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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Molecular Dynamics Simulations of Aldol Condensation Catalyzed by Alkylamine-Functionalized Crystalline Silica Surfaces

Molecular dynamics simulations are performed to investigate the cooperatively catalyzed aldol condensation between acetone and 4-nitrobenzaldehyde on alkylamine (or alkylenamine)-grafted silica surfaces, focusing on the mechanism of the catalytic activation of the acetone and 4-nitrobenzaldehyde by the acidic surface silanols followed by the nucleophilic attack of the basic amine functional group toward the activated reactant. From the analysis of the correlations between the catalytically active acid-base sites and reactants, it is concluded that the catalytic cooperativity of the acid-base pair can be affected by two factors: 1) the competition between the silanol and the amine (or enamine) to form a hydrogen bond with a reactant and 2) the flexibility of the alkylamine (or alkylenamine) backbone. Increasing the flexibility of the alkylamine facilitates the nucleophilic attack of the amine on the reactants. From the molecular dynamics simulations, it is found that C 3 propylamine and C 4 butylamine linkers exhibit the highest probability of reaction, which is consistent with the experimental observation that the activity of the aldol reaction on mesoporous silica depends on the length of alkylamine grafted on the silica surface. Furthermore, this simulation work serves as a pioneering study demonstrating how the molecular simulation approach can be successfully employed to investigate the cooperative catalytic activity of such bifunctional acid-base catalysts.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture

Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Effect of water on structure and dynamics of [BMIM][PF{sub 6}] ionic liquid: An all-atom molecular dynamics simulation investigation

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF{sub 6}]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

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

Adaptive variational quantum dynamics simulations with compressed circuits and fewer measurements

The adaptive variational quantum dynamics simulation (AVQDS) method performs real-time evolution of quantum states using automatically generated parametrized quantum circuits that often contain substantially fewer gates than Trotter circuits. Here we report an improved version of the method, which we call AVQDS(T), by porting the tiling efficient trial circuits with rotations implemented simultaneously technique. The algorithm adaptively adds layers of disjoint unitary gates to the ansatz circuit so as to keep the McLachlan distance, a measure of the accuracy of the variational dynamics, below a fixed threshold. Here we perform benchmark noiseless AVQDS(T) simulations of quench dynamics in local spin models and compare with an alternative adaptive variational approach on quantum resource requirement. Quantum dynamical simulations implementing realistic noise channels are also reported. Finally, we propose a way to substantially alleviate the measurement overhead of AVQDS(T) while maintaining high accuracy by synergistically integrating quantum circuit calculations on quantum processing units with classical calculations using, e.g., tensor networks to evaluate the quantum geometric tensor. We showcase that this approach enables AVQDS(T) to deliver more accurate results than simulations using a fixed ansatz of comparable final depth for a significant time duration with fewer quantum resources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Clustering effects in ionic polymers: Molecular dynamics simulations

Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Tensile testing of Fe and FeCr nanowires using molecular dynamics simulations

Using molecular dynamics, we have studied the behaviour of cylindrical [001]-oriented Fe and FeCr nanowires under uniaxial tensile strain with both an embedded atom method (EAM) and a Tersoff-like bond order potential. The mechanical properties were analysed and the deformation mechanism was studied and compared between the potentials. The effects of chromium content and size of the wire were studied. Both potentials show elongation by deformation twinning in the 〈111〉/(211) system resulting in a significantly stiffer and stronger [110]-axial nanowire. The pure iron nanowires are elastically softer than bulk iron and an addition of chromium has both a softening and weakening effect. The bond order potential shows a strong dependence on chromium concentration, while the dependence is considerably weaker for the EAM potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass: Insights from molecular dynamics simulations

We have carried out classical molecular dynamics simulations in order to get insight into the atomistic mechanisms of the deformation during nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass. In terms of the glass hardness, we have found that the primary factor affecting the decrease of hardness after irradiation is depolymerization rather than free volume, and we argue that this is a general trend applicable to other borosilicate glasses with similar compositions. We have analyzed the changes of the short- and medium-range structures under deformation and found that the creation of oxygen triclusters is an important mechanism in order to describe the deformation of highly polymerized borosilicate glasses and is essential in the understanding of the folding of large rings under stress. We have equally found that the less polymerized glasses present a higher amount of relative densification, while the analysis of bond-breaking during the nanoindentation has showed that shear flow is more likely to appear around sodium atoms. The results provided in this study can be proven to be useful in the interpretation of experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Ab initio molecular dynamics simulations of AlN responding to low energy particle radiation

