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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Understanding the mechanisms of amorphous creep through molecular simulation

Significance The individual and collective molecular displacements in an amorphous solid undergoing plastic deformation are simulated by an atomistic method that allows incremental motions to be observed over a time window of fractions of seconds. Because the timescale matches well with the conditions of experimental measurements, simulation details provide dynamical evidence for the fundamental mechanisms of amorphous creep. In particular, knowledge of the interplay between diffusion (flow) and mechanical deformation processes enables us to explain the stress and temperature behavior of the experimental data as well as the validity of model descriptions of molecular mechanisms in terms of spatially and temporally heterogeneous fluctuations.

42 ENGINEERING↗
DOE OSTI2025

A comparison of probabilistic generative frameworks for molecular simulations

Generative artificial intelligence is now a widely used tool in molecular science. Despite the popularity of probabilistic generative models, numerical experiments benchmarking their performance on molecular data are lacking. Here, in this work, we introduce and explain several classes of generative models, broadly sorted into two categories: flow-based models and diffusion models. We select three representative models: neural spline flows, conditional flow matching, and denoising diffusion probabilistic models, and examine their accuracy, computational cost, and generation speed across datasets with tunable dimensionality, complexity, and modal asymmetry. Our findings are varied, with no one framework being the best for all purposes. In a nutshell, (i) neural spline flows do best at capturing mode asymmetry present in low-dimensional data, (ii) conditional flow matching outperforms other models for high-dimensional data with low complexity, and (iii) denoising diffusion probabilistic models appear the best for low-dimensional data with high complexity. Our datasets include a Gaussian mixture model and the dihedral torsion angle distribution of the Aib9 peptide, generated via a molecular dynamics simulation. We hope our taxonomy of probabilistic generative frameworks and numerical results may guide model selection for a wide range of molecular tasks.

Artificial intelligence↗
DOE OSTI2015

Toward the understanding of hydration phenomena in aqueous electrolytes from the interplay of theory, molecular simulation, and experiment

We confront the microstructural analysis of aqueous electrolytes and present a detailed account of the fundamentals underlying the neutron scattering with isotopic substitution (NDIS) approach for the experimental determination of ion coordination numbers in systems involving both halides anions and oxyanions. We place particular emphasis on the frequently overlooked ion-pairing phenomenon, identify its microstructural signature in the neutron-weighted distribution functions, and suggest novel techniques to deal with either the estimation of the ion-pairing magnitude or the correction of its effects on the experimentally measured coordination numbers. We illustrate the underlying ideas by applying these new developments to the interpretation of four NDIS test-cases via molecular simulation, as convenient dry runs for the actual scattering experiments, for representative aqueous electrolyte solutions at ambient conditions involving metal halides and nitrates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Charge fluctuations from molecular simulations in the constant-potential ensemble

We revisit the statistical mechanics of charge fluctuations in capacitors. In constant-potential classical molecular simulations, the atomic charges of electrode atoms are treated as additional degrees of freedom which evolve in time so as to satisfy the constraint of fixed electrostatic potential for each configuration of the electrolyte. The present work clarifies the role of the overall electroneutrality constraint, as well as the link between the averages computed within the Born–Oppenheimer approximation and that of the full constant-potential ensemble. This allows us in particular to derive a complete fluctuation–dissipation relation for the differential capacitance, that includes a contribution from the charge fluctuations (around the charges satisfying the constant-potential and electroneutrality constraints) also present in the absence of an electrolyte. We provide a simple expression for this contribution from the elements of the inverse of the matrix defining the quadratic form of the fluctuating charges in the energy. We then illustrate numerically the validity of our results, and recover the expected continuum result for an empty capacitor with structureless electrodes at large inter-electrode distances. By considering a variety of liquids between graphite electrodes, we confirm that this contribution to the total differential capacitance is small compared to that induced by the thermal fluctuations of the electrolyte.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2009

The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

Hinkley, J.A.↗
DOE OSTI2023

Molecular Simulations of the Chain Length Dependent Adsorption of C7‐C14 n ‐Alkanes in ZIF‐8

Recent experiments show that the diffusivities of C8 and C10 n-alkanes in ZIF-8 are higher than those of C7 and C9, respectively. We investigated this unusual ‘odd-even' effect by simulating the adsorption of C7-C14 n-alkanes in ZIF-8 using hybrid Monte Carlo molecular simulations. The resultant adsorption isotherms, guest-host energies, isosteric heats, and chain length distributions are analyzed for trends among the n-alkanes. ZIF-8 cages filled with n-alkanes are characterized using a combination of image processing and data science to quantify the differences in packing that occur with chain length. In conclusion, results indicate that packing changes drastically from C7 to C8 and from C9 to C10, which is consistent with the diffusion trends previously reported in experiments.

