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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Molecular Dynamics Simulation of the Structure and Properties of CaO-SiO{sub 2}-CaF{sub 2} Slag Systems

As a fundamental slag system in metallurgical processes, the CaO-SiO{sub 2}-CaF{sub 2} system, its properties, and related microstructures are of critical importance. The effect of the binary basicity and addition of CaF{sub 2} on the structure and viscosity of CaO-SiO{sub 2}-CaF{sub 2} slag were investigated using molecular dynamics simulations and Fourier transform infrared spectrometry. The average bond lengths of Si-O, Ca-O, and O-O were 1.61, 2.31, and 2.61 Å, respectively, and the coordinate number of Si remained constant. O-Si-O maintained an angle of 109.2, which was considered to be unaffected by the basicity changes. With increasing basicity, the network connectivity degrees Q{sup 3} and Q{sup 4} decreased, and the microstructure of the melt was significantly simpler. The effect of CaF{sub 2} on the depolymerization of the network structure was not obvious, and CaF{sub 2} acted mainly as a diluent. The calculations showed that the viscosity decreased upon setting up a ratio of nonbridging oxygen over tetrahedrally coordinated atoms (NBO/T). A good linear relationship was confirmed between the viscosity of the molten slag and the NBO/T.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

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

Structures of fluoride containing aluminosilicate low activity nuclear waste glasses: A molecular dynamics simulations study

Fluorine and other halides commonly exist in nuclear waste forms, and due to their volatile nature, halide retention poses an issue affecting waste loading during vitrification. The compositional effect on fluorine incorporation in aluminosilicate glasses is investigated through molecular dynamics simulations. Oxygen and fluorine coordination numbers around glass former and modifier cations, bond angle distributions, and medium range structure features such as Q n distributions, ring size distributions and neutron diffraction structure factors were calculated. It was found that fluorine has higher preference to bond to Ca 2+ than to Na + , both in the melt and the glass, and there is no Si-F bond formation in the glass but they do exist in the melt. Consequently, CaO for Na 2 O substitution can be an effective way to help fluorine retention without significantly changing the glass chemistry. Furthermore, these results thus provide insights on fluorine incorporation in the aluminosilicate nuclear waste glasses and the strategy on how to improve fluorine retention both in the glass and the melt.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles

Far from the static, idealized conformations deposited into structural databases, proteins are highly dynamic molecules that undergo conformational changes on temporal and spatial scales that may span several orders of magnitude. These conformational changes, often intimately connected to the functional roles that proteins play, may be obscured by traditional biophysical techniques. Over the past 40 years, molecular dynamics (MD) simulations have complemented these techniques by providing the “hidden” atomistic details that underlie protein dynamics. However, there are limitations of the degree to which molecular simulations accurately and quantitatively describe protein motions. Here we show that although four molecular dynamics simulation packages (AMBER, GROMACS, NAMD, and il mm) reproduced a variety of experimental observables for two different proteins (engrailed homeodomain and RNase H) equally well overall at room temperature, there were subtle differences in the underlying conformational distributions and the extent of conformational sampling obtained. This leads to ambiguity about which results are correct, as experiment cannot always provide the necessary detailed information to distinguish between the underlying conformational ensembles. Furthermore, the results with different packages diverged more when considering larger amplitude motion, for example, the thermal unfolding process and conformational states sampled, with some packages failing to allow the protein to unfold at high temperature or providing results at odds with experiment. While most differences between MD simulations performed with different packages are attributed to the force fields themselves, there are many other factors that influence the outcome, including the water model, algorithms that constrain motion, how atomic interactions are handled, and the simulation ensemble employed. Here four different MD packages were tested each using best practices as established by the developers, utilizing three different protein force fields and three different water models. Differences between the simulated protein behavior using two different packages but the same force field, as well as two different packages with different force fields but the same water models and approaches to restraining motion, show how other factors can influence the behavior, and it is incorrect to place all the blame for deviations and errors on force fields or to expect improvements in force fields alone to solve such problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective

The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. Furthermore, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Thermal conductivity of tungsten: Effects of plasma-related structural defects from molecular-dynamics simulations

We report results on the lattice thermal conductivities of tungsten single crystals containing nanoscale-sized pores or voids and helium (He) nanobubbles as a function of void/bubble size and gas pressure in the He bubbles based on molecular-dynamics simulations. For reference, we calculated lattice thermal conductivities of perfect tungsten single crystals along different crystallographic directions at room temperature and found them to be about 10% of the overall thermal conductivity of tungsten with a weak dependence on the heat flux direction. The presence of nanoscale voids in the crystal causes a significant reduction in its lattice thermal conductivity, which decreases with increasing void size. Filling the voids with He to form He nanobubbles and increasing the bubble pressure leads to further significant reduction of the tungsten lattice thermal conductivity, down to ~20% of that of the perfect crystal. The anisotropy in heat conduction remains weak for tungsten single crystals containing nanoscale-sized voids and He nanobubbles throughout the pressure range examined. Analysis of the pressure and atomic displacement fields in the crystalline region that surrounds the He nanobubbles reveals that the significant reduction of tungsten lattice thermal conductivity in this region is due to phonon scattering from the nanobubbles, as well as lattice deformation around the nanobubbles and formation of lattice imperfections at higher bubble pressure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1991