Ab initio molecular dynamics simulations of low energy recoil events in wurtzite AlN have been performed to determine threshold displacement energies, defect production and evolution mechanisms, role of partial charge transfer during the process, and the influence of irradiation-induced defects on the properties of AlN. Here, the results show that the threshold displacement energies, E d , along the direction parallel to the basal planes are smaller than those perpendicular to the basal planes. The minimum E d values are determined to be 19 eV and 55 eV for N and Al atom, respectively, which occur along the [$\overline{11}20$] direction. In general, the threshold displacement energies for N are smaller than those for Al atom, indicating the N defects would be dominant under irradiation. The defect production mechanisms have been analyzed. It is found that charge transfer and redistribution for both the primary knock-on atom and the subsequent recoil atoms play a significant role in defect production and evolution. Similar to the trend in oxide materials, there is a nearly linear relationship between E d and the total amount of charge transfer at the potential energy peak in AlN, which provides guidance on the development of charge-transfer interatomic potentials for classic molecular dynamics simulations. Finally, the response behavior of AlN to low energy irradiation is qualitatively investigated. The existence of irradiation-induced defects significantly modifies the electronic structure, and thus affects the magnetic, electronic and optical properties of AlN. In conclusion, these findings further enrich the understanding of defects in the wide bandgap semiconductor of AlN.

36 MATERIALS 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 OSTI2014

The VENUS/NWChem Software Package. Tight Coupling Between Chemical Dynamics Simulations and Electronic Structure Theory

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling. The two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface which accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

chemical dynamics simulation↗
DOE OSTI2024

Kernel fusion in atomistic spin dynamics simulations on Nvidia GPUs using tensor core

In atomistic spin dynamics simulations, the time cost of constructing the space- and time-displaced pair correlation function in real space increases quadratically as the number of spins N, leading to significant computational effort. The GEMM subroutine can be adopted to accelerate the calculation of the dynamical spin-spin correlation function, but the computational cost of simulating large spin systems (>40000 spins) on CPUs remains expensive. In this work, we perform the simulation on the graphics processing unit (GPU), a hardware solution widely used as an accelerator for scientific computing and deep learning. Here we show that GPUs can accelerate the simulation up to 25-fold compared to multi-core CPUs when using the GEMM subroutine on both. To hide memory latency, we fuse the element-wise operation into the GEMM kernel using CUTLASS that can improve the performance by 26% ~ 33% compared to implementation based on cuBLAS. Furthermore, we perform the on-the-fly calculation in the epilogue of the GEMM subroutine to avoid saving intermediate results on global memory, which makes the large-scale atomistic spin dynamics simulation feasible and affordable.

97 MATHEMATICS AND COMPUTING↗
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↗
DOE OSTI2023

Efficient fully-coherent quantum signal processing algorithms for real-time dynamics simulation

Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the simulation of electronic dynamics, which plays an essential role in chemical reactions, non-equilibrium dynamics, and material design. These systems are time-dependent, which requires that the corresponding simulation algorithm can be successfully concatenated with itself over different time intervals to reproduce the overall coherent quantum dynamics of the system. In this paper, we quantify such simulation algorithms by the property of being fully-coherent: the algorithm succeeds with arbitrarily high success probability 1 − δ while only requiring a single copy of the initial state. Here we subsequently develop fully-coherent simulation algorithms based on quantum signal processing (QSP), including a novel algorithm that circumvents the use of amplitude amplification while also achieving a query complexity additive in time t, ln(1/δ), and ln(1/ϵ) for error tolerance ϵ: $Θ‖\mathscr{H}‖|t|+ln(1/ϵ)+ln(1/δ)$. Furthermore, we numerically analyze these algorithms by applying them to the simulation of the spin dynamics of the Heisenberg model and the correlated electronic dynamics of an H2 molecule. Since any electronic Hamiltonian can be mapped to a spin Hamiltonian, our algorithm can efficiently simulate time-dependent ab initio electronic dynamics in the circuit model of quantum computation. Accordingly, it is also our hope that the present work serves as a bridge between QSP-based quantum algorithms and chemical dynamics, stimulating a cross-fertilization between these exciting fields.

