Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “MOLECULAR SIMULATION”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Effect of layer bending on montmorillonite hydration and structure from molecular simulation

Conceptual models of smectite hydration include planar (flat) clay layers that undergo stepwise expansion as successive monolayers of water molecules fill the interlayer regions. However, X-ray diffraction (XRD) studies indicate the presence of interstratified hydration states, suggesting non-uniform interlayer hydration in smectites. Additionally, recent theoretical studies have shown that clay layers can adopt bent configurations over nanometer-scale lateral dimensions with minimal effect on mechanical properties. Therefore, in this study we used molecular simulations to evaluate structural properties and water adsorption isotherms for montmorillonite models composed of bent clay layers in mixed hydration states. Results are compared with models consisting of planar clay layers with interstratified hydration states (e.g. 1W–2W). The small degree of bending in these models (up to 1.5 Å of vertical displacement over a 1.3 nm lateral dimension) had little or no effect on bond lengths and angle distributions within the clay layers. Except for models that included dry states, porosities and simulated water adsorption isotherms were nearly identical for bent or flat clay layers with the same averaged layer spacing. Similar agreement was seen with Na- and Ca-exchanged clays. In conclusion, while the small bent models did not retain their configurations during unconstrained molecular dynamics simulation with flexible clay layers, we show that bent structures are stable at much larger length scales by simulating a 41.6×7.1 nm 2 system that included dehydrated and hydrated regions in the same interlayer.

58 GEOSCIENCES↗
DOE OSTI2016

What can molecular simulation do for global warming?

Carbon capture is necessary to reduce CO 2 emissions from burning fossil fuels, which has led to global warming. Molecular simulations offer chemical insights and design principles for new separation media and for understanding the separation process. In this review, we summarize recent applications of simulation methods from ab initio and density functional theory to classical molecular dynamics and Grand canonical Monte Carlo in understanding ionic liquids and porous carbonaceous materials for CO 2 separation, especially the postcombustion CO 2 / N 2 separation. We highlight design and simulation of the porous two‐dimensional ( 2D ) materials as the highly selective membranes for CO 2 separation. Simulated structure–property relationships for the materials are discussed in connection to the corresponding chemisorption, physisorption, or membrane process. In chemisorption, the focus is on reducing the heat of reaction with CO 2 ; in physisorption, the key is to increase the binding strength via CO 2 ‐philic groups; in membrane process, the key is to increase solubility for ionic‐liquid membranes and to control pore size for 2D materials. Challenges and opportunities for simulating emerging materials are also discussed. WIREs Comput Mol Sci 2016, 6:173–197. doi: 10.1002/wcms.1241 This article is categorized under: Structure and Mechanism > Computational Materials Science Electronic Structure Theory > Density Functional Theory Molecular and Statistical Mechanics > Molecular Interactions

Tian, Ziqi↗
DOE OSTI2020

Predicting chemical reaction equilibria in molten carbonate fuel cells via molecular simulations

It has been recently suggested that hydroxide ions can be formed in the electrolyte of molten carbonate fuel cells when water vapor is present. The hydroxide can replace carbonate in transporting electrons across the electrolyte, thereby reducing the CO 2 separation efficiency of the fuel cell although still producing electricity. In this work, we obtain the equilibrium concentration of hydroxide in five molten alkali carbonate salts from molecular simulations. The results reveal that there can be a substantial amount of hydroxide in the electrolyte at low partial pressures of CO 2 . In addition, we find that the equilibrium concentration of molecular water dissolved in the electrolyte is over two orders of magnitude higher than that of CO 2 . Increasing the size and polarizability (or in other words reducing the “hardness”) of the cations present in the electrolyte can reduce the hydroxide fraction, but at the cost of lowering ionic conductivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)-Water Interface

The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces

As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and nanoporous materials, and (3) simple functional form which facilitates incorporation into a variety of simulation codes. Here, we review applications of Clayff to model bulk phases and interfaces not included in the original parameter set and recent modifications for modeling surface terminations such as hydroxylated nanoparticle edges. Overall, we conclude with a discussion of expectations for future developments.

