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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
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 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 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↗
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↗
DOE OSTI2023

Investigating structure and dynamics of unentangled poly(dimethyl- co -diphenyl)siloxane via molecular dynamics simulation

Polysiloxane is one of the most important polymeric materials in technological use. Polydimethylsiloxane displays glass-like mechanical properties at low temperatures. Incorporation of phenyl siloxane, via copolymerization for example, improves not only the low-temperature elasticity but also enhances its performance over a wide range of temperatures. Copolymerization with the phenyl component can significantly change the microscopic properties of polysiloxanes, such as chain dynamics and relaxation. However, despite much work in the literature, the influence of such changes is still not clearly understood. In this work, we systematically study the structure and dynamics of random poly(dimethyl- co -diphenyl)siloxane via atomistic molecular dynamics simulations. As the molar ratio Φ of the diphenyl component increases, we find that the size of the linear copolymer chain expands. At the same time, the chain-diffusivity slows down by over an order of magnitudes. In conclusion, the reduced diffusivity appears to be a result of a complex interplay between the structural and dynamic changes induced by phenyl substitution.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Self-Healing Nanomaterials: Multimillion-Atom Reactive Molecular Dynamics Simulations

Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH 3 NH 3 PbI 3 . Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH 3 NH 3 sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.

14 SOLAR ENERGY↗
NASA NTRS1996

Two-Dimensional Dynamic Simulation of a Continuous Foil Bearing

In this paper, the two dimensional(radial and circumferential) transient Navier-Stokes equations are used to solve the hydrodynamic problem in conjunction with the time dependent motion of the journal, and the deformable, spring supported foil. The elastic deformation of the foil and its supports are simulated by a finite element model. The time-dependent Navier-Stokes formulation is used to solve for the interaction between the fluid lubricant, the motion of the journal and the deformable foil boundary. The steady state, the quasi-transient and the full transient dynamic simulation of the foil-fluid journal interaction are examined on a comparative basis. For the steady state simulation, the fluid lubricant pressures are evaluated for a particular journal position, by means of an iterative scheme until convergence is achieved in both the fluid pressures and the corresponding foil deformation. For the quasi-transient case, the transient motion of the journal is calculated using a numerical integration scheme for the velocity and displacement of the journal. The deformation of the foil is evaluated through numerical iteration in feedback mode with the fluid film pressure generated by the journal motion until convergence at every time step is achieved. For the full transient simulation, a parallel real-time integration scheme is used to evaluate simultaneously the new journal position and the new deformed shape of the foil at each time step. The pressure of the fluid lubricant is iterated jointly with the corresponding journal position and the deformed foil geometry until convergence is achieved. A variable time-stepping Newmark-Beta integration procedure is used to evaluate the transient dynamics at each time step of the bearing.

Braun, M. Jack↗
DOE OSTI2021

Evaluation of Force Fields for Molecular Dynamics Simulations of Platinum in Bulk and Nanoparticle Forms

Here, understanding the size- and shape-dependent properties of platinum nanoparticles is critical for enabling the design of nanoparticle-based applications with optimal and potentially tunable functionality. Toward this goal, we evaluated nine different empirical potentials with the purpose of accurately modeling faceted platinum nanoparticles using molecular dynamics simulation. First, the potentials were evaluated by computing bulk and surface properties - surface energy, lattice constant, stiffness constants, and the equation of state - and comparing these to prior experimental measurements and quantum mechanics calculations. Then, the potentials were assessed in terms of the stability of cubic and icosahedral nanoparticles with faces in the {100} and {111} planes, respectively. Although none of the force fields predicts all the evaluated properties with perfect accuracy, one potential - the embedded atom method formalism with a specific parameter set - was identified as best able to model platinum in both bulk and nanoparticle forms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Assessing Melting and Solid–Solid Transition Properties of Choline Chloride via Molecular Dynamics Simulations

Choline chloride (ChCl) is used extensively as a hydrogen bond donor in deep eutectic solvents (DESs). However, determining its melting properties experimentally is challenging due to decomposition upon melting, leading to widely varying literature values. Accurate melting properties are crucial for understanding the solid–liquid phase behavior of ChCl-containing DESs. Here, we employ molecular dynamics simulations to compute the phase transitions of ChCl, testing a variety of atomistic force fields. We find that the results are sensitive to the choice of force field, but a melting temperature of 627 K and a melting enthalpy of 7.8 kJ/mol seem most reasonable, in good agreement with some literature values. Furthermore, we suggest these as the likely melting properties of ChCl, though the results are tentative due to limited experimental data for the liquid ChCl phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2017

Plausible Compositions of the Seven TRAPPIST-1 Planets Using Long-Term Dynamical Simulations

TRAPPIST-1 is a nearby ultra-cool dwarf that is host to a remarkable planetary system consisting of seven transiting planets. The orbital properties and radii of the planets have been well constrained, and recently, the masses of the inner six planets have been measured with additional ground- and space-based photometric observations. Large uncertainties in these mass measurements have prevented a robust analysis of the planetary compositions. Here, we perform many thousands of N-body dynamical simulations with planet properties perturbed from the observed values and identify those that are stable for millions of years. This allows us to identify self-consistent orbital solutions that can be used in future studies. From our range of dynamical masses, we find that most of the planets are consistent with an Earth-like composition, where TRAPPIST-1f is likely to have a volatile-rich envelope.