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

Reactive Molecular Dynamics Simulation of Kerogen Thermal Maturation and Cross-Linking Pathways

For this study, molecular dynamics simulations were performed with a ReaxFF reactive force field to investigate bond breaking and bond formation mechanisms during the early thermal maturation of kerogen and potential crosslinking pathways towards a three-dimensional (3D) quasi-infinite molecular network (crosslinked kerogen). Starting with small ensembles of high molecular mass models for immature type I Green River Shale kerogen (Kerogen 1-I), top of the oil window type II kerogen (Kerogen 2-L), and low maturity type III kerogen (Kerogen 3-L), low molecular mass species including H 2 O, H 2 S, C 2 H 4 , C 3 H 6 were produced as the maturities of the remaining kerogens increased. Highly reactive fragments, which are not detected in pyrolysis experiments, were also produced. Further, the crosslinking mechanism in the newly develop polymeric kerogen networks appears to be highly complex and it is influenced by the nature of the kerogen. Covalent —C—S—, —C—O— and —C—C— bonds are the primary crosslinks that structurally binds kerogen monomers together. The trends observed in the thermochemical transformation of kerogen and the kerogen crosslinking pathways are consistent with the theoretical and experimental studies reported in the scientific literature. The reactive force field molecular dynamics simulation provides a potentially valuable alternative approach to the development of a realistic 3D molecular network of kerogen. However, the conversion of kerogen molecules into a 3D molecular network was low.

02 PETROLEUM↗
DOE OSTI2023

The selective heating effect of microwave irradiation on a binary mixture of water and polyethylene oxide: a molecular dynamics simulation approach

In this study, we investigate the molecular mechanisms of a microwave-driven selective heating process by performing molecular dynamics simulations for three different systems including pure water, pure polyethylene oxide (PEO), and water-PEO mixed systems in the presence of a microwave with two different intensities of electric field such as 0.001 V/Å -1 and 0.01 V/Å -1 at a frequency of 100 GHz. First, from performing molecular dynamics simulations of CO and CO 2 in the presence of the microwave, it is confirmed that the molecular dipole moment is responsible for the rotational motion induced by the oscillating electric field. Second, by analyzing the MD simulations of the pure water system, we discover that the dipole moment of water exhibits a time lag with respect to the microwave. During the heating process, however, the temperature, kinetic, and potential energies increase synchronously with the oscillating electric field of the microwave, showing that the heating of the water system is caused by the molecular reaction of water to the microwave. Comparing the water-PEO mixed system to the pure water and pure PEO systems, the water-PEO mixed system has a higher heating rate than the pure PEO system but a lower heating rate than the pure water system. Therefore, we conclude that heating the water-PEO mixed system is driven by water molecules selectively activated by microwave irradiation. Furthermore, we also calculate the diffusion coefficients of water molecules and PEO chains by describing their mean square displacements, demonstrating that the diffusion coefficients are increased in the presence of microwaves for both water and PEO in pure and mixed systems. Lastly, during the microwave heating process, the structures of the water-PEO mixed system are altered as a function of the intensity of electric field, which is mainly driven by the response of water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?

Ensemble docking in drug discovery or chemical biology uses dynamical simulations of target proteins to generate binding site conformations for docking campaigns. We demonstrate that 600 ns molecular dynamics simulations of four G-protein-coupled receptors in their membrane environments generate ensembles of protein configurations that, collectively, are selected by 70–99% of the known ligands of these proteins. Thus, the process of ligand recognition by conformational selection can be reproduced by combining molecular dynamics and docking calculations. Clustering of the molecular dynamics trajectories, however, does not necessarily identify the protein conformations that are most often selected by the ligands.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Recovering position-dependent diffusion from biased molecular dynamics simulations

All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

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

Synthesis of formamide and related organic species in the interstellar medium via chemical dynamics simulations

We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion–molecule reactions in the gas phase were considered: NH{sub 3}OH{sup +}, NH{sub 2}OH{sub 2}{sup +}, H{sub 2}COH{sup +}, and NH{sub 4} {sup +} for the ions and NH{sub 2}OH, H{sub 2}CO, and NH{sub 3} for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH{sub 2}OH{sub 2}{sup +} + H{sub 2}CO reaction can produce an isomer, NH{sub 2}OCH{sub 2}{sup +}, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH{sub 2}CH{sub 2}{sup +}. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