Gain in computational efficiency by vectorization in the dynamic simulation of multi-body systems

An improved technique for the identification and extraction of the exact quantities associated with the degrees of freedom at the element as well as the flexible body level is presented. It is implemented in the dynamic equations of motions based on the recursive formulation of Kane et al. (1987) and presented in a matrix form, integrating the concepts of strain energy, the finite-element approach, modal analysis, and reduction of equations. This technique eliminates the CPU intensive matrix multiplication operations in the code's hot spots for the dynamic simulation of the interconnected rigid and flexible bodies. A study of a simple robot with flexible links is presented by comparing the execution times on a scalar machine and a vector-processor with and without vector options. Performance figures demonstrating the substantial gains achieved by the technique are plotted.

Amirouche, F. M. L.↗
DOE OSTI2016

Homogeneous hydride formation path in α-Zr: Molecular dynamics simulations with the charge-optimized many-body potential

A formation path for homogeneous γ hydride formation in hcp α-Zr, from solid solution to the ζ and then the γ hydride, was demonstrated using molecular static calculations and molecular dynamic simulations with the charge-optimized many-body (COMB) potential. Hydrogen has limited solubility in α-Zr. Once the solubility limit is exceeded, the stability of solid solution gives way to that of coherent hydride phases such as the ζ hydride by planar precipitation of hydrogen. At finite temperatures, the ζ hydride goes through a partial hcp-fcc transformation via 1/3 <1¯100> slip on the basal plane, and transforms into a mixture of γ hydride and α-Zr. In the ζ hydride, slip on the basal plane is favored thermodynamically with negligible barrier, and is therefore feasible at finite temperatures without mechanical loading. The transformation process involves slips of three equivalent shear partials, in contrast to that proposed in the literature where only a single shear partial was involved. The adoption of multiple slip partials minimizes the macroscopic shape change of embedded hydride clusters and the shear strain accumulation in the matrix, and thus reduces the overall barrier needed for homogeneous γ hydride formation. In conclusion, this formation path requires finite temperatures for hydrogen diffusion without mechanical loading. Therefore, it should be effective at the cladding operating conditions.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

Experimental and molecular dynamics simulation study of structure of liquid and amorphous Ni 62 Nb 38 alloy

The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni 62 Nb 38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate the AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni–Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. We report the analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to T g and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni 62 Nb 38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Coarse-grained explicit-solvent molecular dynamics simulations of semidilute unentangled polyelectrolyte solutions

In this study, we present results from explicit-solvent coarse-grained molecular dynamics (MD) simulations of fully charged, salt-free, and unentangled polyelectrolytes in semidilute solutions. The inclusion of a polar solvent in the model allows for a more physical representation of these solutions at concentrations, where the assumptions of a continuum dielectric medium and screened hydrodynamics break down. The collective dynamic structure factor of polyelectrolytes, S(q, t), showed that at q > q*, where q* = 2π/ξ is the polyelectrolyte peak in the structure factor S(q) and ξ is the correlation length, the relaxation time obtained from fits to stretched exponential was $\tau$ KWW ~ q -3 , which describes unscreened Zimm-like dynamics. This is in contrast to implicit-solvent simulations using a Langevin thermostat where $\tau$ KWW ~ q -2 . At q < q*, a crossover region was observed that eventually transitions to another inflection point $\tau$ KWW ~ q -2 at length scales larger than ξ for both implicit- and explicit-solvent simulations. The simulation results were also compared to scaling predictions for correlation length, ξ ~ c$-½\atop{p}$, specific viscosity, η sp ~ c$½\atop{p}$, and diffusion coefficient, D ~ c$0\atop{p}$, where c p is the polyelectrolyte concentration. The scaling prediction for ξ holds; however, deviations from the predictions for η sp and D were observed for systems at higher c p , which are in qualitative agreements with recent experimental results. This study highlights the importance of explicit-solvent effects in molecular dynamics simulations, particularly in semidilute solutions, for a better understanding of polyelectrolyte solution behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations

Positional fluctuations of an atom in a protein can be described as motion in an effective local energy minimum created by the surrounding protein atoms. The dependence of atomic fluctuations on both temperature (T) and pressure (P) has been used to probe the nature of these minima, which are generally described as harmonic in experiments such as x-ray crystallography and neutron scattering. Here, a quasiharmonic analysis method is presented in which the P-T dependence of atomic fluctuations is in terms of an intrinsic isobaric thermal expansivity αP and an intrinsic isothermal compressibility κT. The method is tested on previously reported mean-square displacements from P-T molecular dynamics simulations of lysozyme, which were interpreted to have a pressure-independent dynamical transition Tg near 200 K and a change in the pressure dependence near 480 MPa. Our quasiharmonic analysis of the same data shows that the P-T dependence can be described in terms of αP and κT where below Tg, the temperature dependence is frozen at the Tg value. In addition, the purported transition at 480 MPa is reinterpreted as a consequence of the pressure dependence of Tg and the quasiharmonic frequencies. The former also indicates that barrier heights between substates are pressure dependent in these data. Furthermore, the insights gained from this quasiharmonic analysis, which was of the energy landscape near the native state of a protein, suggest that similar analyses of other simulations may be useful in understanding such phenomena as pressure-induced protein unfolding.