Quarles, B.↗
NASA NTRS2017

Plausible Compositions of the Seven TRAPPIST-1 Planets Using Long-Term Dynamical Simulations

TRAPPIST-1 is a nearby ultra-cool dwarf that is host to a remarkable planetary system consisting of seven transiting planets. The orbital properties and radii of the planets have been well constrained, and recently, the masses of the inner six planets have been measured with additional ground- and space-based photometric observations. Large uncertainties in these mass measurements have prevented a robust analysis of the planetary compositions. Here, we perform many thousands of N-body dynamical simulations with planet properties perturbed from the observed values and identify those that are stable for millions of years. This allows us to identify self-consistent orbital solutions that can be used in future studies. From our range of dynamical masses, we find that most of the planets are consistent with an Earth-like composition, where TRAPPIST-1f is likely to have a volatile-rich envelope.

B. Quarles↗
NASA NTRS2017

Plausible Compositions of the Seven TRAPPIST-1 Planets Using Long-Term Dynamical Simulations

TRAPPIST-1 is a nearby ultra-cool dwarf that is host to a remarkable planetary system consisting of seven transiting planets. The orbital properties and radii of the planets have been well constrained, and recently, the masses of the inner six planets have been measured with additional ground- and space-based photometric observations. Large uncertainties in these mass measurements have prevented a robust analysis of the planetary compositions. Here, we perform many thousands of N-body dynamical simulations with planet properties perturbed from the observed values and identify those that are stable for millions of years. This allows us to identify self-consistent orbital solutions that can be used in future studies. From our range of dynamical masses, we find that most of the planets are consistent with an Earth-like composition, where TRAPPIST-1f is likely to have a volatile-rich envelope.

B. Quarles↗
DOE OSTI2018

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models

Understanding protein conformational variability remains a challenge in drug discovery. The issue arises in protein kinases, whose multiple conformational states can affect the binding of small-molecule inhibitors. To overcome this challenge, we propose a comprehensive computational framework based on Markov state models (MSMs). Our framework integrates the information from explicit-solvent molecular dynamics simulations to accurately rank-order the accessible conformational variants of a target protein. We tested the methodology using Abl kinase with a reference and blind-test set. Only half of the Abl conformational variants discovered by our approach are present in the disclosed X-ray structures. We report the approach successfully identified a protein conformational state not previously observed in public structures but evident in a retrospective analysis of Lilly in-house structures: the X-ray structure of Abl with WHI-P154. Using a MSM-derived model, the free energy landscape and kinetic profile of Abl was analyzed in detail highlighting opportunities for targeting the unique metastable states.

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

Assessment of the impact of reactor residence time distribution on non-equilibrium product selectivity of polypropylene pyrolysis using reactive molecular dynamics simulations

Mass residence time distribution (RTD) is considered to be an important factor controlling the product selectivity in the pyrolysis of biomass and plastic wastes along with the pyrolysis chemistry. However, due to the complex pyrolysis chemistry of biomass and plastic waste, the coupling between the reaction chemistry, RTD, and product selectivity is challenging to understand. Here, we introduce a reaction molecular dynamics-based method to examine pyrolysis chemistry and species timescales to assess the impact of RTD on product selectivity and yield. To validate this method, reactive molecular dynamics simulations were conducted for polypropylene pyrolysis and its non-equilibrium product selectivity using 6 different RTDs. We find that the RTD and the reaction chemistry control the peak non-equilibrium product concentrations. The peak monomer (C 3 H 6 ) concentration during pyrolysis can be increased by up to 25 % by using a narrow RTD in the case of polypropylene pyrolysis. We also find that product selectivity is strongly affected by the average residence time and RTD. This coupling between the reaction chemistry, RTD, and product selectivity highlights the need to understand detailed reaction chemistry to control RTD and optimize non-equilibrium product selectivity during polymer and biomass pyrolysis. The present method provides a new way to design RTD for reactors to reach maximized product selectivity of plastic waste and biomass.

33 ADVANCED PROPULSION SYSTEMS↗