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Results for “Dynamical 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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2016

Molecular dynamics simulations reveal that water diffusion between graphene oxide layers is slow

Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 14% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. As a result, slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Proton radiation effects in indium oxide using cascade molecular dynamics simulations

Metal oxide (MO) semiconductors, characterized by their wide band gaps and notable charge transport properties, are promising candidates for electronic applications in extreme environments, including near-Earth space. However, atomistic simulations of radiation–matter interactions in MOs remain challenging due to the limitations of existing interatomic potentials, which often fail to capture both the short-range repulsive forces essential for radiation damage modeling and the long-range electrostatic effects governing defect evolution. In this work, we develop a customized interatomic potential tailored for radiation damage simulations in indium oxide (In 2 O 3 ) as a model system, a representative MO material. Our potential integrates the Ziegler-Biersack-Littmark potential to accurately describe short-range interactions with Buckingham and Coulombic potentials to account for long-range forces. We perform molecular dynamics simulations of low-energy proton irradiation using this custom potential. We employ the primary knock-on atom (PKA) cascade method to study atomic displacements and primary defect formation. Simulations were conducted for 1 keV proton irradiation in four randomly chosen directions, and PKA-driven defect analyses at 5, 10, and 15 keV to examine the effects of direction and energy level on damage generation. Our results provide insight into the impact of irradiation direction and energy level on the cascade evolution and defect formation mechanisms.

Atomistic simulations↗
DOE OSTI2019

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Significance A major challenge in biology is characterizing the structural flexibility of intrinsically disordered proteins (IDPs). Ensemble-averaged experimental data do not provide the underlying protein structures. Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. We report that enhancing the sampling of the simulations can generate an ensemble of IDP structures in quantitative agreement with scattering and NMR, without the need for biasing the simulation or reweighting the results. The demonstration of established simulation technology that produces accurate physical models of flexible biosystems may pave the way to relating conformational flexibility to biological function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Molecular dynamics simulation of radiation damage in CaCd{sub 6} quasicrystal cubic approximant up to 10 keV

Due to the peculiar nature of the atomic order in quasicrystals, examining phase transitions in this class of materials is of particular interest. Energetic particle irradiation can provide a way to modify the structure locally in a quasicrystal. To examine irradiation-induced phase transitions in quasicrystals on the atomic scale, we have carried out molecular dynamics simulations of collision cascades in CaCd{sub 6} quasicrystal cubic approximant with energies up to 10 keV at 0 and 300 K. The results show that the threshold energies depend surprisingly strongly on the local coordination environments. The energy dependence of stable defect formation exhibits a power-law dependence on cascade energy, and surviving defects are dominated by Cd interstitials and vacancies. Only a modest effect of temperature is observed on defect survival, while irradiation temperature increases lead to a slight increase in the average size of both vacancy clusters and interstitial clusters.

36 MATERIALS SCIENCE↗
DOE OSTI2013

The liquid surface of chiral ionic liquids as seen from molecular dynamics simulations combined with intrinsic analysis

We present molecular-level insight into the liquid/gas interface of two chiral room-temperature ionic liquids (RTILs) derived from 1-n-butyl-3-methylimidazolium bromide ([bmim][Br]); namely, (R)-1-butyl-3-(3-hydroxy-2-methylpropyl)imidazolium bromide (hydroxypropyl) and 1-butyl-3-[(1R)-nopyl]imidazolium bromide (nopyl). We use our currently developed force field which was validated against the experimental bulk density, heat of vaporization, and surface tension of [bmim][Br]. The force field for the RTILs adopts the Chemistry at Harvard Molecular Mechanics (CHARMM) parameters for the intramolecular and repulsion-dispersion interactions along with the reduced partial atomic charges based on ab initio calculations. The net charges of the ions are around ±0.8e, which mimic the anion to cation charge transfer and many-body effects. Molecular dynamics simulations in the slab geometry combined with the intrinsic interface analysis are employed to provide a detailed description of the RTIL/gas interface in terms of the structural and dynamic properties of the interfacial, sub-interfacial, and central layers at a temperature of 300 K. The focus is on the comparison of the liquid/gas interface for the chiral RTILs with the interface for parent [bmim][Br]. The structure of the interface is elucidated by evaluating the surface roughness, intrinsic atomic density profiles, and orientation ordering of the cations. The dynamics of the ions at the interfacial region is characterized by computing the survival probability, and normal and lateral self-diffusion coefficients in the layers.

