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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Molecular dynamics simulation of vacancy and void effects on strain-induced martensitic transformations in Fe-50 at.% Ni model concentrated solid solution alloy

Strain-induced martensitic transformations can improve the strength and ductility of some face centered cubic (FCC) metals and alloys. Irradiation-induced defects such as vacancies, dislocation loops, and voids activate martensitic transformations over a wider range of mechanical loading conditions than in pristine material. Furthermore, the mechanisms underlying irradiation-enabled martensite transformations remain unclear. In this work, we use molecular dynamics simulations to study the effect of vacancies and voids on strain-induced martensitic transformations in a model concentrated solid solution alloy Fe-50 at.% Ni. It has been found that single vacancies have no resolvable effect on the transformation because they reduce the stacking fault energy by a relatively insignificant margin and do so only if the vacancy is located on the stacking fault plane. Voids, however, activate the martensite transformation through shear strain accumulation around the void due to dislocation pileup. The larger the void, the more pronounced this effect.

36 MATERIALS SCIENCE↗
NASA NTRS1983

Structural considerations for a software life cycle dynamic simulation model

This paper presents the results of a preliminary study into the prospects for simulating the software implementation and maintenance life cycle process, with the aim of producing a computerized tool for use by management and software engineering personnel in project planning, tradeoff studies involving product, environmental, situational, and technological factors, and training. The approach taken is the modular application of a 'flow of resource' concept to the systems dynamics simulation modeling technique. The software life cycle process is represented as a number of stochastic, time-varying, interacting work tasks that each achieves one of the project milestones. Each task is characterized by the item produced, the personnel applied, and the budgetary profile.

Tausworthe, R. C.↗
DOE OSTI2021

Molecular dynamics simulations of energy accommodation between gases and polymers for ultra-low thermal conductivity insulation

Determining the energy accommodation between gases and solids is essential to developing porous thermal insulation materials with ultra-low effective thermal conductivity that reduce energy use, greenhouse gas emissions, and fossil fuel consumption. The energy accommodation coefficients of most gases, however, have been rarely studied, especially with respect to solids that have relatively high thermal resistivity, e.g., polymers. Here, by using all-atom nonequilibrium molecular dynamics simulations, we reveal the accommodation coefficients of He, Ar, N 2 , and O 2 with polymers, mainly polystyrene. We find that their values are around 0.51, 0.72, 0.79, and 0.90, respectively, suggesting a critical reexamination of the commonly used theoretical maximum value of 1. We have also conducted experiments and validated the value for air, which is about 0.81. Such a change in accommodation coefficients can lead to a reduction of about 70%, 50%, 35%, and 20% in the thermal conductivity of He, Ar, N 2 , and O 2 gases in nano pores (below 100 nm) or at low pressures (below 1 millibar). With these new accommodation coefficients, we find that in a 10 nm pore with ambient pressure at 300 K, the gas thermal conductivity of He, Ar, N 2 , and O 2 in porous polystyrene can be as low as 9.7 × 10 –4 , 3.4 × 10 –4 , 7.3 × 10 –4 , and 8.5 × 10 –4 W·m –1 ·K –1 , respectively, which are two to three orders of magnitude lower than their bulk values, promising higher thermal resistivity of insulation materials. This work reveals the fundamental energy exchange between gases and polymers, providing important guidance for designing high-performance thermal insulation materials for various applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Non-equilibrium molecular dynamics simulation to evaluate the effect of confinement on fluid flow in silica nanopores

The flow of fluids in nano-confinement has applications in separations, water purification, medical systems and in the recovery of fluids in petroleum systems. It is believed that fluids do not obey continuum laws when flowing in nanopores (or in confinement). This paper attempts to shed light on various nano confinement effects such as fluid-wall interactions, pore size and molecular geometry, using molecular dynamic simulation. Here, water, hexane, and methanol flow behaviors were simulated for pore diameters ranging from 1 to 8 nm. In addition to the density analysis of the confined fluids, the fluid flows in saturated nanopores were simulated by the sectional flow method. Water and methanol molecules were completely stabilized in the 1 nm pore. Hexane molecules could not enter the 1 nm pore, due to geometric considerations. For the 2 – 8 nm pores, all fluids showed reduced flow rate compared to the Hagen–Poiseuille flow, due to an interfacial molecular layer stabilized at the pore surface. Flow reduction observed in these studies is contrary to significant flow enhancements observed for fluid flow in carbon nanotubes of similar dimensions. Water flow showed almost constant stick length for all the pore sizes. Methanol flow had the largest stick length. Hexane flow was reduced because of overcrowding of molecules at the pore surface. The effect of confinement diminished with an increase in pore diameter.

