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Results for “Molecular Dynamics Simulations”

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 19 records
All sourcesNASA NTRSDOE OSTI
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 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 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 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 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 OSTI2019

Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations

Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon in a living organism. But this MD technique produces large-size and long-timescale data that are inherently high-dimensional and occupies many terabytes of data. Processing this immense amount of data in a meaningful way is becoming increasingly difficult. Therefore, specific dimensionality reduction algorithm using deep learning technique has been employed here to embed the high-dimensional data in a lower-dimension latent space that still preserves the inherent molecular characteristics i.e. retains biologically meaningful information. Subsequently, the results of the embedding models are visualized for model evaluation and analysis of the extracted underlying features. However, most of the existing visualizations for embeddings have limitations in evaluating the embedding models and understanding the complex simulation data. We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations. Our system enables exploration and discovery of meaningful and semantic embedding results and supports the understanding and evaluation of results by the quantitatively described features of the MD simulations (even without specific labels).

Chae, Junghoon↗
DOE OSTI2019

Transferable Kinetic Monte Carlo Models with Thousands of Reactions Learned from Molecular Dynamics Simulations

Molecular dynamics (MD) simulation of complex chemistry typically involves thousands of atoms propagating over millions of time steps, generating a wealth of data. Traditionally these data are used to calculate some aggregate properties of the system and then discarded, but we propose that these data can be reused to study related chemical systems. Using approximate chemical kinetic models and methods from statistical learning, we study hydrocarbon chemistries under extreme thermodynamic conditions. We discover that a single MD simulation can contain sufficient information about reactions and rates to predict the dynamics of related yet different chemical systems using kinetic Monte Carlo (KMC) simulation. Our learned KMC models identify thousands of reactions and run four orders of magnitude faster than MD. In conclusion, the transferability of these models suggests that we can viably reuse data from existing MD simulations to accelerate future simulation studies and reduce the number of new MD simulations required.

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

The alloying element dependence of the local lattice deformation and the elastic properties of Ni{sub 3}Al: A molecular dynamics simulation

Molecular dynamics (MD) together with the modified analytical embedded atom method (MAEAM) is employed to study the alloying elements (Re, Ru, Co, and Ta) dependence of the elastic properties of L1{sub 2}-Ni{sub 3}Al. The investigations indicate that the calculated elastic properties of Ni{sub 3}Al are in reasonable agreement with the previous results. The substituting formation energies of the alloying elements in Ni{sub 3}Al are calculated to determine the site preference. It is found out that Re, Ru, and Ta atoms prefer to occupy the Al sites, and the Co atom prefers to occupy the Ni site. Based on Re, Ru, and Ta substituting the 1st, 2nd, 3rd, and 4th nearest-neighbor atoms, we ascertain that the substituting manners of these alloying elements have a decisive effect on the bulk modulus and the local crystal lattice of Ni{sub 3}Al. Moreover, for Re, the bonding interaction plays a predominant role in the improvement in the bulk modulus of Ni{sub 3}Al, whereas the size effect of Ru and Ta on the improvement in the bulk modulus is more obvious. Finally, the potential reasons of which the alloying elements enhance the bulk modulus are discussed in details.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Structure, solvation, and dynamics of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: A molecular dynamics simulation study

Molecular dynamics simulations of complexes of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} with 3-hydroxyflavone (flavonol, 3HF) and ClO {sub 4}{sup −} in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations’ first solvation shells. Formation of the cation–3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg{sup 2+} is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca{sup 2+}, Sr{sup 2+}, and BaClO {sub 4}{sup +} with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg{sup 2+} with disrupted H-bonding. It was shown that additional stabilization of the [MgClO{sub 4}(3HF)]{sup +} and [BaClO{sub 4}(3HF)]{sup +} complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt{sup 2+} from one side and ClO {sub 4}{sup −}, 3HF, and AN in the cations’ coordination shell from another side implies quite weak interaction between cation, anion, and ligands in the investigated complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Mechanisms for hyperthermal polyatomic hydrocarbon modification of PMMA surfaces from molecular dynamics simulations

Classical molecular dynamics simulations are performed to determine the mechanisms by which hyperthermal hydrocarbon polyatomics, which are present in low-energy plasmas, chemically modify polymer surfaces. In particular, C 2 H, CH 3 , and C 3 H 5 are deposited on an amorphous poly (methyl methacrylate) (PMMA) substrate with kinetic energies of 4, 10, 25, and 50 eV and compared to the deposition of H at the same energies. The short-range forces on the atoms are determined using the second generation reactive empirical many-body potential, while the long-range forces are determined using a Lennard-Jones potential. The simulations predict that at all these incident energies, the chemical modification of the PMMA is limited to within a nanometer of the surface. Atoms, fragments, and incident polyatomics are further predicted to chemically attach to specific sites on the PMMA monomers at low energies and to attach to a wider range of sites at higher energies. However, no appreciable cross-linking between polymer chains is predicted to occur. Variation in the penetration depth of the deposited polyatomics or H is correlated to differences in their size and bond saturation. The greatest extent of chemical modification of the PMMA surface slab is achieved for C 2 H deposition with 50 eV of kinetic energy.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Predicting 1 H NMR relaxation in Gd 3+ -aqua using molecular dynamics simulations

