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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 1,639 records · Page 91
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. Here, in this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.

Hamiltonians↗
DOE OSTI2016

An implicit divalent counterion force field for RNA molecular dynamics

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Thermophysical properties of α−Pu{sub 2}O{sub 3}: A new potential model

α−Pu{sub 2}O{sub 3} is an important material among plutonium based materials in nuclear industry. Pure plutonium surfaces quickly oxidizes into α−Pu{sub 2}O{sub 3} and PuO{sub 2} which are in the form of layers one on another. Here we have investigated thermal properties of α−Pu{sub 2}O{sub 3} by molecular dynamics simulation by using a partially ionic semi-empirical rigid ion potential. Mechanical properties, thermal expansion, and heat capacity are calculated. Results were compared with available experimental data and quantum calculation [2]. Due to the experimental limitations such as toxicity and radiation effects, studying the physical properties of such materials from molecular dynamics simulations have vital importance.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Understanding supercooling mechanism in sodium sulfate decahydrate phase-change material

Salt hydrate-based phase-change materials are considered promising for future heat storage applications in residential heating/cooling systems. Smooth phase transition from the liquid to solid phase and vice versa is essential for effective heat exchanger; however, supercooling in salt hydrates delays the onset of liquid–solid phase transition. We investigate the molecular level mechanism of supercooling in sodium sulfate decahydrate (SSD). SSD is a complex salt hydrate whose properties are governed by electrostatic forces that include pure Coulombic interactions as well as hydrogen bonds. Experimentally, we examine the importance of a nucleator in reducing supercooling temperatures. We investigated the effect of various mass concentrations of a borax nucleator on a decrease of supercooling temperatures. Molecular dynamics simulation techniques are used to obtain a basic understanding of supercooling in SSD. We observe that by introducing borax as a nucleator, there is a decrease in the supercooling temperature before nucleation. Our molecular dynamics simulations show that long-range electrostatics between sodium and sulfate ion pairs and that with polar water molecules is responsible for delayed nucleation in SSD that results in supercooling, and also, dynamics of charged molecules slows down. The lack of crystallization leads to amorphous structures in supercooled SSD.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mean force kinetic theory applied to self-diffusion in supercritical Lennard-Jones fluids

A new kinetic-theory-based calculation of the self-diffusion coefficient for dense supercritical Lennard-Jones fluids is presented. The mean force kinetic theory, which was recently developed for transport in dense plasmas, is applied for the calculation of diffusion in dense neutral fluids. The calculation only requires the pair distribution function, a quantity that is readily calculable from equilibrium statistical mechanics for many systems, including the Lennard-Jones fluid. The self-diffusion coefficients are compared with calculations from molecular dynamics simulations, and good agreement at high density is demonstrated, even in the vicinity of the solid–fluid coexistence line. A comparison of different kinetic models with molecular dynamics simulations demonstrates that the transport coefficients have important contributions due to particle interaction via a potential of mean force and local correlations, which increase the collision rate. The new calculations compare well to those from free-volume theory and overcome a limitation of this theory that prevents its use in systems that interact via long range monotonic potentials. It is expected that this approach will also apply to other systems, including neutral-plasma and neutral-electrolyte mixtures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Modulating electronic coupling at the quantum dot/molecule interface by wavefunction engineering