42 ENGINEERING↗
DOE OSTI2025

Sticking Coefficients of Fusion Reactor Impurities from Molecular Dynamics Simulations for the Design of Cryopumps

A cryopump can be utilized as an impurity removal component of a direct internal recirculation (DIR) system for the fusion fuel cycle. The DIR facilitates a low fuel inventory by continuously pumping unburnt fuel while removing impurities from the fusion exhaust stream. A cryopump can target multiple impurity species by maintaining a temperature lower than the gas triple-point temperature that promotes desublimation. The desublimation/condensation of gases in cryopumps can be characterized by the sticking coefficient, which is defined as the probability for a gas particle to stick to a (cryo-)surface upon collision. The sticking coefficient is one of the important design/operation parameters for cryopumps, and it depends on a variety of surface and gas properties. Here, in this study, molecular dynamics simulations were utilized to estimate the sticking coefficients of typical fusion gas impurity species N 2 , CO 2 , and CH 4 over a Cu surface for a range of gas temperatures and surface coverages. The molecular dynamics study showed that the sticking coefficients for gases decrease with an increase in gas temperature. The presence of a single full monolayer of condensate on the metallic surface showed an adverse effect on the sticking of gases; however the sticking improved with two full monolayers of condensate on the surface. The sticking of gases over the mixed condensate on a surface was more favorable than the condensate of the same species for N 2 and CH 4 , with an exception for CO 2 , which showed a decrease in sticking over the mixed condensate.

cryopump↗
DOE OSTI2018

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations

We present that borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. Lastly, the results shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Fast Li-Ion Transport in Amorphous Li 2 Si 2 O 5 : An Ab Initio Molecular Dynamics Simulation

The present study reports an ab-initio molecular dynamics (AIMD) simulation of ionic diffusion in the amorphous Li 2 Si 2 O 5 in a temperature range of 573–823 K. The results show that the amorphous Li 2 Si 2 O 5 is primarily a Li + conductor with negligible O 2- and Si 4+ contributions. The obtained activation energy of 0.47 eV for Li + diffusion is higher than Na + in the analogue amorphous Na 2 Si 2 O 5 , but close to other types of Li + conductors. The predicted Li + conductivity is on the order of 10 -2 S·cm -1 at 623–823 K. Our simulations also reveal that Li + in the amorphous Li 2 Si 2 O 5 diffuses via a hopping mechanism between the nearest sites in the channels formed by two adjacent SiO 4 layers.

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

Molecular Dynamics Simulations Reveal a Novel Mechanism for ATP Inhibition of Insulin Degrading Enzyme

Regulation of brain levels of the Amyloid-β 42 (Aβ42) polypeptide by IDE has recently been linked with possible routes for new therapies against Alzheimer’s disease (AD). One important aspect is the regulatory mechanism of IDE by ATP, which is an IDE activator in degrading small peptides and an inhibitor in degrading larger peptides, such as Aβ42. This relationship was investigated in this study. We present molecular dynamics simulations of Aβ42 complexed with IDE, in the absence or presence of either ATP or excess Na + and Cl – ions. Results suggest a previously unreported inhibition mechanism that depends on charge-induced structural modifications in the active site and interactions simultaneously involving ATP, Aβ42, and IDE. Such interactions exist only when both ATP and Aβ42 are simultaneously present in the catalytic chamber. This mechanism results in allosteric, noncompetitive inhibition with apparent decrease of substrate affinity, in accordance with experiment.

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

The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

Pruitt, Spencer R.↗
DOE OSTI2015

HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

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

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H) -ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

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

Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator

RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Homogeneous states in driven granular mixtures: Enskog kinetic theory versus molecular dynamics simulations

The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The combined action of both forces attempts to model the interaction of the mixture with a bath or surrounding fluid. The problem is studied by means of two independent and complementary routes. First, the Enskog kinetic equation with a Fokker-Planck term describing interactions of particles with thermostat is derived. Then, a scaling solution to the Enskog kinetic equation is proposed where the dependence of the scaled distributions φ{sub i} of each species on the granular temperature occurs not only through the dimensionless velocity c = v/v{sub 0} (v{sub 0} being the thermal velocity) but also through the dimensionless driving force parameters. Approximate forms for φ{sub i} are constructed by considering the leading order in a Sonine polynomial expansion. The ratio of kinetic temperatures T{sub 1}/T{sub 2} and the fourth-degree velocity moments λ{sub 1} and λ{sub 2} (which measure non-Gaussian properties of φ{sub 1} and φ{sub 2}, respectively) are explicitly determined as a function of the mass ratio, size ratio, composition, density, and coefficients of restitution. Second, to assess the reliability of the theoretical results, molecular dynamics simulations of a binary granular mixture of spheres are performed for two values of the coefficient of restitution (α = 0.9 and 0.8) and three different solid volume fractions (ϕ = 0.00785, 0.1, and 0.2). Comparison between kinetic theory and computer simulations for the temperature ratio shows excellent agreement, even for moderate densities and strong dissipation. In the case of the cumulants λ{sub 1} and λ{sub 2}, good agreement is found for the lower densities although significant discrepancies between theory and simulation are observed with increasing density.