Atomistic molecular dynamics simulations are used to predict 1 H NMR T 1 relaxation of water from paramagnetic Gd 3+ ions in solution at 25 °C. Simulations of the T 1 relaxivity dispersion function r 1 computed from the Gd 3+ – 1 H dipole–dipole autocorrelation function agree within ≃8% of measurements in the range f 0 ≃ 5 ↔ 500 MHz, without any adjustable parameters in the interpretation of the simulations, and without any relaxation models. Here the simulation results are discussed in the context of the Solomon-Bloembergen-Morgan inner-sphere relaxation model, and the Hwang-Freed outer-sphere relaxation model. Below f 0 ≲ 5 MHz, the simulation overestimates r 1 compared to measurements, which is used to estimate the zero-field electron-spin relaxation time. The simulations show potential for predicting r 1 at high frequencies in chelated Gd 3+ contrast-agents used for clinical MRI.

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

Interfaces of dicationic ionic liquids and graphene: a molecular dynamics simulation study

Molecular dynamics simulations were performed to investigate the interfacial structure and capacitance of electrical double layers (EDLs) in dicationic ionic liquids (DILs) 1-alkyl-3-dimethylimidazolium tetrafluoroborate [Cn(mim)2](BF4)2 (n = 3, 6, 9), with respect to a baseline of a monocationic ionic liquid [C3mim][BF4], near planar carbon electrodes consisting of graphene sheets. The simulation results show that an adsorbed layer with double peaks is exclusively found for [C3(mim)2](BF4)2, while a single peak of the other three cations is observed at the neutral electrode, due to the difference in ion–wall interaction and cation–anion association. As the electrode becomes negatively charged, the second peak of [C3(mim)2]2+ is dramatically reduced, whereas those of [C6(mim)2]2+ and [C9(mim)2]2+ become non-trivial. The capacitance–potential curve of EDLs in DILs manifests a transition from camel shape to bell shape as the cation chain length increases, which is attributed to the enlargement of ion adsorption (per unit charge) on the electrode and the decrease of attractive interaction between ions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations

Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.

BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗
DOE OSTI2023

Equation of state for He bubbles in W and model of He bubble growth and bursting near W{100} surfaces derived from molecular dynamics simulations

Abstract Molecular dynamics (MD) simulations are performed to derive an equation of state (EOS) for helium (He) bubbles in tungsten (W) and to study the growth of He bubbles under a W(100) surface until they burst. We study the growth as a function of the initial nucleation depth of the bubbles. During growth, successive loop-punching events are observed, accompanied by shifts in the depth of the bubble towards the surface. Subsequently, the MD data are used to derive models that describe the conditions that cause the loop punching and bursting events. Simulations have been performed at 500, 933, 1500, 2000, and 2500 K to fit the parameters in the models. To compute the pressure in the bubble at the loop punching and bursting events from the models, we derive an EOS for He bubbles in tungsten with an accompanying volume model to compute the bubble volume for a given number of vacancies ( $$N_\text {V}$$ N V ), He atoms ( $$N_\text {He}$$ N He ), and temperature ( T ). To derive the bubble EOS, we firstly derive the EOS for a free He gas. The derived free-gas EOS can accurately predict all MD data included in the analysis (which span up to 54 GPa at 2500 K). Subsequently, the bubble EOS is derived based on the free-gas EOS by correcting the gas density to account for the interaction between He and W atoms. The EOS for the bubbles is fitted to data from MD simulations of He bubbles in bulk W that span a wide range of gas density and sizes up to about 3 nm in diameter. The pressure of subsurface bubbles at the loop punching events as calculated using the bubble-EOS and the volume model agrees well with the pressure obtained directly from the MD simulations. In the loop punching model, for bubbles consisting of $$N_\text {V}$$ N V vacancies and $$N_\text {He}$$ N He helium atoms, the $$N_\text {He}/N_\text {V}$$ N He / N V ratio that causes the event, the resulting increase in $$N_\text {V}$$ N V , and the associated shift of the bubble depth are formulated as a function of $$N_\text {V}$$ N V and T . In the bursting model, a bubble must simultaneously reach a certain depth and $$N_\text {He}/N_\text {V}$$ N He / N V ratio in order to burst. The burst depth and $$N_\text {He}/N_\text {V}$$ N He / N V are also modeled as a function of $$N_\text {V}$$ N V and T . The majority of the loop punching events occur at bubble pressures between 20 and 60 GPa, depending on the bubble size and temperature. The larger the bubble and the higher the temperature, the lower the bubble pressure. Furthermore, our results indicate that at a higher temperature, a bubble can burst from a deeper region.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