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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗
NASA NTRS1993

A fast recursive algorithm for molecular dynamics simulation

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

Jain, A.↗
DOE OSTI2022

Investigation of plasmon relaxation mechanisms using nonadiabatic molecular dynamics

Hot carriers generated from the decay of plasmon excitation can be harvested to drive a wide range of physical or chemical processes. However, their generation efficiency is limited by the concomitant phonon-induced relaxation processes by which the energy in excited carriers is transformed into heat. However, simulations of dynamics of nanoscale clusters are challenging due to the computational complexity involved. Here, in this paper, we adopt our newly developed Trajectory Surface Hopping (TSH) nonadiabatic molecular dynamics algorithm to simulate plasmon relaxation in Au 20 clusters, taking the atomistic details into account. The electronic properties are treated within the Linear Response Time-Dependent Tight-binding Density Functional Theory (LR-TDDFTB) framework. The relaxation of plasmon due to coupling to phonon modes in Au 20 beyond the Born–Oppenheimer approximation is described by the TSH algorithm. The numerically efficient LR-TDDFTB method allows us to address a dense manifold of excited states to ensure the inclusion of plasmon excitation. Starting from the photoexcited plasmon states in Au 20 cluster, we find that the time constant for relaxation from plasmon excited states to the lowest excited states is about 2.7 ps, mainly resulting from a stepwise decay process caused by low-frequency phonons of the Au 20 cluster. Furthermore, our simulations show that the lifetime of the phonon-induced plasmon dephasing process is ~10.4 fs and that such a swift process can be attributed to the strong nonadiabatic effect in small clusters. Our simulations demonstrate a detailed description of the dynamic processes in nanoclusters, including plasmon excitation, hot carrier generation from plasmon excitation dephasing, and the subsequent phonon-induced relaxation process.

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

Load-Displacement Relation and Gap Distribution Between Rough Surfaces: Partial Differential Equations Approach

We develop a theoretical model to predict the load-displacement relation and probability density function for gaps between contacting rough surfaces. We derive partial differential equations from the previous model (Joe et al., 2018), and extend them to the non-adhesive contact problem. The predictions of the present theory are compared with numerical results using the Green's function molecular dynamics algorithm, and a good agreement is obtained.

adhesion↗
DOE OSTI2025

Initial position optimization in molecular dynamics simulations for a Coulomb system

A new algorithm for molecular dynamics (MD) simulations is developed to optimize plasma particle distributions at given initial temperatures. By combining velocity scaling and reassignment, the method effectively eliminates the initial rise and oscillation in temperatures observed with randomly distributed positions. These rises and oscillations are undesired numerical artifacts observed in conventional plasma MD simulations, arising from unoptimized particle positions. The algorithm demonstrates temperature relaxation without initial rises or oscillations, as well as precise flow velocity relaxation, enabling accurate measurement of relaxation times. The code is accelerated using graphics processing units for parallel processing, enhancing the study of plasma dynamics. The proposed method for distributing physically valid particles in MD simulations enables accurate studies of intrinsic collision processes in plasmas, including the dynamics of strongly coupled plasmas, plasma–wave interactions, and transport phenomena in magnetized plasmas. The paper concludes with a discussion of potential applications and future enhancements to the algorithm.

Jo, Jawon (ORCID:0009000924193285)↗
NASA NTRS2017

Modeling Chemical Reactions in Classical Molecular Dynamics Simulations

An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.

Jacob R Gissinger↗
NASA NTRS2000

Annual Research Briefs - 2000: Center for Turbulence Research

This report contains the 2000 annual progress reports of the postdoctoral Fellows and visiting scholars of the Center for Turbulence Research (CTR). It summarizes the research efforts undertaken under the core CTR program. Last year, CTR sponsored sixteen resident Postdoctoral Fellows, nine Research Associates, and two Senior Research Fellows, hosted seven short term visitors, and supported four doctoral students. The Research Associates are supported by the Departments of Defense and Energy. The reports in this volume are divided into five groups. The first group largely consists of the new areas of interest at CTR. It includes efficient algorithms for molecular dynamics, stability in protoplanetary disks, and experimental and numerical applications of evolutionary optimization algorithms for jet flow control. The next group of reports is in experimental, theoretical, and numerical modeling efforts in turbulent combustion. As more challenging computations are attempted, the need for additional theoretical and experimental studies in combustion has emerged. A pacing item for computation of nonpremixed combustion is the prediction of extinction and re-ignition phenomena, which is currently being addressed at CTR. The third group of reports is in the development of accurate and efficient numerical methods, which has always been an important part of CTR's work. This is the tool development part of the program which supports our high fidelity numerical simulations in such areas as turbulence in complex geometries, hypersonics, and acoustics. The final two groups of reports are concerned with LES and RANS prediction methods. There has been significant progress in wall modeling for LES of high Reynolds number turbulence and in validation of the v(exp 2) - f model for industrial applications.

