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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Dynamic Structure of Magnetized High Energy Density Plasmas (Final Report)

This report summarizes results of project DE-SC0022202 ``Dynamic Structure of Magnetized High Energy Density Plasmas,'' which was originally funded for the period 08/01/2021 - 7/31/2022, but was no-cost extended to 7/31/2023. The primary objectives of the work, as stated in the original proposal, were ``develop a theory to describe a novel state of magnetized high energy density plasmas, benchmark the theory using first-principles molecular dynamics simulations, and apply the results to develop a means to interpret x-ray scattering measurements in future experiments.'' These were the goals of the original project proposal, which was for a 3 year project. The project was ultimately funded for 1 year, and so the work completed focused on the goals described for only the first year of the proposed work. This included further developing a kinetic theory for strongly magnetized plasmas, applying it to compute fluid-scale (MHD) transport coefficients, and to test the predictions using molecular dynamics simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Pseudoelastic deformation in Mo-based refractory multi-principal element alloys

Phase diagrams supported by density functional theory methods can be crucial for designing high-entropy alloys that are subset of multi-principal-element alloys. We present phase and property analysis of quinary (MoW) x Zr y (TaTi) 1-x-y refractory high-entropy alloys from combined Calculation of Phase Diagram (CALPHAD) and density-functional theory results, supplemented by molecular dynamics simulations. Both CALPHAD and density-functional theory analysis of phase stability indicates a Mo-W-rich region of this quinary has a stable single-phase body-centered-cubic structure. We report first quinary composition from Mo-W-Ta-Ti-Zr family of alloy with pseudo-elastic behavior, i.e., hysteresis in stress-strain. Our analysis shows that only Mo-W-rich compositions of Mo-W-Ta-Ti-Zr, i.e., Mo+W, show reproducible hysteresis in stress-strain responsible for pseudo-elastic behavior. The (MoW) 85 Zr 7.5 (TaTi) 7.5 was down-selected based on temperature-dependent phase diagram analysis and molecular dynamics simulations predicted elastic behavior that reveals twinning-assisted pseudoelastic behavior. While mostly unexplored in body-centered-cubic crystals, twinning is a fundamental deformation mechanism that competes against dislocation slip in crystalline solids. Furthermore, this alloy shows identical cyclic deformation characteristics during uniaxial < 100 > loading, i.e., the pseudoelasticity is isotropic in loading direction. Additionally, a temperature increase from 77 to 1,500 K enhances the elastic strain recovery in load-unload cycles, offering possibly control to tune the pseudoelastic behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Design of high polarization low switching barrier hybrid improper ferroelectric perovskite oxide superlattices

Hybrid improper ferroelectricity is a useful tool to design ABO 3 /A'BO 3 polar superlattices from non polar building blocks. In this study, we have designed high polarization-low switching barrier hybrid improper ferroelectric superlattices with efficient polarization, and polarization-magnetization switching properties above room temperature, using density functional theory and ab initio molecular dynamics simulations. Superlattices with a chemical formula of (AAlO 3 ) m /(A'AlO 3 ) n , where m/n = 1/1, 1/3, 3/1, 1/5 and 5/1, A, A' = Lanthanide and Y cations are considered to outline the design principles behind polarization switching and (LaFeO 3 ) 3 /(CeFeO 3 ) 1 is investigated for polarization-magnetization switching. We find that the unconventional switching paths via out-of-phase rotation Q R- (a 0 a 0 c - ) and tilt precession QTP always yield lower switching barrier compared to those via in-phase rotation Q R+ (a 0 a 0 c + ) and tilt QT (a - a - c 0 ) of BO 6 octahedra. Results from ab initio molecular dynamics simulations estimate the temperature at which the lowest energy barrier can be overcome. Furthermore, it is possible to tune the polarization switching barrier by tuning the tolerance factor, A,A' cation radius mismatch and super lattice periodicity. For switching via Q R- , the switching barrier varies exponentially with rotation angle, indicating how high switching barrier is expected for systems, away from cubic symmetry. We provide a recipe to overcome such a bottleneck by tuning superlattice periodicity. Finally, we have proposed the multiferroic device application concept through a proposed polarization-temperature hysteresis loop and magnetization switching.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Anomalous entropy-driven kinetics of dislocation nucleation

The kinetics of dislocation reactions, such as dislocation multiplication, controls the plastic deformation in crystals beyond their elastic limit, therefore critical mechanisms in a number of applications in materials science. We present a series of large-scale molecular dynamics simulations that shows that one such type of reactions, the nucleation of dislocation at free surfaces, exhibit unconventional kinetics, including unexpectedly large nucleation rates under compression, very strong entropic stabilization under tension, as well as strong non-Arrhenius behavior. These unusual kinetics are quantitatively rationalized using a variational transition state theory approach coupled with an efficient numerical scheme for the estimation of vibrational entropy changes. These results highlight the need for a variational treatment of the kinetics to quantitatively capture dislocation reaction kinetics, especially at low-to-moderate strains where large deformations are required to activate reactions. These observations suggest possible explanations to previously observed unconventional deformation kinetics in both molecular dynamics simulations and experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗
DOE OSTI2022

