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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 559 records · Page 31

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cinema:Snap: Real-time tools for analysis of dynamic diamond anvil cell experiment data

We report we developed tools and a workflow for real-time analysis of data from dynamic diamond anvil cell experiments performed at user light sources. These tools allow users to determine the phases of matter observed during the compression of materials in order to make decisions during an experiment to improve the quality of experimental results and maximize the use of scarce experimental facility time. The tools fill a gap in dynamic compression data analysis tools that are real-time, are flexible to the needs of high-pressure scientists, connect to automated processing of results, can be easily incorporated into workflows with existing tools and data formats, and support remote experimental data analysis workflows. Specific analytics developed include novel automated two-peak analysis for overlapping peaks and multiple phases, coordinated views of pressure and temperature values, full-compression contour plots, and configurable views of integrated x-ray diffraction. We present an experimental use case to show how the tools produce real-time analytics that help the scientists revise parameters for the next compression

47 OTHER INSTRUMENTATION↗

Path integral molecular dynamics: A high-fidelity approach to quantum dynamics of electrons

We investigate electron transport in the uniform electron gas using ring-polymer molecular dynamics (RPMD). Working in the weakly coupled, non-degenerate regime, we use RPMD to probe how the onset of quantum diffraction effects at high temperature reshapes electron–electron collisions and leads to a classical-to-quantum crossover in macroscopic transport properties. Static thermodynamics obtained with RPMD are consistent with the weak-coupling equation of state, confirming correct quantum Boltzmann sampling. Real-time transport extracted from mean square displacements exhibits the expected ballistic-to-diffusive transition and a systematic reduction of the electronic self-diffusivity as quantum effects strengthen, due to quantum diffraction modifying electron–electron collisions. Direct ring-polymer scattering simulations reveal diffractive “softening” of binary deflections, providing a micro-to-macro link between collision physics and diffusion. The present study establishes RPMD as a quantitative, trajectory-based tool for electron transport across the classical–quantum crossover and furnishes benchmarks for improving Coulomb-log interpolation models. We outline extensions to multi-component plasmas and a path to incorporate Fermi–Dirac statistics within path-integral dynamics.

Electronic transport↗

In situ x-ray diffraction study of dynamically compressed α -cristobalite using a dynamic diamond anvil cell

Here we present results of the dynamic compression of α -cristobalite up to a pressure of 106 GPa with the use of the dynamic diamond anvil cell. X-ray diffraction images were recorded at different ramp compression and decompression rates to investigate in situ the high-pressure phase transitions of α -cristobalite. Our results suggest that the pressure onset of the phase transformation of α -cristobalite to cristobalite II, cristobalite X-I, and ultimately to seifertite ( α – PbO 2 type SiO 2 ) is dependent on the applied compression rates and stress conditions of the experiment. Increasing compression rates in general shift the studied phase transitions to higher pressures. Furthermore, our results indicate for single crystals under hydrostatic conditions a suppression of a phase transition from cristobalite X-I to seifertite at pressures of up to 82 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Dynamic compression effects of H 2 ⁡O in a dynamic diamond anvil cell: Origin of metastable ice VII and its crystal growth kinetics

We report on the structural verification of metastable ice VII solidifying in the phase space of ice VI at 1.80 GPa at room temperature. Using time-resolved (TR) x-ray diffraction and TR ruby luminescence paired with high-speed microphotography utilizing a dynamic diamond anvil cell, an initial compression rate range from 0.12 to 95.84 GPa/s was explored. The solidification pressure of metastable ice VII has a potential sigmoidal dependence upon compression rate with a turnover compression rate of ∼80 GPa/s. The preferred crystallization of ice VII in the stability field of ice VI is due to the increased nucleation rate of ice VII over ice VI at 1.77 GPa that is driven by the surface energy difference between the liquid and solid phases along with the change in Gibbs free energy of solidification. The dynamic pressure-volume–compression behaviors of ice phases (VI and VII) show a lattice stiffening in both phases, especially during the compression loading. It is also found that the compression rate greatly affects the solid-solid phase transition between ice VI and VII but does not affect the liquid-solid transition between water and ice VI as much. Lastly, a third phase transition was found to occur after metastable ice VII transforms into high-density amorphous (HDA) ice, which could be a disordered hydrogen-bonded network configuration of ice VII forming out of HDA ice facilitated by the decoupling of the oxygen movement and reorientation of the H 2⁡ O molecule. These results demonstrate the complexity of a seemingly simple molecule H 2⁡ O, how it can readily change its static properties with the modification of (de)compression rate, and highlight the need to use multiple TR structural and spectroscopic probes at higher time resolutions to realize the most comprehensive understanding.