Source record↗
DOE OSTI2025

Energy-efficient, Large-scale Molecular Dynamics Simulations via Hardware- and Algorithm-level Optimization

This work aims to develop a framework for energy-efficient computing that will enable molecular dynamics (MD) simulations of large-scale phenomena with atomic precision and simultaneously remove computational bottlenecks limiting the speed of MD simulations. We seek to implement such an approach through the development of surrogate models for the interatomic force calculation combined with the use of mixed numerical precision formats. For a model system of neutral atoms (only pairwise interactions), significant force calculation efficiency improvements were achieved, without detrimental effects on atomic structures or average energies, using single precision, by developing a surrogate model (deep neural network), and by quantizing this surrogate model. For a model system of charged atoms, the reciprocal-space calculation of electrostatic interactions was identified as the main bottleneck, and the development of a surrogate model should be pursued to achieve an estimated one-order-of-magnitude additional speedup.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗
NASA NTRS1998

Observation and Modeling of Single Wall Carbon Nanotube Bend Junctions

Single wall carbon nanotube (SWNT) bends, with diameters from approx. 1.0 to 2.5 nm and bend angles from 18 deg. to 34 deg., are observed in catalytic decomposition of hydrocarbons at 600 - 1200 C. An algorithm using molecular dynamics simulation (MD) techniques is developed to model these structures that are considered to be SWNT junctions formed by topological defects (i.e. pentagon-heptagon pairs). The algorithm is used to predict the tube helicities and defect configurations for bend junctions using the observed tube diameters and bend angles. The number and arrangement of the defects at the junction interfaces are found to depend on the tube helicities and bend angle. The structural and energetic calculations using the Brenner potential show a number of stable junction configurations for each bend angle with the 34 deg. bends being more stable than the others. Tight binding calculations for local density of state (LDOS) and transmission coefficients are carried out to investigate electrical properties of the bend junctions.

Han, Jie↗
DOE OSTI2022

Exact Factorization Adventures: A Promising Approach for Non-Bound States

Modeling the dynamics of non-bound states in molecules requires an accurate description of how electronic motion affects nuclear motion and vice-versa. The exact factorization (XF) approach offers a unique perspective, in that it provides potentials that act on the nuclear subsystem or electronic subsystem, which contain the effects of the coupling to the other subsystem in an exact way. We briefly review the various applications of the XF idea in different realms, and how features of these potentials aid in the interpretation of two different laser-driven dissociation mechanisms. We present a detailed study of the different ways the coupling terms in recently-developed XF-based mixed quantum-classical approximations are evaluated, where either truly coupled trajectories, or auxiliary trajectories that mimic the coupling are used, and discuss their effect in both a surface-hopping framework as well as the rigorously-derived coupled-trajectory mixed quantum-classical approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

Menon, Madhu↗
DOE OSTI2023

Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects

We numerically investigate an adaptive version of the parareal algorithm in the context of molecular dynamics. This adaptive variant has been originally introduced in [1]. We focus here on test cases of physical interest where the dynamics of the system is modelled by the Langevin equation and is simulated using the molecular dynamics software LAMMPS. In this work, the parareal algorithm uses a family of machine-learning spectral neighbor analysis potentials (SNAP) as fine, reference, potentials and embedded-atom method potentials (EAM) as coarse potentials. We consider a self-interstitial atom in a tungsten lattice and compute the average residence time of the system in metastable states. Our numerical results demonstrate significant computational gains using the adaptive parareal algorithm in comparison to a sequential integration of the Langevin dynamics. We also identify a large regime of numerical parameters for which statistical accuracy is reached without being a consequence of trajectorial accuracy.

36 MATERIALS SCIENCE↗