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

Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin

Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. Additionally, the functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response. We recently initiated the biophysical and dynamical investigation of several vertebrate RNase homologs and observed that clustering residue dynamics appear to be linked with the phylogeny and biological specificity of several members. Here we report the 1 H, 13 C and 15 N backbone resonance assignments of human EDN (RNase 2) and its molecular dynamics simulation on the microsecond timescale, providing means to pursue this comparative atomic-scale functional and dynamical analysis by NMR and computation over multiple time frames.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Nanoporous silica gel structures and evolution from reactive force field-based molecular dynamics simulations

Nanoporous silica-rich gel formed on silicate glass surfaces during dissolution in aqueous environment is critical in elucidating the corrosion mechanisms and the long-term residual dissolution behaviors. Silica gel models were created using two types of methods with reactive force field-based molecular dynamics simulations. The results show that the remnant silica gels created from the ISG bulk structure have a more isolated and closed pore morphology and slightly higher glass network connectivity. This contrasts with the gel structures created by hydrogarnet defect formation that exhibit more connected pore morphologies. The remnant gel structures show lower water diffusivity which was explained by the nano-confinement effect of water molecules due to frequent interactions of water molecules with adjacent silica walls and the more isolated pore morphology in the remnant gel structures. These results reveal the complexity in terms of micro and atomic structures of these silica gels, and both structure features have impact on water transport in the gel layer hence the passivating effect that controls the long-term dissolution behavior of these glasses.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Molecular dynamics simulations of evaporation-induced nanoparticle assembly

While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present large scale molecular dynamics simulations of the evaporation-induced assembly of nanoparticles suspended in a liquid that evaporates in a controlled fashion. The quality of the nanoparticle crystal formed just below the liquid/vapor interface is found to be better at relatively slower evaporation rates, as less defects and grain boundaries appear. This trend is understood as the result of the competition between the accumulation and diffusion times of nanoparticles at the liquid/vapor interface. When the former is smaller, nanoparticles are deposited so fast at the interface that they do not have sufficient time to arrange through diffusion, which leads to the prevalence of defects and grain boundaries. Our results have important implications in understanding assembly of nanoparticles and colloids in non-equilibrium liquid environments.

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

Preparation, temperature dependent structural, molecular dynamics simulations studies and electrochemical properties of LiFePO{sub 4}

Highlights: • LiFePO{sub 4} compound was prepared by carbothermal reduction method. • In-situ XRD studies were carried out on LiFePO{sub 4} at various temperatures. • Dedicated imperial potentials used to explain the variation of lattice constants. • It exhibited reversible capacity of 140 (±5) mAh g{sup −1}, stable up to 400 cycles. - Abstract: LiFePO{sub 4} was prepared using carbothermal reduction method. In-situ temperature dependent structural studies were carried using X-ray diffraction. Molecular dynamics simulations were conducted for the LiFePO{sub 4} using empirical potentials developed using bond valence approach to investigate the structural variations. Electrochemical behaviour of LiFePO{sub 4} was evaluated using cyclic voltammetry and galvanostatic cycling studies at room temperature. Charge–discharge cycling studies showed a reversible capacities 140 (±5) mAh g{sup −1} at the end of 50th cycle and these capacity values were stable up to 400 cycles and almost nil capacity fade between 50 and 400 cycles, showing excellent capacity retention, low capacity fading. The cyclic voltammetry studies showed a main cathodic and anodic redox peaks at 3.34 and 3.5 V vs. Li, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Reactive Molecular Dynamics Simulations of the Atomic Oxygen Impact on Epoxies with Different Chemistries