In this work, we use wavefunction engineering by varying the size of Quantum Dots (QDs) and tuning the delocalization (or diffuseness) of frontier orbitals of an acceptor molecule to modulate charge transfer dynamics at the QD/molecule interface. For this purpose, we apply our recently developed bulk-adjusted linear combination of atomic orbitals (BA-LCAO) approach for nanostructures and a density functional theory (DFT) for the acceptor molecules. These electronic structure calculations, combined with extensive molecular dynamics simulations using a fragmented molecular mechanics (FraMM) force field, reveal intimate details of charge transfer across the QD/Acceptor interface. For the spherical wurtzite-(CdSe) 201 and (CdSe) 693 nanostructures, as model QDs with respective 2.8 and 4.1 nm diameters, and anthraquinone-2,3-dicarboxylic acid and its derivatives with the 7-OH, 7-OF, 10-BH, and 10-CH 2 substituents, as model molecular acceptors, we find that (1) both the electron donating and withdrawing groups greatly enhance hole transfer by means of diffusing the acceptor HOMO; (2) electron transfer is affected only by the electron donating groups; (3) solvent effects are largely negligible for the orbital overlaps, and (4) consistent with spatial confinement theories, the electron density of the smaller QD penetrates farther into the vacuum than the corresponding density of the larger QD leading to stronger coupling with the acceptor. These findings suggest that (a) one can effectively control charge transfer across the QD/molecule interface by either changing the size of the QD or by tuning diffuseness of frontier orbitals of the acceptor molecule and (b) the combination of the recently developed BA-LCAO approach for QDs with a DFT for the acceptor molecules, facilitated by the use of the FraMM force field and extensive molecular dynamics simulations, provide qualitatively accurate description of charge transfer dynamics at the QD/acceptor interface.

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

Generalized 3D beam dynamics model for industrial traveling wave linacs design and simulations

Beam dynamics simulations in traveling wave (TW) accelerating structures with significant beam loading is a challenging problem. Some codes are capable of calculating the TW electromagnetic fields, and some can track particles through such fields, but most cannot treat both self-consistently. A few commercial codes can model the physics correctly at the expense of many processor-hour computations to obtain converged self-consistent solutions. However, simple, accurate equations of motion for intensive beam dynamics in TW accelerating structure analysis have been previously obtained by Masunov and subsequently implemented in the Hellweg code, which was developed at the Moscow Engineering-Physics Institute. Hellweg is based on equations that allow fast simulations of beam dynamics while taking into account such effects as beam loading, space charge, and external magnetic fields. In this paper, we describe in detail some recent improvements to the Hellweg physics kernel. We have generalized the Masunov results into a 3D set of equations of motion, which include all spatial components of the radiofrequency (RF) and external magnetic fields. We have also improved the Lapostolle space charge model to the general 3D ellipsoid form for any dimensions’ ratio, consideration for the particles outside the beam core, and the fields from the neighboring bunches that can exist in the real machine. These modifications allow approaching the Hellweg accuracy to the self-consistent commercial codes while keeping the simulation time short, which is essential during the linac design and optimization stage. The implementation of these new capabilities in Hellweg is carefully benchmarked against other codes and analytical calculations. The code is freely available with an open source license.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Coordinate transformation methodology for simulating quasistatic elastoplastic solids

Molecular dynamics simulations frequently employ periodic boundary conditions where the positions of the periodic images are manipulated in order to apply deformation to the material sample. For example, Lees-Edwards conditions use moving periodic images to apply simple shear. Here, we examine the problem of precisely comparing this type of simulation to continuum solid mechanics. We employ a hypo-elastoplastic mechanical model, and develop a projection method to enforce quasi-static equilibrium. We introduce a simulation framework that uses a fixed Cartesian computational grid on a reference domain, and imposes deformation via a time-dependent coordinate transformation to the physical domain. As a test case for our method, we consider the evolution of shear bands in a bulk metallic glass using the shear transformation zone theory of amorphous plasticity. We examine the growth of shear bands in simple shear and pure shear conditions as a function of the initial preparation of the bulk metallic glass.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive

In both continuum hydrodynamics simulations and also multimillion atom reactive molecular dynamics simulations of shockwave propagation in single crystal pentaerythritol tetranitrate (PETN) containing a cylindrical void, we observed the formation of an initial radially symmetric hot spot. By extending the simulation time to the nanosecond scale, however, we observed the transformation of the small symmetric hot spot into a longitudinally asymmetric hot region extending over a much larger volume. Performing reactive molecular dynamics shock simulations using the reactive force field (ReaxFF) as implemented in the LAMMPS molecular dynamics package, we showed that the longitudinally asymmetric hot region was formed by coalescence of the primary radially symmetric hot spot with a secondary triangular hot zone. We showed that the triangular hot zone coincided with a double-shocked region where the primary planar shockwave was overtaken by a secondary cylindrical shockwave. The secondary cylindrical shockwave originated in void collapse after the primary planar shockwave had passed over the void. A similar phenomenon was observed in continuum hydrodynamics shock simulations using the CTH hydrodynamics package. Furthermore, the formation and growth of extended asymmetric hot regions on nanosecond timescales has important implications for shock initiation thresholds in energetic materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Simulating Neutron Stars with Solid Quark Cores: Rotations, Oscillations, and Binary Mergers [Slides]

