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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural evolution in Au- and Pd-based metallic glass forming liquids and the case for improved molecular dynamics force fields

The results of a combined experimental and computational investigation of the structural evolution of Au 81 Si 19 , Pd 82 Si 18 , and Pd 77 Cu 6 Si 17 metallic glass forming liquids are presented. Electrostatically levitated metallic liquids are prepared, and synchrotron x-ray scattering studies are combined with embedded atom method molecular dynamics simulations to probe the distribution of relevant structural units. Metal–metalloid based metallic glass forming systems are an extremely important class of materials with varied glass forming ability and mechanical processibility. High quality experimental x-ray scattering data are in poor agreement with the data from the molecular dynamics simulations, demonstrating the need for improved interatomic potentials. The first peak in the x-ray static structure factor in Pd 77 Cu 6 Si 17 displays evidence for a Curie–Weiss type behavior but also a peak in the effective Curie temperature. In conclusion, a proposed order parameter distinguishing glass forming ability, 1/(S(T,q 1 )−1, shows a peak in the effective Curie temperature near a crossover temperature established by the behavior of the viscosity, T A .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗
DOE OSTI2023

Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects

We numerically investigate an adaptive version of the parareal algorithm in the context of molecular dynamics. This adaptive variant has been originally introduced in [1]. We focus here on test cases of physical interest where the dynamics of the system is modelled by the Langevin equation and is simulated using the molecular dynamics software LAMMPS. In this work, the parareal algorithm uses a family of machine-learning spectral neighbor analysis potentials (SNAP) as fine, reference, potentials and embedded-atom method potentials (EAM) as coarse potentials. We consider a self-interstitial atom in a tungsten lattice and compute the average residence time of the system in metastable states. Our numerical results demonstrate significant computational gains using the adaptive parareal algorithm in comparison to a sequential integration of the Langevin dynamics. We also identify a large regime of numerical parameters for which statistical accuracy is reached without being a consequence of trajectorial accuracy.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Polymers in Deep Eutectic Solvents

The project investigated the behavior of polymers in ionic liquids such as deep eutectic solvents using an array of techniques. These included the development of atomistic force fields, coarse graining these force fields to the united atom level, large scale molecular dynamics (MD) simulations using new thermostat algorithms, and machine learning (ML) methods for the phase behavior. The project demonstrated the feasibility and accuracy of first principles force fields for ionic liquids, deep-eutectic solvents, and urea-water mixtures. A novel hierarchical coarse graining method was then used to develop accurate and efficient united-atom models, using which microsecond simulations were performed for polymers in ionic liquids. These simulations were in quantitative agreement with experiment, thus resolving previous controversies. Methods were also developed to obtain the potential of mean force between complex ions in solution. Finally, supervised ML methods were developed for the phase behavior of polymers in ionic liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

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

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

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

Effect of Flexibility in Molecular Simulations of Carbon Dioxide Adsorption and Diffusion in a Cuprous Triazolate Framework

Using fixed atom force fields to model gas adsorption in flexible metal organic frameworks (MOFs) is known to pose difficulties in accurately reproducing and predicting experimental results. This paper studies the difference in accuracy between flexible and fixed atom force fields in reproducing CO 2 adsorption measurements in MAF-2 ([Cu(etz)]∞ (MAF-2, Hetz) 3,5-diethyl-1,2,4-triazole), an NbO-type triazolate scaffold with a bcu cavity system and attached ethyl groups. The flexible force field used to run the hybrid molecular dynamics and grand canonical Monte Carlo calculations were generated using the QuickFF software incorporating van der Waals parameters from the Universal Force Field (UFF) and density derived electrostatic and chemical (DDEC) charges. The fixed atom force field used was composed of UFF van der Waals parameters together with DDEC charges. The calculations were run at 298 K and at pressures of 0.1, 0.3, 0.5, 0.8, and 1 bar. It was observed that for this MOF the rigid force field overpredicted gas adsorption, whereas the flexible force field values closely matched experimental data. In the flexible structure, the freely moving ethyl groups of MAF-2 hindered adsorption, reducing the interaction energy between CO 2 and the N atoms of the triazolate framework as well as reducing the size of the largest cavity diameter. Here, the combination of these factors led to improved prediction of adsorption values with the flexible forcefield as compared to the rigid forcefield, demonstrating the need for modeling MOFs in a way more indicative of their behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