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

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

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

Characterization of radiation damage in TiO 2 using molecular dynamics simulations

Molecular dynamics simulations are carried out to characterize irradiation effects in TiO 2 rutile, for wide ranges of temperatures (300–900 K) and primary knock-on atom (PKA) energies (1–10 keV). The number of residual defects decreases with increased temperature and decreased PKA energy, but is independent of PKA type. In the ballistic phase, more oxygen than titanium defects are produced, however, the primary residual defects are titanium vacancies and interstitials. Defect clustering depends on the PKA energy, temperature, and defect production. For some 10 keV PKAs, the largest cluster of vacancies at the peak of the ballistic phase and after annealing has up to ≈1200 and 100 vacancies, respectively. For the 10 keV PKAs at 300 K, the energy storage, primarily in residual Ti vacancies and interstitials, is estimated at 140–310 eV. It decreases with increased temperature to as little as 5–180 eV at 900 K. In conclusion, selected area electron diffraction patterns and radial distribution functions confirm that although localized amorphous regions form during the ballistic phase, TiO 2 regains full crystallinity after annealing.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Early age volume changes in metakaolin geopolymers: Insights from molecular simulations and experiments

The early age volume changes occurring during the geopolymerisation reaction are not sufficiently understood yet, due to shortage of experimental data and theoretical models. This work presents new results on chemical and autogenous deformation of sodium-activated geopolymers from metakaolin, focussing on the first 72 h of reaction. The results show that the geopolymers undergo early-age chemical expansion, not shrinkage. A model is proposed to explain the experimental result, leveraging recent advances from molecular simulations. The model predicts how the extent of chemical expansion is controlled by confined water in the molecular structure of the geopolymer. However, despite this underlying chemical expansion, geopolymer samples undergo autogenous shrinkage at the macroscale, which excludes self-desiccation as the origin of autogenous deformation. A better insight is gained by monitoring the kinetics of geopolymerisation using isothermal and differential calorimetry. Two kinetic regimes are identified, with apparent activation energies of approximately 90 kJ/mol and 70 kJ/mol. This suggests that two microscopic mechanisms concur to determine the early-age volume changes of geopolymer pastes.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Strengths and Weaknesses of Molecular Simulations of Electrosprayed Droplets

The origin and the magnitude of the charge in a macroion are critical questions in mass spectrometry analysis coupled to electrospray and other ionization techniques that transfer analytes from the bulk solution into the gaseous phase via droplets. In many circumstances, it is the later stages of the existence of a macroion in the containing solvent drop before the detection that determines the final charge state. Experimental characterization of small (with linear dimensions of several nanometers) and short-lived droplets is quite challenging. Molecular simulations in principle may provide insight exactly in this challenging for experiments regime. We discuss the strengths and weaknesses of the molecular modeling of electrosprayed droplets using molecular dynamics. We illustrate the limitations of the molecular modeling in the analysis of large macroions and specifically proteins away from their native states. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Advanced Potential Energy Surfaces for Molecular Simulation

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

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

Atomic Movies of Laser-Induced Structural and Phase Transformations from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations of laser-materials interactions are playing an important role in investigation of complex and highly non-equilibrium processes involved in short pulse laser processing and surface modification. This role is defined by the ability of MD simulations to reveal in-depth information on the structural and phase transformations induced by the laser excitation and, at the same time, to provide clear visual representations, or “atomic movies,” of laser-induced dynamic processes. This chapter provides a brief overview of recent progress in the description of laser coupling and relaxation of photo-excited states in metals, semiconductors, insulators and molecular systems within the general framework of the classical MD technique and presents several examples of MD simulations of laser melting, generation of crystal defects, photomechanical spallation, explosive boiling and molecular entrainment in laser ablation. Possible directions of future progress in atomistic modeling of laser-materials interactions and the potential role of MD simulations in the design of an integrated multiscale computational model capable of accounting for interrelations between processes occurring at different time- and length-scales are discussed.

Classical Molecular Dynamic↗
DOE OSTI2016

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that the fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.

42 ENGINEERING↗
DOE OSTI2017

A novel energy conversion based method for velocity correction in molecular dynamics simulations

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt

The homogeneous nucleation of crystals of the ionic liquid [dmim{sup +}][Cl{sup −}] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589–2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10{sup 10} cm{sup −3} s{sup −1} was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.

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

Assessing the Impact of Point Defects on Molecular Diffusion in ZIF-8 Using Molecular Simulations

Because defects are ubiquitous in materials, they may play an important role in affecting the performance of materials in practical applications. In this paper, we investigate the influence of point defects on the diffusion of molecules including water, hydrocarbons, and acid gases in zeolitic imidazolate framework-8 (ZIF-8) using molecular simulations. To make these simulations possible, we introduce a force field that extends previous descriptions of pristine ZIF-8 to include experimentally relevant point defects. In general, the point defects we examined increase the local hopping rate for molecular diffusion, suggesting that low concentrations of these defects will not dominate long-range molecular diffusion in ZIF-8.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