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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Berni Julian Alder, theoretical physicist and inventor of molecular dynamics, 1925–2020

Berni Julian Alder, one of the leading figures in the invention of molecular dynamics simulations used for a wide array of problems in physics and chemistry, died on September 7th, 2020. His career, spanning more than 65 years, transformed statistical mechanics, many body physics, the study of chemistry and the microscopic dynamics of fluids, by making atomistic computational simulation (in parallel with traditional theory and experiment) a new pathway to unexpected discoveries. Among his many honors, the CECAM prize, recognizing exceptional contributions to the simulation of the microscopic properties of matter is named for him. He was awarded the National Medal of Science by President Obama in 2008.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Amplifying Nanoparticle Reinforcement through Low Volume Topologically Controlled Chemical Coupling

Here, we present a streamlined method to covalently bond hydroxylated carbon nanotubes (CNOH) within a polyphenol matrix, all achieved through a direct, solvent-free process. Employing an extremely small concentration of CNOH (0.01% w/w) along with topologically contrasting linkers led to a maximum of 5-fold increase in modulus and a 25% enhancement in tensile strength compared to the unaltered matrix, an order of magnitude greater reinforcement (w/w) compared to state-of-the-art melt-processed nanocomposites. Through dynamic mechanical analysis, low field solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we uncovered the profound influence of linker’s conformational degrees of freedom on the segmental dynamics and therefore the material’s properties.

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

Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fast Na diffusion and anharmonic phonon dynamics in superionic Na 3 PS 4

The design of new solid electrolytes (SEs) hinges on identifying and tuning relevant descriptors. Phonons describe the atomic dynamics in crystalline materials and provide a basis to encode possible minimum energy pathways for ion migration, but anharmonic effects can be large in SEs. Identifying and controlling the pertinent phonon modes coupled most strongly with ionic conductivity, and assessing the role of anharmonicity, could therefore pave the way for discovering and designing new SEs via phonon engineering. In this work, we investigate phonons in Na 3 PS 4 and their coupling to fast Na diffusion, using a combination of neutron scattering, ab initio molecular dynamics (AIMD), and extended molecular dynamics based on machine-learned potentials. We identify that anharmonic soft-modes at the Brillouin zone boundary of the anharmonically stabilized cubic phase constitute key phonon modes that control the Na diffusion process in Na 3 PS 4 . We demonstrate how these strongly anharmonic phonon modes enable Na-ions to hop along the minimum energy pathways. Further, the quasi-elastic neutron scattering (QENS) measurements, supplemented with ab initio and machine-learned molecular dynamics simulations, probe the Na diffusivity and diffusion mechanism. These results offer detailed microscopic insights into the dynamic mechanism of fast Na diffusion and provide an avenue to search for further Na solid electrolytes.

42 ENGINEERING↗
DOE OSTI2021

Effects of interaction strength of associating groups on linear and star polymer dynamics

A small number of associating groups incorporated onto a polymer backbone have dramatic effects on the mobility and viscoelastic response of the macromolecules in melts. These associating groups assemble, driving the formation of clusters, whose lifetime affects the properties of the polymers. In this study, we probe the effects of the interaction strength on the structure and dynamics of two topologies, linear and star polymer melts, and further investigate blends of associative and non-associating polymers using molecular dynamics simulations. Polymer chains of approximately one entanglement length are described by a bead–spring model, and the associating groups are incorporated in the form of interacting beads with an interaction strength between them that is varied from 1 to 20 k B T. We find that, for all melts and blends, interaction of a few k B T between the associating groups drives cluster formation, where the size of the clusters increases with increasing interaction strength. These clusters act as physical crosslinkers, which slow the chain mobility. Blends of chains with and without associating groups macroscopically phase separate for interaction strength between the associating groups of a few k B T and above. For weakly interacting associating groups, the static structure function S(q) is well fit by functional form predicted by the random phase approximation where a clear deviation occurs as phase segregation takes place, providing a quantitative assessment of phase segregation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Improving the electrostatic design of the Jefferson Lab 300 kV DC photogun

