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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

Structure of Boron Nitride Nanotubes: Tube Closing Vs. Chirality

The structure of boron nitride nanotubes is investigated using a generalized tight-binding molecular dynamics method. It is shown that dynamic relaxation results in a wavelike or "rippled" surface in which the B atoms rotate inward and the N atoms move outward, reminiscent of the surface relaxation of the III-V semiconductors. More importantly, the three different morphologies of the tube closing with flat, conical and amorphous ends, as observed in experiments, are shown to be directly related to the tube chiralities. The abundance of flat end tubes observed in experiments is, thus, shown to be an indication of the greater stability of "zig-zag" BN tubes over the "arm-chair" tubes under experimental conditions.

Srivastava, Deepak↗
NASA NTRS2000

Computer Modeling of the Earliest Cellular Structures and Functions

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

Pohorille, Andrew↗
NASA NTRS2006

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

Rodriquez-Gomez, D.↗
NASA NTRS2008

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Saether, E.↗
DOE OSTI2020

Fission Product Diffusion in Silicon Carbide: As Revealed by Computer Simulations and Experimental Measurements

The diffusion and release of fission products through silicon carbide in the tri-structural isotropic (TRISO) fuel particles remain unsolved for decades. The underlying mechanism is quite challenging to be determined. To help unveil the mysterious story, the current work applies molecular dynamics method to show the stability of silver, palladium, ruthenium and iodine as an interstitial and their atomic diffusion along coincident site lattice (CSL) boundary, especially ?3 grain boundary (GB). The major finding presents a much faster diffusion along GB than in bulk for all elements considered. The reasonably close estimate to experiments and simulations where available has confirmed the important role of grain boundary diffusion of Ag and Pd in SiC. However, the discrepancy addressed in Ag with measurements from fuel studies suggest a more complicated mechanism, which might be in correlation with high energy grain boundaries or the presence of crack. The subsequent characterization of Ru and I distribution in SiC-PyC-SiC diffusion couples, which have been ion irradiated at 900?C to 10 dpa and 20 dpa, has performed by secondary ion mass spectrometry (SIMS) analysis. The experiment measurements correlate well with the grain boundary diffusion by simulation, which provide further evidences that the grain boundary diffusion cannot be neglected once the fission products are accessible at the grain boundary.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Systems and methods for generating a molecular dynamic graded lattice structure and their application to additive manufacturing

Systems and methods for generating molecular dynamic graded lattice structures that can be used as infill for additively manufactured articles. Molecular dynamically generated lattice infill is based on force balancing a node distribution instead of a circle packing. Field data can be utilized to adjust the spacing of the node distribution according to a force balance equilibrium model that accounts for the field expected to be experienced by the article being additively manufactured. The resultant non-uniform honeycomb structures from force-balancing robustly and efficiently address the connection issues with traditional non-uniform lattice structures.

Kim, Seokpum↗
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↗
DOE OSTI2020

Method of information entropy for convergence assessment of molecular dynamics simulations

The lack of a reliable method to evaluate the convergence of molecular dynamics simulations has contributed to discrepancies in different areas of molecular dynamics. Here, the method of information entropy is introduced to molecular dynamics for stationarity assessment. The Shannon information entropy formalism is used to monitor the convergence of the atom motion to a steady state in a continuous spatial domain and is also used to assess the stationarity of calculated multidimensional fields such as the temperature field in a discrete spatial domain. It is demonstrated in this work that monitoring the information entropy of the atom position matrix provides a clear indicator of reaching steady state in radiation damage simulations, non-equilibrium molecular dynamics thermal conductivity computations, and simulations of Poiseuille and Couette flow in nanochannels. A main advantage of the present technique is that it is non-local and relies on fundamental quantities available in all molecular dynamics simulations. Unlike monitoring average temperature, the technique is applicable to simulations that conserve total energy such as reverse non-equilibrium molecular dynamics thermal conductivity computations and to simulations where energy dissipates through a boundary as in radiation damage simulations. The method is applied to simulations of iron using the Tersoff/ZBL splined potential, silicon using the Stillinger–Weber potential, and to Lennard–Jones fluid. Its applicability to both solids and fluids shows that the technique has potential for generalization to other areas in molecular dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
DOE OSTI2021

An Ab Initio Multiple Cloning Method for Non-Adiabatic Excited-State Molecular Dynamics in NWChem

The recently developed ab-initio multiple cloning (AIMC) approach based on the multicongurational Ehrenfest (MCE) method provides a powerful and accurate way of describing the excited-state dynamics of molecular systems. The AIMC method is a controlled approximation to non-adiabatic dynamics with a particular strength in the proper description of decoherence effects due to branching of vibrational wavepackets at a level crossing. In this work, we report a new implementation of the AIMC algorithm in the open source NWChem computational chemistry program. The framework combines linear-response time-dependent density functional theory with Ehrenfest mean-eld theory to determine the equations of motion for classical trajectories. The multi-dimensional wave function is decomposed into a superposition of Gaussian coherent states guided by Ehrenfest trajectories (i.e., MCE approach), which can clone with fully quantum mechanical amplitudes and phases. By using an efficient time-derivative based non-adiabatic coupling approach within the AIMC method, all observable are calculated on-the-y in the non-adiabatic molecular dynamics process. As a representative example, we apply our implementation to study the ultrafast photoinduced electronic and vibrational energy transfer in a pyridine molecule. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer are discussed. This new AIMC implementation provides a high-level non-adiabatic molecular dynamics framework for simulating photoexcited dynamics in complex molecular systems and experimentally relevant ultrafast spectroscopic probes, such as nonlinear coherent optical and X-ray signals.