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

Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Wettability of Two-Dimensional Carbon Allotropes from Molecular Simulations

Force-field Monte Carlo and Molecular Dynamics simulations are used to compare wetting behaviors of model carbon sheets mimicking neat graphene, its saturated derivative, graphane, and related planar allotropes penta-graphene, γ-graphyne, and ψ-graphene in contact with aqueous droplets or an aqueous film confined between parallel carbon sheets. Atomistic and area-integrated surface/water potentials are found to be essentially equivalent in capturing moderate differences between the wetting free energies of tested substrates. Despite notable differences in mechanical and electric properties of distinct allotropes, the predicted allotrope/water contact angles span a narrow window of weakly hydrophilic values. Contact angles in the range of 80 ± 10° indicate modest hydration repulsion incapable of competing with van der Waals attraction between carbon particles. Poor dispersibility in neat water is hence a common feature of studied materials.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Depletion of the Protein Hydration Shell with Increasing Temperature Observed by Small-Angle X-ray Scattering and Molecular Simulations

The hydration shell is an integral part of proteins since it plays key roles in conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remains less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp small-angle X-ray scattering (T-ramp SAXS) from 255 to 335 K with molecular simulations to demonstrate that the hydration shells of the IgG-binding domain of Protein G (GB3) and the villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T-ramp SAXS data and explicit-solvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive, depleting hydration shells. The depletion is caused not merely by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T-ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view of the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.

electron density↗
NASA NTRS2004

[Using Molecular Simulations to Understand Complex Nanoscale Dynamic Phenomena in Polymer Solutions]

The first half of the project concentrated on molecular simulation studies of the translocation of model molecules for single-stranded DNA through a nanosized pore. This has resulted in the publication, Translocation of a polymer chain across a nanopore: A Brownian dynamics simulation study, by Pu Tian and Grant D. Smith, JOURNAL OF CHEMICAL PHYSICS VOLUME 119, NUMBER 21 1 DECEMBER 2003, which is attached to this report. In this work we carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient) designed to mimic an electrostatic field. The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient). We focused on the latter case in our studies. Calculation of radius of gyration of the translocating chain at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tube-like pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied. Attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

Smith, Grant↗
DOE OSTI2021

Probing the thermodynamics and kinetics of ethylene carbonate reduction at the electrode–electrolyte interface with molecular simulations

Understanding the formation of the solid-electrolyte interphase (SEI) in lithium-ion batteries (LIBs) is an ongoing area of research due to its high degree of complexity and the difficulties encountered by experimental studies. Herein, we investigate the initial stage of SEI growth, the reduction reaction of ethylene carbonate (EC), from both a thermodynamic and kinetic approach with theory and molecular simulation. We employed both the potential distribution theorem (PDT) and the SMD implicit solvent model to EC solvation for the estimation of reduction potentials of Li$^+$, EC, and Li$^+$-solvating EC (s-EC), as well as reduction rate constants of EC and s-EC. We find that solvation effects greatly influence these quantities of interest, particularly the Li$^+$/Li reference electrode potential in EC solvent. Further, we also compute the inner- and outer-sphere reorganization energies for both EC and s-EC at the interface of liquid EC and a hydroxyl-terminated graphite surface, where total reorganization energies are predicted to be 76.6 and 88.9 kcal/mol, respectively. With the computed reorganization energies, we estimate reduction rate constants across a range of overpotentials and show that EC has a larger electron transfer rate constant than s-EC at equilibrium, despite s-EC being more thermodynamically favorable. Furthermore, this manuscript demonstrates how ion solvation effects largely govern the prediction of reduction potentials and electron transfer rate constants at the electrode-electrolyte interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a Quantum Drude Oscillator. • We present the first general implementation of Quantum Drude Oscillators in the molecular dynamics package QDO-MD. • We highlight the successful construction of a new, transferable molecular model of water: QDO-water. - Graphical abstract:.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Molecular Simulation of the Catalytic Regeneration of n BuLi through a Hydrometalation Route