Neutron stars feature complexity from GR, QM, particle physics and nuclear physics effects which cannot be investigated in the lab up to the densities in their core. GWs from binary neutron star mergers are on the rise to provide more insight into the physics inside NSs. There is a possibility that involves crystalline, color-superconducting quark matter, with implications towards altering the GW signal if NSs harbor this exotic matter. There are no 3D dynamical simulations of solid quark matter inside Neutron stars. We perform the first 3D dynamical simulations of solid quark matter inside NSs. These are performed in the Newtonian Approximation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in Brachypodium cesa1 S830N

Here, we present a study into the mechanisms of primary cell wall cellulose formation in grasses, using the model cereal grass Brachypodium distachyon. The exon found adjacent to the BdCESA1 glycosyltransferase QXXRW motif was targeted using Targeting Induced Local Lesions in Genomes (TILLING) and sequencing candidate amplicons in multiple parallel reactions (SCAMPRing) leading to the identification of the Bdcesa1 S830N allele. Plants carrying this missense mutation exhibited a significant reduction in crystalline cellulose content in tissues that rely on the primary cell wall for biomechanical support. However, Bdcesa1 S830N plants failed to exhibit the predicted reduction in plant height. In a mechanism unavailable to eudicotyledons, B. distachyon plants homozygous for the Bdcesa1 S830N allele appear to overcome the loss of internode expansion anatomically by increasing the number of nodes along the stem. Stem biomechanics were resultantly compromised in Bdcesa1 S830N . The Bdcesa1 S830N missense mutation did not interfere with BdCESA1 gene expression. However, molecular dynamic simulations of the CELLULOSE SYNTHASE A (CESA) structure with modelled membrane interactions illustrated that Bdcesa1 S830N exhibited structural changes in the translated gene product responsible for reduced cellulose biosynthesis. Molecular dynamic simulations showed that substituting S830N resulted in a stabilizing shift in the flexibility of the class specific region arm of the core catalytic domain of CESA, revealing the importance of this motion to protein function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Solitons and protein folding: An In Silico experiment

Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Probing DNA clamps with single-molecule force spectroscopy

Detailed mechanisms of DNA clamps in prokaryotic and eukaryotic systems were investigated by probing their mechanics with single-molecule force spectroscopy. Specifically, the mechanical forces required for the Escherichia coli and Saccharomyces cerevisiae clamp opening were measured at the single-molecule level by optical tweezers. Steered molecular dynamics simulations further examined the forces involved in DNA clamp opening from the perspective of the interface binding energies associated with the clamp opening processes. In combination with additional molecular dynamics simulations, we identified the contact networks between the clamp subunits that contribute significantly to the interface stability of the S.cerevisiae and E. coli clamps. These studies provide a vivid picture of the mechanics and energy landscape of clamp opening and reveal how the prokaryotic and eukaryotic clamps function through different mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

On the origin and behavior of irradiation-induced c-component dislocation loops in magnesium

C-component dislocation loops are one of the unique defects in hexagonal close-packed (hcp) crystals that promote the accelerated growth and void formation under irradiation. In this paper, we report in situ observation of c-component dislocation loop formation in Mg under electron irradiation with emphasis on their atomic structures. Aberration-corrected scanning transmission electron microscopy imaging is utilized to reveal four possible types of double-layer loops, which were identified as different types of stacking fault and dislocation core structures. Triple- and quadruple-layer c-component dislocation loops were also observed. The formation mechanisms of the four types of double-layer loops were revealed via molecular dynamics simulations. The experimentally observed formation rate of the single- and double-layer dislocation loops is controlled by their formation energies. Finally, our direct experimental observations in combination with molecular dynamics simulations provide fundamental insight into the mechanisms governing nucleation and growth of the c-component dislocation loops as well as their interactions, which could potentially help with future development of irradiation-resistant materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Flow of long chain hydrocarbons through carbon nanotubes (CNTs)