Chemical bonding↗

Smoothed dissipative particle dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations

Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for both bulk hydrodynamics and interfacial fluctuations. Interfacial surface tension is modeled by imposing a pairwise force between SDPD particles. We show that the relationship between the model parameters and surface tension, previously derived under the assumption of zero thermal fluctuation, is accurate for fluid systems at low temperature but overestimates the surface tension for intermediate and large thermal fluctuations. To analyze the effect of thermal fluctuations on surface tension, we construct a coarse-grained Euler lattice model based on the mean field theory and derive a semi-analytical formula to directly relate the surface tension to model parameters for a wide range of temperatures and model resolutions. We demonstrate that the present method correctly models the dynamic processes, such as bubble coalescence and capillary spectra across the interface.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Correlating dynamic microstructure to observed color in electrophoretic displays via in situ small-angle x-ray scattering

Electrophoretic deposition (EPD) is an industrially relevant and scalable technique used to form particle deposits from colloidal suspensions. Highly concentrated particle suspensions generally prevent real-time in situ microscopy observations which limit the characterization of EPD films to ex situ, or postprocessed, laboratory techniques. For dynamic systems, such as tunable amorphous photonic crystals (APCs), only reversible deposits are formed during the EPD process. Since reversible deposits cannot be characterized with standard ex situ methods, the particle-particle and particle-field interactions that govern the displayed color and crystallinity of these systems are not well understood. In this paper, we present in situ small-angle x-ray scattering and UV-Vis techniques for measuring both the structural and optical response of an APC under applied electric fields. Furthermore, we also develop a computational model based on colloidal interactions to explain the observed change in the interparticle spacing of APCs due to the applied electric field which correlates to displayed color. Ultimately, this work provides a new in situ characterization method that could be expanded for other dynamic, tunable colloidal systems.

36 MATERIALS SCIENCE↗

Roles of Dynamic State Estimation in Power System Modeling, Monitoring and Operation

—Power system dynamic state estimation (DSE) remains an active research area. This is driven by the absence of accurate models, the increasing availability of fast-sampled, time synchronized measurements, and the advances in the capability, scalability, and affordability of computing and communications. This paper discusses the advantages of DSE as compared to static state estimation, and the implementation differences between the two, including the measurement configuration, modeling framework and support software features. The important roles of DSE are discussed from modeling, monitoring and operation aspects for today’s synchronous machine dominated systems and the future power electronics-interfaced generation systems. Several examples are presented to demonstrate the benefits of DSE on enhancing the operational robustness and resilience of 21st century power system through time critical applications. Future research directions are identified and discussed, paving the way for developing the next generation of energy management systems.

Zhao, Junbo↗

Nonresonant pump/probe electronic Raman scattering within nonequilibrium dynamical mean-field theory

We develop the theory for nonresonant Raman scattering of strongly correlated electrons in time-resolved pump-probe experiments. The electrons are initially pumped with an intense pulse of light and then a probe pulse measures the Raman response function after an adjustable time delay. Here, we describe how the width of the probe pulse and the strength of the electron correlations affect the Raman cross section. The theory is developed for the case of B 1g symmetry, where incident and scattered light are polarized perpendicular to each other. We illustrate the exact solution with the Falicov-Kimball model, which is solved via nonequilibrium dynamical mean-field theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Molecular Polaritonics: Chemical Dynamics Under Strong Light–Matter Coupling

Chemical manifestations of strong light–matter coupling have recently been a subject of intense experimental and theoretical studies. Here we review the present status of this field. Section 1 is an introduction to molecular polaritonics and to collective response aspects of light–matter interactions. Section 2 provides an overview of the key experimental observations of these effects, while Section 3 describes our current theoretical understanding of the effect of strong light–matter coupling on chemical dynamics. A brief outline of applications to energy conversion processes is given in Section 4. Pending technical issues in the construction of theoretical approaches are briefly described in Section 5. Finally, the summary in Section 6 outlines the paths ahead in this exciting endeavor.

Chemistry↗

Variable Dynamic Testbed Vehicle: Dynamics Analysis

The Variable Dynamic Testbed Vehicle (VDTV) concept has been proposed as a tool to evaluate collision avoidance systems and to perform driving-related human factors research. The goal of this study is to analytically investigate to what extent a VDTV with adjustable front and rear anti-roll bar stiffnesses, programmable damping rates, and four-wheel-steering can emulate the lateral dynamics of a broad range of passenger vehicles.