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

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

In this work, we describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.

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

Properties of Ti/TiC Interfaces from Molecular Dynamics Simulations

Titanium carbide is used as a primary component in coating materials, thin films for electronic devices, and composites. Here, the structure of coherent and semicoherent interfaces formed between close-packed TiC (111) and Ti (0001) is investigated in classical molecular dynamics simulations. The forces on the atoms in the simulations are determined using a newly developed TiC potential under the framework of the third-generation charge optimized many-body (COMB 3 ) suite of potentials. The work of adhesion energies for the coherent interfaces is calculated and compared with the predictions of density functional theory calculations. In the case of relaxed semicoherent interfaces, a two-dimensional (2D) misfit dislocation network is predicted to form that separates the interface into different regions in which the positions of the atoms are similar to the positions at the corresponding coherent interfaces. After the interface is annealed at an elevated temperature, the climb of edge dislocations is activated which modifies the 2D misfit dislocation network and increases the work of adhesion. These findings can be used as inputs for sequential larger simulation models to understand and predict the macroscopic properties of TiC/Ti interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquidlike motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally, the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall, our findings increase our understanding of the connection between molecular motions and diffraction data and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular Dynamics Simulation of Pore-Size Effects on Gas Adsorption Kinetics in Zeolites

Strong gas-mineral interactions or slow adsorption kinetics require a molecular-level understanding of both adsorption and diffusion for these interactions to be properly described in transport models. In this combined molecular simulation and experimental study, noble gas adsorption and mobility is investigated in two naturally abundant zeolites whose pores are similar in size (clinoptilolite) and greater than (mordenite) the gas diameters. Simulated adsorption isotherms obtained from grand canonical Monte Carlo simulations indicate that both zeolites can accommodate even the largest gas (Rn). However, gas mobility in clinoptilolite is significantly hindered at pore-limiting window sites, as seen from molecular dynamics simulations in both bulk and slab zeolite models. Further, experimental gas adsorption isotherms for clinoptilolite confirm the presence of a kinetic barrier to Xe uptake, resulting in the unusual property of reverse Kr/Xe selectivity. Finally, a kinetic model is used to fit the simulated gas loading profiles, allowing a comparison of trends in gas diffusivity in the zeolite pores.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Capacitance of Carbon Nanotube/Graphene Composite Electrodes with [BMIM + ][BF$_4^–$]/Acetonitrile: Fixed Voltage Molecular Dynamics Simulations

The capacitance of nanoporous carbon electrode materials is dictated by the physical interactions with electrolyte ions and molecules at the accessible interior electrode surface. While significant progress has been made in designing and synthesizing carbon materials with well-defined and relatively homogeneous nanoporosity, the majority of materials remain heterogeneous, and the resulting properties reflect an average over this distribution. In this regard, computer simulations can be a valuable tool to predict or validate structure/property relationships by systematically investigating well-defined, model electrode morphologies. In this work, we utilize fixed-voltage molecular dynamics simulations to predict structure/capacitance relationships for five different model morphologies of carbon nanotube/graphene (CNT/G) composite electrodes with 1-butyl-3-methylimidazolium tetrafluoroborate/acetonitrile electrolyte. The CNT/G electrode models are inspired by experimental “layer-by-layer” syntheses and strike a balance between realism and computational tractability. Comparison between different model electrode architectures elucidates important structure/property relationships. We find that CNT/graphene contact points serve as “hot spots” with significantly enhanced charge separation relative to the rest of the electrode. Furthermore, we demonstrate a specific nanoconfinement motif that provides substantial 3–4$\times$ enhancement of local capacitance, resulting in a ~40% increase of the total electrode differential capacitance. Because the accessible surface area of the model CNT/G electrodes is precisely determined, a comparison of per-area capacitance across systems is unambiguous. Our results thus complement a prior computational demonstration of capacitance enhancement in nanoconfinement while elucidating additional interaction motifs at CNT/G electrochemical interfaces.

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

Nano-crystallization and magnetic mechanisms of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy by ab initio molecular dynamics simulation

Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH{sub 3}F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. {sup 13}C NMR chemical shifts of a CH{sub 3}F/CH{sub 4}/TBME sH hydrate and a temperature analysis of the {sup 2}H NMR powder lineshapes of a CD{sub 3}F/THF sII and CD{sub 3}F/TBME sH hydrate, displayed evidence that the populations of CH{sub 4} and CH{sub 3}F in the D and D{sup ′} cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH{sub 3}F and TBME/CH{sub 4} sH hydrates showed that the presence of CH{sub 3}F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH{sub 3}F and THF/CH{sub 4} sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH{sub 3}F molecules between adjacent small cages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