Recovery of MOF-5 from Extreme High-Pressure Conditions Facilitated by a Modern Pressure Transmitting Medium

Here mechanisms underlying the mechanically induced amorphization of metal-organic frameworks (MOFs) are of current interest, and both high-pressure experimentation and molecular dynamics simulations have been used to reveal the fundamentals of load bearing, deformation, and pressure-induced amorphization (PIA) in these highly porous materials. Unfortunately, MOFs are typically highly susceptibility to amorphization, which limits the conditions under which they can be processed and used. However, their flexible structures can be stabilized to high pressures by incorporating guest species into the framework matrix. In this study, a large molecule pressure transmitting medium (DAPHNE 7575 ) is used as a structure-fortifying guest species to stabilize the prototypical MOF -5 to ultra-high pressures ( >9 GPa) and enable the recovery of crystalline material upon decompression. Structural changes associated with the penetration of the pressure transmitting medium on compression are examined using a combination of high pressure synchrotron powder diffraction and molecular dynamics simulations. This work enhances the understanding of PIA in MOFs while showcasing a potential route for the stabilization of MOFs to surprisingly high-pressures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein

Ensembles of amino acid side chains often dominate the interfacial interactions of intrinsically disordered proteins; however, backbone contributions are far from negligible. Using a combination of nanoscale force measurements and molecular dynamics simulations, we demonstrated with analogous mussel-mimetic adhesive peptides and peptoids both 34 residues long that highly divergent adhesive/cohesive outcomes can be achieved on mica surfaces by altering backbone chemistry only. The Phe, Tyr, and Dopa containing peptoid variants used in this study deposited as dehydrated and incompressible films that facilitated analysis of peptoid side chain contributions to adhesion and cohesion. For example, whereas Phe and Dopa peptoids exhibited similar cohesion, Dopa peptoids were ~3 times more adhesive than Phe peptoids on mica. Compared with the peptides, Phe peptoid achieved only ~20% of Phe containing peptide adhesion, but the Dopa peptoids were >2-fold more adhesive than the Dopa peptides. Cation-π interactions accounted for some but not all of the cohesive interactions. Finally, our results were corroborated by molecular dynamics simulations and highlight the importance of backbone chemistry and the potential of peptoids or peptoid/peptide hybrids as wet adhesives and primers.

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

Mechanical behavior of ultralight nickel metamaterial

The mechanical response of ultralight kagomé structures consisting of hollow nickel (Ni) nanotubes and solid Ni nanorods to compression is studied using molecular dynamics simulations. In both kagomé architectures, 16[112] Shockley partial dislocations and twin formation are observed under compression. The structure made from solid nanorods shows deformation near both the nodes and beams of the kagomé lattice. The hollow kagomé architecture has a higher yield point than the solid kagomé structure. The deformation in the hollow nanotube structure is mostly localized in the nodal region for strains less than 11%. At higher strains, the deformation sets in all the struts and nodes of the hollow kagomé lattice. Owing to this two-stage deformation mechanism, the hollow Ni nanotube kagomé structure shows less bending and greater toughness than the solid Ni nanorod kagomé architecture.

Rajak, Pankaj (ORCID:0000000263446056)↗
DOE OSTI2020

Tuning the melting point of selected ionic liquids through adjustment of the cation’s dipole moment.

In prior research with thermally robust salts [Cassity et al., PCCP, 2017, 19, 31560] it was noted that an increase in the dipole moment of the cation generally led to a decrease in the melting point. Molecular dynamics simulations of the liquid state revealed that an increased dipole moment reduces cation-cation repulsions through dipole-dipole alignment. This was believed to reduce the liquid phase enthalpy, which would tend to lower the melting point of the IL. Here, we also test this principle by replacing hydrogen atoms with fluorine atoms at selected positions within the cation. This allows us to alter the electrostatics of the cation without substantially affecting the sterics. Furthermore, the strength of the dipole moment can be controlled by choosing different positions within the cation for replacement. We studied variants of four different parent cations paired with bistriflimide and determined their melting points, and enthalpies and entropies of fusion through DSC experiments. The decreases in the melting point were determined to be enthalpically driven. We found that the dipole moment of the cation, as determined by quantum chemical calculations, is inversely correlated with the melting point of the given compound. Molecular dynamics simulations of the crystalline and solid states of two isomers showed differences in their enthalpies of fusion that closely matched those seen experimentally. Moreover, this reduction in the enthalpy of fusion was determined to be caused by an increase in the enthalpy of the crystalline state. We provide evidence that dipole-dipole interactions between cations leads to the formation of cationic domains in the crystalline state. These cationic associations partially block favourable cation–anion interactions, which are recovered upon melting. If, however, the dipole- dipole interactions between cations is too strong they have a tendency to form glasses. This study provides a design rule for lowering the melting point of structurally similar ILs by altering their dipole moment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Raman studies of hydrogen trapped in As 4 O 6 ·2H 2 at high pressure and low temperature