Variable Dynamic Testbed Vehicle VDTV collision av↗

A System Dynamics Model of Early-Stage Transition Dynamics in the Bioproducts Industry

The U.S. Department of Energy, Bioenergy Technologies Office has a broad understanding of different conversion processes that produce bioproducts (chemicals derived from biomass feedstocks) and the techno-economic attributes of those processes. However, bioproducts have in many cases proven to be difficult to scale up to commercial production, and there is currently a need for greater understanding around the possible successful scenarios for advancing the bioproducts industry. Insight into the myriad factors that impact the success of individual bioproducts and the growth of the bioproducts industry will enable bioproduct stakeholders to evaluate strategies for development and investment that could achieve the greatest impact. An understanding of these factors will also enable the identification of synergies between the bioproducts and biofuels industries that occur through shared learning and co-production. The Bioproduct Transition Dynamics (BTD) model explores questions such as the following: what are the factors that separate a successful, commercially produced bioproduct like succinic acid from one that never progresses beyond bench-scale lab research? Can these factors be influenced by stakeholders, and to what extent? The BTD model uses system dynamics to capture the impacts of investor decision-making, bioproduct techno-economics, and end use factors during the early stages of bioproduct development. Key components of the BTD model include techno-economic benchmarks that inform the investor decision-making process, failures and setbacks in development and the resulting need for additional work, and the impacts of effective or ineffective management during each development stage. These factors and their interactions are tracked through bench-scale laboratory research, piloting, demoing, and the construction and operation of the first commercial-scale plant. Bioproduct development is linked to the biofuels industry through a shared-learning model, enabling the benefit to biofuels from bioproduct technology and feedstock supply chain development to be quantified. A wide variety of bioproducts can be analyzed using the BTD model, including bioproducts that have been developed through economic or policy-driven mechanisms, and those with either niche (low volume) or scalable (high volume) demand. The BTD model also has the potential to apply to technology development processes outside the bioproducts industry; background research performed for this project has shown that the early stages of technology development are similar, and impacted by similar factors, regardless of the exact industry. This presentation will cover the BTD model logic, input data, validation process, and results of a sensitivity analysis based on techno-economic data for succinic acid. The sensitivity analysis was performed to identify factors with the largest impact on the eventual success or failure of a bioproduct. Results indicate that management effectiveness, which affects how efficiently money spent is converted into technological advancements, is the single most important factor in determining whether a bioproduct reaches commercial-scale production. The capacity of the first commercial plant and the type of biomass feedstock used, as well as the presence of government support in the form of cost-sharing, were also identified as significant factors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

Significance A major challenge of protein crystallography is to accurately describe protein structure variations. Whereas Bragg peaks only yield a picture in which the variations are superimposed, diffuse X-ray scattering (diffraction between the peaks) reports on the way different atoms move together and can be used to increase the accuracy of models. We have performed a molecular-dynamics (MD) simulation of crystalline staphylococcal nuclease, yielding a rich picture of functionally important motions. This simulation is 100-fold longer than previous studies and yields reproducible calculations of diffuse intensity, overcoming a major challenge in the field. Experimental data support the MD models and indicate that diffuse scattering can be used both to validate and to improve MD simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative In Situ Studies of Dynamic Fracture in Brittle Solids Using Dynamic X-ray Phase Contrast Imaging

Here, we demonstrate the use of X-ray phase contrast imaging with sub-microsecond temporal resolution to obtain quantitative visualization of dynamic fracture processes in brittle solids. We examine an amorphous solid (fused silica), a ceramic single crystal (single-crystal quartz), and a polycrystalline ceramic (boron carbide), in the form of single-edge notched specimens loaded using a three-point apparatus at nominal strain rates up to ~800 s -1 . We observe that the crack tip speed for boron carbide is relatively independent of mode I stress intensity factor rate ($\dot{K}$ I ) for these rates of loading, while that of fused silica and single-crystal quartz increases with $\dot{K}$ I . Further, for the amorphous and single crystal cases, we observe the development of a crack tip instability in the form of crack branching as the crack tip speed approaches 45% of the Rayleigh wave speed. This suggests that strain-rate-dependent mechanisms contribute to crack branching. Such mechanisms may, in turn, affect the macroscopic fracture properties of these materials.

36 MATERIALS SCIENCE↗