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

Advancing material modeling in hydrocodes using a concurrent finite-element and molecular dynamics multiscale framework

We present a multiscale simulation framework that couples the finite-element method with molecular dynamics. Bypassing traditional equations of state (EOS) by using in-line atomistic simulations, the method offers the advantage of incorporating detailed microscale physics not easily represented with coarse-grained models. Coupling consistency with the continuum code is ensured through the use of lifting and restriction operators, in line with heterogeneous multiscale methods. The concurrent continuum-atomistic framework is validated through comparison with experimental results and conventional EOS models, and demonstrated in a shock-driven hydrodynamic flow simulation under extreme conditions. We further evaluate the framework's usability by comparing it to state-of-the-art EOS models of deuterium. A computational performance study reveals that the atomistic EOS evaluation is a feasible alternative to conventional approaches, and demonstrates a weak scaling of 99% efficiency. These results highlight the framework's potential for large-scale multiscale modeling across a broad range of materials and conditions.

Computer science↗
DOE OSTI2022

Nonadiabatic Molecular Dynamics Simulations Based on Time-Dependent Density Functional Tight-Binding Method

Nonadiabatic excited-state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamic (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. Here, the nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Further, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well that obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Towards sharp error analysis of extended Lagrangian molecular dynamics

The extended Lagrangian molecular dynamics (XLMD) method provides a useful framework for reducing the computational cost of a class of molecular dynamics simulations with constrained latent variables. The XLMD method relaxes the constraints by introducing a fictitious mass ε for the latent variables and solving a set of singularly perturbed ordinary differential equations. While favorable numerical performance of XLMD has been demonstrated in several different contexts in the past decade, mathematical analysis of the method remains scarce. Here, we propose the first error analysis of the XLMD method in the context of a classical polarizable force field model. While the dynamics with respect to the atomic degrees of freedom are general and nonlinear, the key mathematical simplification of the polarizable force field model is that the constraints on the latent variables are given by a linear system of equations. We prove that when the initial value of the latent variables is compatible in a sense that we define, XLMD converges as the fictitious mass ε is made small with $\mathscr{O}$(ε) error for the atomic degrees of freedom and with $\mathscr{O}$($\sqrt{ε}$) error for the latent variables, when the dimension of the latent variable d' is 1. Furthermore, when the initial value of the latent variables is improved to be optimally compatible in a certain sense, we prove that the convergence rate can be improved to $\mathscr{O}$(ε) for the latent variables as well. Numerical results verify that both estimates are sharp not only for d'=1, but also for arbitrary d'. In the setting of general d', we do obtain convergence, but with the non-sharp rate of $\mathscr{O}$($\sqrt{ε}$) for both the atomic and latent variables.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Generation of the TSL for Zirconium Hydrides from Ab Initio Methods

Zirconium hydride (ZrHx) is a moderator material used in TRIGA and other reactors that may exist in multiple phases with varying stoichiometry, which include the δ phase and the ϵ phase. Current ENDF/B-VIII.0 ZrHx thermal scattering law (TSL) evaluations do not distinguish between phases. These sub-libraries were generated with the LEAPR module of NJOY using historic phonon spectra derived from a central force model and assume incoherent elastic scattering for both bound hydrogen and zirconium, which neglects the effects of crystal structures important for scattering from zirconium bound in ZrHx. In this work, the TSLs for hydrogen and zirconium bound in δ-ZrHx and ϵ-ZrH2 were generated from phonon spectra derived from modern ab initio lattice dynamics methods and ab initio molecular dynamics. Subsequently, TSLs for hydrogen and zirconium in ZrHx and ZrH2 were generated using the Full Law Analysis Scattering System Hub (FLASSH) code. The built-in generalized coherent elastic routine was used to generate the previously neglected elastic contribution from zirconium for this material. The present TSLs provide both a re-evaluation of the current ZrH sub-libraries and expansion of the set of TSLs available for the examination of neutrons in systems with zirconium hydride, permitting explicit treatment of δ and ϵ phases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Scale translation yields insights into gas adsorption under nanoconfinement

This work describes a scale-translating simulation framework to investigate gas adsorption behavior in nanoconfined pores. The framework combines molecular simulations (MSs), equation of state (EoS), and lattice Boltzmann (LB) simulations. MSs reveal the physics of methane adsorption in nano-sized pores, where input values of fugacity coefficients are optimized based on EoS predictions. Then, an LB free-energy model, which incorporates a viral EoS, upscales intermolecular forces and estimates adsorption behavior via a proposed fluid–wall interaction model. Armed with the values of the LB interaction parameter as a function of pressure, the LB model is used to predict fluid behavior in irregular nanopores, and the results are validated against reference MS data. The LB model is then used to study adsorption behavior at a continuum scale in representative organic shale nanopores based on finely characterized Vaca Muerta shale samples. Furthermore, the results show that methane adsorption could significantly increase contained fluids by 10%–25% in pores smaller than 20 nm. However, in larger pores (40 nm to 90 nm), adsorption's impact diminishes to 2%–3%, suggesting sorption's negligible role beyond a 40 nm pore size.

74 ATOMIC AND MOLECULAR PHYSICS↗