In this work, Raman spectroscopic measurements of the arsenolite–hydrogen inclusion compound As 4 O 6 ·2H 2 were performed in diamond anvil cells at high pressure and variable temperature down to 80 K. The experimental results were complemented by ab initio molecular dynamics simulations and phonon calculations. Observation of three hydrogen vibrons in As 4 O 6 ·2H 2 is reported in the entire temperature and pressure range studied (up to 24 GPa). While the experiments performed with protium and deuterium at variable temperatures allowed for the assignment of two vibrons as Q 1 (1) and Q 1 (0) transitions of ortho and para spin isomers of hydrogen trapped in the inclusion compound, the origin of the third vibron could not be unequivocally established. Low-temperature spectra revealed that the lowest-frequency vibron is actually composed of two overlapping bands of A g and T 2g symmetries dominated by H 2 stretching modes as predicted by our previous density functional theory calculations. We observed low-frequency modes of As 4 O 6 ·2H 2 vibrations dominated by H 2 “librations,” which were missed in a previous study. A low-temperature fine structure was observed for the J = 0 → 2 and J = 1 → 3 manifolds of hydrogen trapped in As 4 O 6 ·2H 2 , indicating the lifting of degeneracy due to an anisotropic environment. A non-spherical distribution was captured by molecular dynamics simulations, which revealed that the trajectory of H 2 molecules is skewed along the crystallographic $\langle$111$\rangle$ direction. Last but not least, low-temperature synchrotron powder x-ray diffraction measurements on As 4 O 6 ·2H 2 revealed that the bulk structure of the compound is preserved down to 5 K at 1.6 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2015

Fracture of Carbon Nanotube - Amorphous Carbon Composites: Molecular Modeling

Carbon nanotubes (CNTs) are promising candidates for use as reinforcements in next generation structural composite materials because of their extremely high specific stiffness and strength. They cannot, however, be viewed as simple replacements for carbon fibers because there are key differences between these materials in areas such as handling, processing, and matrix design. It is impossible to know for certain that CNT composites will represent a significant advance over carbon fiber composites before these various factors have been optimized, which is an extremely costly and time intensive process. This work attempts to place an upper bound on CNT composite mechanical properties by performing molecular dynamics simulations on idealized model systems with a reactive forcefield that permits modeling of both elastic deformations and fracture. Amorphous carbon (AC) was chosen for the matrix material in this work because of its structural simplicity and physical compatibility with the CNT fillers. It is also much stiffer and stronger than typical engineering polymer matrices. Three different arrangements of CNTs in the simulation cell have been investigated: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. The SWNT and MWNT array systems are clearly idealizations, but the SWNT bundle system is a step closer to real systems in which individual tubes aggregate into large assemblies. The effect of chemical crosslinking on composite properties is modeled by adding bonds between the CNTs and AC. The balance between weakening the CNTs and improving fiber-matrix load transfer is explored by systematically varying the extent of crosslinking. It is, of course, impossible to capture the full range of deformation and fracture processes that occur in real materials with even the largest atomistic molecular dynamics simulations. With this limitation in mind, the simulation results reported here provide a plausible upper limit on achievable CNT composite properties and yield some insight on the influence of processing conditions on the mechanical properties of CNT composites.

Jensen, Benjamin D.↗
DOE OSTI2022

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ~5-50 cm -1 . This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effect of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal/mol -1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

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

Three-dimensional atomic packing in amorphous solids with liquid-like structure

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Shape-preserving amorphous-to-crystalline transformation of CaCO3 revealed by in situ TEM

Organisms use inorganic ions and macromolecules to regulate crystallization from amorphous- precursors, endowing natural biominerals with complex morphologies and enhanced properties. The mechanisms by which modifiers enable these shape preserving transformations are poorly understood. We used in situ liquid-phase transmission electron microscopy to follow the evolution from amorphous calcium carbonate to calcite in the presence of additives. A combination of contrast analysis and infrared spectroscopy shows that Mg ions, which are widely present in seawater and biological fluids, alter the transformation pathway in a concentration-dependent manner. The ions bring excess (structural) water into the amorphous bulk so that a direct transformation is triggered by dehydration in the absence of morphological changes. Molecular dynamics simulations suggest Mg-incorporated water induces structural fluctuations, allowing transformation without the need to nucleate a separate crystal. Thus, the obtained calcite retains the original morphology of the amorphous state, biomimetically achieving the morphological control of crystals seen in biominerals

crystallization, biomineralization, calcium carbon↗