics was recently shown to be a useful tool to understand and interpret the coupling of nuclei, electrons, and photons in cavity settings. Here, we provide a detailed analysis of its structure for exactly solvable systems that model two phenomena: cavity-induced suppression of proton-coupled electron-transfer and its dependence on the initial state, and cavity-induced electronic excitation. We demonstrate the inadequacy of simply using a weighted average of polaritonic surfaces to determine the dynamics. Such a weighted average misses a crucial term that redistributes energy between the nuclear and the polaritonic systems, and this term can in fact become a predominant term in determining the nuclear dynamics when several polaritonic surfaces are involved. Evolving an ensemble of classical trajectories on the exact potential energy surface reproduces the nuclear wavepacket quite accurately, while evolving on the weighted polaritonic surface fails after a short period of time. The implications and prospects for application of mixed quantum-classical methods based on this surface are discussed.

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

Hydrogen Bonding and Its Effect on the Orientational Dynamics of Water Molecules inside Polyelectrolyte Brush-Induced Soft and Active Nanoconfinement

Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules attain the configuration of a “brush”: these PE brushes, due to their ability to form hydrogen bonds (HBs) with water via the PE functional groups, act as a source of soft and active nanoconfinement for the brush-trapped water molecules. In this paper, we study the effects of PE brush-induced confinement on the structure, dynamics and energetics of the water-water and water-PE HBs. Our results indicate a significant weakening of the HBs from bulk to sparsely grafted to densely grafted brushes. i.e., by increasing the degree of brush-induced nanoconfinement. We explain that this weakening of water-water HBs is caused by the disruption of the extended network of water molecules within the brush-induced nanoconfinement. This is confirmed by performing a ring structure analysis of the water molecules, which yields a reduction in the average ring size at higher degrees of brush-induced nanoconfinement (i.e., at higher brush grafting densities). Furthermore, we investigate the role of HB on the orientational dynamics of the water molecules. Here, we observe that the rotational motion of the water molecules becomes sluggish inside the PE brushes. Recent findings have indicated that the water and counterions trapped in brush-induced nanoconfinement demonstrate structures (in combination with the PE functional group) analogous to that in “water-in-salt” electrolytes that have seen extensive recent uses for Li-ion battery applications. However, the rotational dynamics of water molecules inside the brush-induced nanoconfinement is found to be distinctly different from that of conventional “water-in-salt” electrolytes in absence of any confinement; therefore, the present study will provide the necessary platform towards conceptualizing polymer-based nanoconfinement for battery applications.

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

Second-Order Chaos Indicators MEGNO2 and OMEGNO2: Theory

Modifications of the Mean Exponential Growth factor of Nearby Orbits (MEGNO) linear variational method called MEGNO2 and OMEGNO2 indicators are introduced. The modifications are based on taking into account not only the linear, but also the nonlinear part of the increment of the phase flow in the divergence among nearby trajectories according to the second-order formulas. The new indicators allow one to determine more quickly the nature of the orbits under study in dynamical systems with zero or small Lyapunov exponents in comparison with the first-order variational indicators. They improve the analysis of regular regions and, in particular, periodic orbits as well as prevent the appearance of spurious structures in the resulting mappings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Atomistic description for temperature-driven phase transitions in BaTiO 3

Barium titanate (BaTiO 3 ) is a prototypical ferroelectric perovskite that undergoes the rhombohedral-orthorhombic-tetragonal-cubic phase transitions as the temperature increases. In this paper, we develop a classical interatomic potential for BaTiO 3 within the framework of the bond-valence theory. The force field is parametrized from first-principles results, enabling accurate large-scale molecular dynamics (MD) simulations at finite temperatures. Overall, our model potential for BaTiO 3 reproduces the temperature-driven phase transitions in isobaric-isothermal ensemble (NPT) MD simulations. This potential allows for the analysis of BaTiO 3 structures with atomic resolution. By analyzing the local displacements of Ti atoms, we demonstrate that the phase transitions of BaTiO 3 exhibit a mix of order-disorder and displacive characters. Besides, from a detailed observation of structural dynamics during phase transition, we discover that the global phase transition is associated with changes in the equilibrium value and fluctuations of each polarization component, including the ones already averaging to zero, Contrary to the conventional understanding that temperature increase generally causes bond-softening transition, the x-polarization component (the one which is polar in both the orthorhombic and the tetragonal phases) exhibits a bond-hardening character during the orthorhombic-to-tetragonal transition. These results provide further insight about the temperature-driven phase transitions in BaTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Carbohydrate‐binding domains facilitate efficient oligosaccharides synthesis by enhancing mutant catalytic domain transglycosylation activity

Abstract Chemoenzymatic approaches using carbohydrate‐active enzymes (CAZymes) offer a promising avenue for the synthesis of glycans like oligosaccharides. Here, we report a novel chemoenzymatic route for cellodextrins synthesis employed by chimeric CAZymes, akin to native glycosyltransferases, involving the unprecedented participation of a “non‐catalytic” lectin‐like domain or carbohydrate‐binding modules (CBMs) in the catalytic step for glycosidic bond synthesis using β‐cellobiosyl donor sugars as activated substrates. CBMs are often thought to play a passive substrate targeting role in enzymatic glycosylation reactions mostly via overcoming substrate diffusion limitations for tethered catalytic domains (CDs) but are not known to participate directly in any nucleophilic substitution mechanisms that impact the actual glycosyl transfer step. This study provides evidence for the direct participation of CBMs in the catalytic reaction step for β‐glucan glycosidic bonds synthesis enhancing activity for CBM‐based CAZyme chimeras by >140‐fold over CDs alone. Dynamic intradomain interactions that facilitate this poorly understood reaction mechanism were further revealed by small‐angle X‐ray scattering structural analysis along with detailed mutagenesis studies to shed light on our current limited understanding of similar transglycosylation‐type reaction mechanisms. In summary, our study provides a novel strategy for engineering similar CBM‐based CAZyme chimeras for the synthesis of bespoke oligosaccharides using simple activated sugar monomers.

Bandi, Chandra Kanth↗
DOE OSTI2022

Deuterium incorporation into cellulose: a mini-review of biological and chemical methods

Isotopic enrichment offers structural insights that are not easily accessible with natural abundance isotopic composition. Deuterated cellulose has attracted considerable attention in the field of neutron scattering studies, providing information about the dynamics, structure of cellulose and its interactions with other plant cell wall components. The deuteration of cellulose also allows the analysis of cellulose hydrogen bonds by FTIR or NMR techniques. The chemical structure of cellulose contains both exchangeable hydroxyl and non-exchangeable alkyl hydrogens. Deuterium incorporation can be divided into two classifications: biological route which incorporates both alkyl and hydroxyl bound deuterium, and chemical route which typically replaces hydroxyl-bound exchangeable hydrogen. Additionally, the biological route involves cultivating plants or microorganisms in a deuterium-enriched medium. The chemical route typically involves an exchange reaction between hydroxyl-bound hydrogen and D 2 O, often facilitating with an alkaline reagent. This review provides an overview of recent advances in deuteration methods and characterization as well as the application of deuterated cellulose.

59 BASIC BIOLOGICAL SCIENCES↗