The pressure-driven flow of long-chain hydrocarbons in nanosized pores is important in energy, environmental, biological, and pharmaceutical applications. This paper examines the flow of hexane, heptane, and decane in carbon nanotubes (CNTs) of pore diameters 1–8 nm using molecular dynamic simulations. Enhancement of water flow in CNTs in comparison to rates predicted by continuum models has been well established in the literature. Our work was intended to observe if molecular dynamic simulations of hydrocarbon flow in CNTs produced similar enhancements. We used the OPLS-AA force field to simulate the hydrocarbons and the CNTs. Our simulations predicted the bulk densities of the hydrocarbons to be within 3% of the literature values. Molecular sizes and shapes of the hydrocarbon molecules compared to the pore size create interesting density patterns for smaller sized CNTs. We observed moderate flow enhancements for all the hydrocarbons (1–100) flowing through small-sized CNTs. For very small CNTs the larger hydrocarbons were forced to flow in a cork-screw fashion. As a result of this flow orientation, the larger molecules flowed as effectively (similar enhancements) as the smaller hydrocarbons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

A laser gyro with a four-mirror square resonator: formulas for simulating the dynamics of the synchronisation zone parameters of the frequencies of counterpropagating waves during the device operation in the self-heating regime

For a laser gyro with a four-mirror square resonator we have developed a mathematical model, which allows one to simulate the temporal behaviour of the synchronisation zone parameters of the frequencies of counterpropagating waves in a situation when the device operates in the self-heating regime and is switched-on at different initial temperatures. (laser gyroscopes)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Neural network potential for Zr–Rh system by machine learning

Zr–Rh metallic glass has enabled its many applications in vehicle parts, sports equipment and so on due to its outstanding performance in mechanical property, but the knowledge of the microstructure determining the superb mechanical property remains yet insufficient. Here, we develop a deep neural network potential of Zr–Rh system by using machine learning, which breaks the dilemma between the accuracy and efficiency in molecular dynamics simulations, and greatly improves the simulation scale in both space and time. Here, the results show that the structural features obtained from the neural network method are in good agreement with the cases in ab initio molecular dynamics simulations. Furthermore, we build a large model of 5400 atoms to explore the influences of simulated size and cooling rate on the melt-quenching process of Zr 77 Rh 23 . Our study lays a foundation for exploring the complex structures in amorphous Zr 77 Rh 23 , which is of great significance for the design and practical application.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Structural transition in sputter-deposited amorphous germanium films by aging at ambient temperature

The structure of amorphous Ge (a-Ge) films prepared by sputter-deposition and the effects of aging at ambient temperature and pressure were studied by pair-distribution-function (PDF) analysis from electron scattering and molecular dynamics simulations. The PDFs of the as-deposited and aged samples for 3–13 months showed that the major peaks for Ge-Ge bonds decrease in intensity and broaden with aging for up to 7 months. In the PDFs of a-Ge of molecular dynamics simulation obtained by quenching liquid at different rates, the major peak intensities of a slowly cooled model are higher than those of a rapidly cooled model. Analyses on short- and medium-range configurations show that the slowly cooled model includes a certain amount of medium-range ordered (MRO) clusters, while the rapidly cooled model includes liquid-like configurations rather than MRO clusters. The similarity between experimental and computational PDFs implies that as-deposited films are similar in structure to the slowly cooled model, whereas the fully aged films are similar to the rapidly cooled model. It is assumed that as they undergo room-temperature aging, the MRO clusters disintegrate and transform into liquid-like regions in the same matrix. This transition in local configurations is discussed in terms of instability and the non-equilibrium of nanoclusters produced by a vapor-deposition process.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