The 300 kV DC high voltage photogun at Jefferson Lab was redesigned to deliver electron beams with a much higher bunch charge and improved beam properties. The original design provided only a modest longitudinal electric field ( E z ) at the photocathode, which limited the achievable extracted bunch charge. To reach the bunch charge goal of approximately few nC with 75 ps full-width at half-maximum Gaussian laser pulse width, the existing DC high voltage photogun electrodes and anode–cathode gap were modified to increase E z at the photocathode. In addition, the anode aperture was spatially shifted with respect to the beamline longitudinal axis to minimize the beam deflection introduced by the non-symmetric nature of the inverted insulator photogun design. We present the electrostatic design of the original photogun and the modified photogun and beam dynamics simulations that predict vastly improved performance. We also quantify the impact of the photocathode recess on beam quality, where recess describes the actual location of the photocathode inside the photogun cathode electrode relative to the intended location. A photocathode unintentionally recessed/misplaced by sub-millimeter distance can significantly impact the downstream beam size.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Mean force emission theory for classical bremsstrahlung in strongly coupled plasmas

This work presents mean force emission theory, which extends the classical theory of bremsstrahlung emission to strongly coupled plasmas. In the high-frequency limit, the theory reduces to solving for the electron trajectory during a binary collision, but where the electron–ion interactions occur through the potential of mean force. In the low-frequency limit, it uses an autocorrelation formalism that captures effects of multiple collisions and strongly correlated motion. The predictions are benchmarked by comparison with first-principles classical molecular dynamics simulations of a fully ionized hydrogen plasma in which all interactions are repulsive. The comparison shows good agreement up to Coulomb coupling strengths of Γ∼30. The theory improves upon traditional models by including strong coupling effects and systematically including the effect of multiple collisions. Furthermore, mean force emission theory provides evidence that the Drude correction factor commonly used in quantum calculations of optical quantities may not be adequate at strong coupling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Multistage nucleation pathway in LiF molten salt mirrors the crystal–melt interface structure

Despite over a century of studies, fundamental questions remain about the processes governing crystal nucleation from melts or solutions. Research over the past three decades has presented mounting evidence for kinetic pathways of crystal nucleation that are more complex than envisioned by the simplest forms of classical theory. Such observations have been presented for colloidal and elemental systems with covalent and metallic bonding. Despite the technological and geochemical importance of molten salts, similar studies for these ionically bonded systems are currently lacking. Here we develop a machine learning interatomic potential for a model ionic system: LiF. The potential features quantum-level accuracy for both liquid and multiple solid polymorphs over wide temperature and pressure ranges and accurately reproduces experimentally measured properties. Thanks to the efficiency of the potential, which enables microsecond-scale molecular dynamics simulations, induction times for nucleation of LiF solids from their melts are computed over a range of undercoolings. With the aid of a set of robust local order parameters established here, the simulations reveal that homogeneous crystal nucleation in undercooled melts preferentially initiates from liquid regions showing slow dynamics and high bond orientational order simultaneously, and the second-shell order of both precritical nuclei and the surface of postcritical nuclei is dominated by hexagonal close packing and body-centered cubic local structure, even though the nucleus core is dominated by face-centered cubic structure corresponding to the stable rocksalt crystal structure. Finally, we establish a connection between the crystallization pathway and the equilibrium crystal-melt interface structure.

Applied Physical Sciences↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Solvation Energy of Ions in a Stockmayer Fluid

We calculate the solvation energy of monovalent and divalent ions in various liquids with coarse-grained molecular dynamics simulations. Our theory treats the solvent as a Stockmayer fluid, which accounts for the intrinsic dipole moment of molecules and the rotational dynamics of the dipoles. Despite the simplicity of the model, we obtain qualitative agreement between the simulations and experimental data for the free energy and enthalpy of ion solvation, which indicates that the primary contribution to the solvation energy arises mainly from the first and possibly second solvation shells near the ions. Our results suggest that a Stockmayer fluid can serve as a reference model that enables direct comparison between theory and experiment and may be invoked to scale up electrostatic interactions from the atomic to the molecular length scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Thermodynamics of high-pressure ice phases explored with atomistic simulations

Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII' and X are the same thermodynamic phase under different conditions, whereas superionic ice VII" has a first-order phase boundary with ice VII'. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

OpenFerro v0.1.0

OpenFerro is a Python package for on-lattice atomistic dynamics simulation of ferroic materials. OpenFerro is based on JAX, a high-performance linear algebra package supporting auto-differentiation and GPU acceleration. OpenFerro is designed to minimize the effort required to build on-lattice Hamiltonian models, and to perform molecular dynamics (MD) and Landau-Lifshitz-Gilbert simulations. Unlike existing codes, OpenFerro provides a unified interface to model different types of local order parameters.

Xie, Pinchen [Lawrence Berkeley National Laborator↗
DOE OSTI2022

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

We report molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. The SLIC/CDC multiscale model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). The SLIC/CDC model predicts Gibbs energies of solvation for a database of 500 solutes in water with average accuracy better than 1 kcal/mol both for experimental measurements and for explicit-solvent molecular dynamics simulations. The separate SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent accessible surface area (SASA) nonpolar energy mode. The SLIC/SASA model predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems and better than 1.6 kcal/mol average accuracy in ionic liquids. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The role of pre-existing heterogeneities in materials under shock and spall

There has been a challenge for many decades to understand how heterogeneities influence the behavior of materials under shock loading, eventually leading to spall formation and failure. Experimental, analytical, and computational techniques have matured to the point where systematic studies of materials with complex microstructures under shock loading and the associated failure mechanisms are feasible. This is enabled by more accurate diagnostics as well as characterization methods. As interest in complex materials grows, understanding and predicting the role of heterogeneities in determining the dynamic behavior becomes crucial. Early computational studies, hydrocodes, in particular, historically preclude any irregularities in the form of defects and impurities in the material microstructure for the sake of simplification and to retain the hydrodynamic conservation equations. Contemporary computational methods, notably molecular dynamics simulations, can overcome this limitation by incorporating inhomogeneities albeit at a much lower length and time scale. This review discusses literature that has focused on investigating the role of various imperfections in the shock and spall behavior, emphasizing mainly heterogeneities such as second-phase particles, inclusions, and voids under both shock compression and release. Pre-existing defects are found in most engineering materials, ranging from thermodynamically necessary vacancies, to interstitial and dislocation, to microstructural features such as inclusions, second phase particles, voids, grain boundaries, and triple junctions. This literature review explores the interaction of these heterogeneities under shock loading during compression and release. Systematic characterization of material heterogeneities before and after shock loading, along with direct measurements of Hugoniot elastic limit and spall strength, allows for more generalized theories to be formulated. Further, continuous improvement toward time-resolved, in situ experimental data strengthens the ability to elucidate upon results gathered from simulations and analytical models, thus improving the overall ability to understand and predict how materials behave under dynamic loading.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multi-site reaction dynamics through multi-fragment density matrix embedding

The practical description of disordered chemical reactions, where the reactions involve multiple species at multiple sites, is presently a challenge using correlated electronic structure methods due to their high computational cost and steep scaling. Here, we describe the gradient theory of multi-fragment density matrix embedding theory, which potentially provides a minimal computational framework to model such processes at the correlated electron level. We present the derivation and implementation of the gradient theory, its validation on model systems and chemical reactions using density matrix embedding, and its application to a molecular dynamics simulation of proton transport in a small water cluster, a simple example of multi-site reaction dynamics.

Chemistry↗
DOE OSTI2024

Four-dimensional phase space tomography from one-dimensional measurements of a hadron beam

In this paper, we use one-dimensional measurements to infer the four-dimensional phase space density of an accumulated proton beam in the Spallation Neutron Source (SNS) accelerator. The reconstruction was performed by maximizing the distribution’s entropy subject to the measurement constraints and thus represents the most conservative inference from the data. The reconstructed distribution reproduces the measured profiles down to the noise level, and simulations indicate that the problem is reasonably well constrained. Similar measurements could serve as benchmarks for beam dynamics simulations in the SNS or hadron accelerators.

43 PARTICLE ACCELERATORS↗