Atomic oxygen (AO) is one of the most abundant species present in the lower earth orbit and is responsible for the aggressive degradation of polymers used in spacecraft structures. In this investigation, we use ReaxFF reactive force field molecular dynamics simulations to evaluate the disintegration of several different thermosetting epoxy polymers subjected to hypervelocity AO impact. Our simulations indicate that epoxy with aromatic curative displays higher resistance to the AO impact because of its stable benzene functionality. Decreased cross-linking density and increased simulation temperature both lead to faster disintegration of the polymer. Our simulation results indicate that ReaxFF force field simulations can be a useful tool to evaluate the response of various thermosetting epoxies to AO impact and identify promising candidate materials for spacecraft applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1989

Six-degree-of-freedom aircraft simulation with mixed-data structure using the applied dynamics simulation language, ADSIM

A realistic simulation of an aircraft in the flight using the AD 100 digital computer is presented. The implementation of three model features is specifically discussed: (1) a large aerodynamic data base (130,00 function values) which is evaluated using function interpolation to obtain the aerodynamic coefficients; (2) an option to trim the aircraft in longitudinal flight; and (3) a flight control system which includes a digital controller. Since the model includes a digital controller the simulation implements not only continuous time equations but also discrete time equations, thus the model has a mixed-data structure.

Savaglio, Clare↗
DOE OSTI2014

Lenard-Balescu calculations and classical molecular dynamics simulations of electrical and thermal conductivities of hydrogen plasmas

Here, we present a discussion of kinetic theory treatments of linear electrical and thermal transport in hydrogen plasmas, for a regime of interest to inertial confinement fusion applications. In order to assess the accuracy of one of the more involved of these approaches, classical Lenard-Balescu theory, we perform classical molecular dynamics simulations of hydrogen plasmas using 2-body quantum statistical potentials and compute both electrical and thermal conductivity from out particle trajectories using the Kubo approach. Our classical Lenard-Balescu results employing the identical statistical potentials agree well with the simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1998

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

Srivastava, Deepak↗
DOE OSTI2023

Molecular Dynamics Simulations of Calcite Fracture in Water

Calcite (CaCO 3 ) is one of the most common minerals in geologic and engineered systems. It is often in contact with aqueous solutions, causing chemically assisted fracture that is critical to understanding the stability of subsurface systems and manmade structures. Calcite fracture was evaluated with reactive molecular dynamics simulations, including the impacts of crack tip geometry (notch), the presence of water, and surface hydroxyl groups. Chemo-mechanical weakening was assessed by comparing the loads where fracture began to propagate. Our analyses show that in the presence of a notch, the load at which crack growth begins is lower, compared to the effect of water or surface hydroxyls. Additionally, the breaking of two adjacent Ca–O bonds is the kinetic limitation for crack initiation, since transiently broken bonds can reform, not resulting in crack growth. In aqueous environments, fresh (not hydroxylated) calcite surfaces exhibited water strengthening. Manual addition of H + and/or OH – species on the (104) calcite surface resulted in chemo-mechanical weakening of calcite by 9%. Achieving full hydroxylation of the calcite surface was thermodynamically and kinetically limited, with only 0.17–0.01 OH/nm 2 surface hydroxylation observed on the (104) surface at the end of the simulations. In conclusion, the limited reactivity of pure water with the calcite surface restricts the chemo-mechanical effects and suggests that reactions between physiosorbed water and localized structural defects may be dominating the chemo-mechanical process in the studies where water weakening has been reported.

Calcite↗
DOE OSTI2023

Molecular dynamics simulations of fission gas xenon (Xe) diffusion at UO 2 grain-boundaries (Rev.1)

The diffusivity of fission gas xenon (Xe) at UO 2 grain-boundaries is one of the most important parameters in mechanistic modeling of fission gas diffusion in UO 2 based nuclear fuels. In this report, we use molecular dynamics simulations to investigate the Xe diffusivity in UO 2 grain-boundaries, employing the many-body potential developed by Cooper, Rushton and Grimes for UO 2 . Three different types of grain-boundaries are investigated, twist Σ5, tilt Σ5, and a random grain-boundary. Diffusion activation energies in the range of 0.39 – 1.46 eV are obtained for the Xe diffusivity. Comparison to results for the uranium vacancy diffusivity from MD simulations employing the same methodology suggests a weak to moderate attractive Xe-uranium vacancy binding energy depending on the grain-boundary type.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