Efficient regeneration of organolithium compounds is a challenging aspect in the process of novel organometathetical catalytic cycles. A new method for Mg production from seawater has been proposed that capitalizes on the rich chemistry of Grignard reagents. Based on a 3-step catalytic cycle with Cp2MClL catalyst (M=Ti, Zr and L select organic ligands), it requires the regeneration of nBuLi. The potential of the proposed approach is evaluated with density functional theory based molecular simulations. The results reveal that the high affinity of Li towards Cl and N results in the formation of alkanes, and the strong coupling of catalyst and BuLi leads to catalyst deactivation. To improve its catalytic performance, we proposed the use of a diamine co-catalyst and a modified catalyst with a ligand that does not contain N, which would help release BuLi from the vicinity of the catalyst. Ab inito molecular dynamics simulations at 298 K in explicit solvent (THF) were used to estimate the Gibb’s free energetics and equilibrium constants obtained from the vibrational density of states. The results show a marked improvement in the free-energetics with lower barriers towards the completion of the catalytic cycle and suppression of de-activation channels. M.-S. L. and B. P. M. were supported by the US Department of Energy (DOE), Advanced Research Projects Agency for Energy performed at the Pacific Northwest National Laboratory (PNNL). V.-A. G. and R. R. were supported by DOE, Office of Science, Office of Basic Energy Sciences-CGBS Catalysis Program. Computational resources were provided by PNNL Research Computing Cluster and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231.

Lee, Mal-Soon (ORCID:000000016851177X)↗
DOE OSTI2014

Determination of the thermodynamic correction factor of fluids confined in nano-metric slit pores from molecular simulation

The multi-component diffusive mass transport is generally quantified by means of the Maxwell-Stefan diffusion coefficients when using molecular simulations. These coefficients can be related to the Fick diffusion coefficients using the thermodynamic correction factor matrix, which requires to run several simulations to estimate all the elements of the matrix. In a recent work, Schnell et al. [“Thermodynamics of small systems embedded in a reservoir: A detailed analysis of finite size effects,” Mol. Phys. 110, 1069–1079 (2012)] developed an approach to determine the full matrix of thermodynamic factors from a single simulation in bulk. This approach relies on finite size effects of small systems on the density fluctuations. We present here an extension of their work for inhomogeneous Lennard Jones fluids confined in slit pores. We first verified this extension by cross validating the results obtained from this approach with the results obtained from the simulated adsorption isotherms, which allows to determine the thermodynamic factor in porous medium. We then studied the effects of the pore width (from 1 to 15 molecular sizes), of the solid-fluid interaction potential (Lennard Jones 9-3, hard wall potential) and of the reduced fluid density (from 0.1 to 0.7 at a reduced temperature T* = 2) on the thermodynamic factor. The deviation of the thermodynamic factor compared to its equivalent bulk value decreases when increasing the pore width and becomes insignificant for reduced pore width above 15. We also found that the thermodynamic factor is sensitive to the magnitude of the fluid-fluid and solid-fluid interactions, which softens or exacerbates the density fluctuations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structure analysis of simulated molecular clouds with the Δ-variance

Here, we employ the Δ-variance analysis and study the turbulent gas dynamics of simulated molecular clouds (MCs). Our models account for a simplified treatment of time-dependent chemistry and the non-isothermal nature of the gas. We investigate simulations using three different initial mean number densities of n 0 = 30, 100 and 300 cm -3 that span the range of values typical for MCs in the solar neighbourhood. Furthermore, we model the CO line emission in a post-processing step using a radiative transfer code. We evaluate Δ-variance spectra for centroid velocity (CV) maps as well as for integrated intensity and column density maps for various chemical components: the total, H 2 and 12 CO number density and the integrated intensity of both the 12 CO and 13 CO (J = 1 → 0) lines. The spectral slopes of the Δ-variance computed on the CV maps for the total and H 2 number density are significantly steeper compared to the different CO tracers. We find slopes for the linewidth–size relation ranging from 0.4 to 0.7 for the total and H 2 density models, while the slopes for the various CO tracers range from 0.2 to 0.4 and underestimate the values for the total and H 2 density by a factor of 1.5–3.0. We demonstrate that optical depth effects can significantly alter the Δ-variance spectra. Furthermore, we report a critical density threshold of 100 cm -3 at which the Δ-variance slopes of the various CO tracers change sign. We thus conclude that carbon monoxide traces the total cloud structure well only if the average cloud density lies above this limit.

79 ASTRONOMY AND ASTROPHYSICS↗
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↗