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

Investigating Alkylsilane Monolayer Tribology at a Single-Asperity Contact with Molecular Dynamics Simulation

Chemisorbed monolayer films are known to possess favorable characteristics for nanoscale lubrication of micro- and nanoelectromechanical systems (MEMS/NEMS). Prior studies have shown that the friction observed for monolayer-coated surfaces features a strong dependence on the geometry of contact. Specifically, tip-like geometries have been shown to penetrate into monolayer films, inducing defects in the monolayer chains and leading to plowing mechanisms during shear, which result in higher coefficients of friction (COF) than those observed for planar geometries. In this work, we use molecular dynamics simulations to examine the tribology of model silica single-asperity contacts under shear with monolayer-coated substrates featuring various film densities. It is observed that lower monolayer densities lead to reduced COFs, in contrast to results for planar systems where COF is found to be nearly independent of monolayer density. This is attributed to a liquid-like response to shear, whereby fewer defects are imparted in monolayer chains from the asperity, and chains are easily displaced by the tip as a result of the higher free volume. This transition in the mechanism of molecular plowing suggests that liquid-like films should provide favorable lubrication at single-asperity contacts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2010

Method of Obtaining High Resolution Intrinsic Wire Boom Damping Parameters for Multi-Body Dynamics Simulations

The goal of NASA's Magnetospheric MultiScale (MMS) mission is to understand magnetic reconnection with sensor measurements from four spinning satellites flown in a tight tetrahedron formation. Four of the six electric field sensors on each satellite are located at the end of 60- meter wire booms to increase measurement sensitivity in the spin plane and to minimize motion coupling from perturbations on the main body. A propulsion burn however, might induce boom oscillations that could impact science measurements if oscillations do not damp to values on the order of 0.1 degree in a timely fashion. Large damping time constants could also adversely affect flight dynamics and attitude control performance. In this paper, we will discuss the implementation of a high resolution method for calculating the boom's intrinsic damping, which was used in multi-body dynamics simulations. In summary, experimental data was obtained with a scaled-down boom, which was suspended as a pendulum in vacuum. Optical techniques were designed to accurately measure the natural decay of angular position and subsequently, data processing algorithms resulted in excellent spatial and temporal resolutions. This method was repeated in a parametric study for various lengths, root tensions and vacuum levels. For all data sets, regression models for damping were applied, including: nonlinear viscous, frequency-independent hysteretic, coulomb and some combination of them. Our data analysis and dynamics models have shown that the intrinsic damping for the baseline boom is insufficient, thereby forcing project management to explore mitigation strategies.

Yew, Alvin G.↗
DOE OSTI2021

Cavity molecular dynamics simulations of vibrational polariton-enhanced molecular nonlinear absorption

We report recent experiments have observed that the chemical and photophysical properties of molecules can be modified inside an optical Fabry– Pérot microcavity under collective vibrational strong coupling (VSC) conditions, and such modification is currently not well understood by theory. In an effort to understand the origin of such cavity-induced phenomena, some recent studies have focused on the effect of the cavity environment on the nonlinear optical response of the molecular subsystem. Here, we use a recently proposed protocol for classical cavity molecular dynamics simulations to numerically investigate the linear and the nonlinear response of liquid carbon dioxide under such VSC conditions following an optical pulse excitation. We find that applying a strong pulse of excitation to the lower hybrid light–matter state, i.e., the lower polariton (LP), can lead to an overall molecular nonlinear absorption that is enhanced by up to two orders of magnitude relative to the excitation outside the cavity. This polariton-enhanced multiphoton absorption also causes an ultrashort LP lifetime (0.2 ps) under strong illumination. Unlike usual polariton relaxation processes—whereby polaritonic energy transfers directly to the manifold of singly excited vibrational dark states—under the present mechanism, the LP transfers energy directly to the manifold of higher vibrationally excited dark states; these highly excited dark states subsequently relax to the manifold of singly excited states with a lifetime of tens of ps. Because the present mechanism is generic in nature, we expect these numerical predictions to be experimentally observed in different molecular systems and in cavities with different volumes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the equivalence of nonequilibrium and equilibrium measurements of slip in molecular dynamics simulations

Here, we show that nonequilibrium and equilibrium measurements of slip are consistent, provided the hydrodynamic wall location associated with the equilibrium measurement is properly taken into account. The latter is a strong function of the fluid state and wall-fluid interaction and cannot be neglected as it typically has been. Our results are based on an alternative approach for calculating the hydrodynamic wall location which alleviates most of the difficulties associated with its calculation via a Green-Kubo integral that appear to have contributed to its neglect. Extensive molecular dynamics simulations are used to validate our approach including a model for calculating the slip length that does not involve a Green-Kubo integral.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