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Results for “Cluster Dynamics Simulations”

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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Tycho: Realistically Simulating Exoplanets within Stellar Clusters. I. Improving the Monte Carlo Approach

To fully understand the diverse population of exoplanets, we must study their early lives within open clusters, the birthplace of most stars with masses >0.5M {sub ⊙} (including those currently in the field). Indeed, when we observe planets within clustered environments, we notice highly eccentric and odd systems that suggest the importance of dynamical pathways created by interactions with additional bodies (as in the case of HD 285507b). However, it has proven difficult to investigate these effects, as many current numerical solvers for the multi-scale N-body problem are simplified and limited in scope. To remedy this, we aim to create a physically complete computational solution to explore the role of stellar close encounters and interplanetary interactions in producing the observed exoplanet populations for both open cluster stars and field stars. We present a new code, Tycho, which employs a variety of different computational techniques, including multiple N-body integration methods, close encounter handling, modified Monte Carlo scattering experiments, and a variety of empirically informed initial conditions. We discuss the methodology in detail, and its implementation within the AMUSE software framework. Approximately 1% of our systems are promptly disrupted by star-star encounters contributing to the rogue planets occurrence rate. Additionally, we find that close encounters which that perturb long-period planets lead to 38.3% of solar-system-like planetary systems becoming long-term unstable.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

An ab initio exciton model for singlet fission

Here we present an ab initio exciton model that extends the Frenkel exciton model and includes valence, charge-transfer, and multiexcitonic excited states. It serves as a general, parameter-free, yet computationally efficient and scalable approach for simulation of singlet fission processes in multichromophoric systems. A comparison with multiconfigurational methods confirms that our exciton model predicts consistent energies and couplings for the pentacene dimer and captures the correct physics. Calculations of larger pentacene clusters demonstrate the computational scalability of the exciton model and suggest that the mixing between local and charge-transfer excitations narrows the gap between singlet and multiexcitonic states. Local vibrations of pentacene molecules are found to facilitate singlet–multiexcitonic state-crossing and hence are important for understanding singlet fission. The exciton model developed in this work also sets the stage for further implementation of the nuclear gradients and nonadiabatic couplings needed for first principles nonadiabatic quantum molecular dynamics simulations of singlet fission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1988

On the collapse and violent relaxation of protoglobular clusters

During the formation of stellar systems such as globular clusters, low-mass subcondensations which eventually form stars must retain a geometric size throughout the collapse process that is small compared to the characteristic distance separating them. If the local velocity dispersion of the subcondensations is small, the overall dimension of the system can decrease substantially before reaching a dynamical equilibrium state. The maximum collapse factor is deduced by examining the growth of the velocity dispersion and the spread in arrival times at the origin caused by local and global fluctuations. It is shown, analytically as well as in a series of N-body simulations, that the maximum reduction in the characteristic dimension of a system of N fragments with an initial homogeneous distribution subject to N exp 1/2 fluctuations is proportional to N exp 1/3. Direct physical collisions between low-mass subcondensations are therefore unlikely to occur in protoglobular clusters. The results are discussed in the context of fragmentation and violent relaxation.

Aarseth, S. J.↗
DOE OSTI2022

Guanosine Dianions Hydrated by One to Four Water Molecules

Intermolecular interactions as those present in molecule…water complexes may profoundly influence the physico-chemical properties of molecules. Here, we carried out an experimentally-computational study on the doubly-deprotonated guanosine monophosphate…water clusters, [dGMP-2H] 2- •nH 2 O (n=1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations. Successive addition of water molecules to [dGMP-2H] 2- increases the experimental adiabatic detachment (ADE) and vertical detachment energy (VDE) by 0.5 to 0.1 eV, depending on the cluster size. In order to choose the representative conformations, we combined MD simulations with a clustering procedure to identify low energy geometries for which ADEs and VDEs were computed at the CAM-B3LYP/6-31++G(d,p) level. Our results demonstrate that the assumed approach lead to the sound geometries and energetics of the studied micro-solvates since the calculated ADEs and VDEs are in pretty good agreement with the experimental characteristics. The evolution of hydrogen bonding with cluster size indicates possibility of the occurrence of proton transfer for clusters comprising a larger number of water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

ACDC (Automated Campbell Diagram Code) [SWR-26-042]

This application provides a web-based graphical user interface to generating Campbell Diagrams and visualizing mode shapes for OpenFAST turbine models. Determining the aeroelastic stability and dynamic characteristics of wind turbines is a critical step in turbine design and analysis. Historically, extracting natural frequencies and mode shapes from OpenFAST—the industry-standard whole-turbine simulation code—has been a fragmented and tedious process. It required manual model configuration, command-line linearization execution, and complex post-processing via proprietary scripts to handle rotating-frame dynamics. To address these workflow bottlenecks, we present the Automated Campbell Diagram Code (ACDC), an open-source graphical software tool developed by the National Laboratory of the Rockies (NLR) under the DOE-funded Distributed Wind Aeroelastic Modeling (dWAM) project. ACDC streamlines the end-to-end linearization and stability analysis workflow into a single, intuitive cross-platform application. The software guides users through OpenFAST model configuration, definition of operating points, and the automated execution of steady-state trim and linearization simulations. Under the hood, ACDC automates the complex mathematical post-processing steps required for rotating systems, including Multi-Blade Coordinate (MBC) transformations, eigenanalysis, and advanced modal tracking utilizing the Modal Assurance Criterion (MAC) and spectral clustering. Finally, ACDC processes these results to automatically generate Campbell diagrams and features a robust 3D visualization engine to animate full-system mode shapes. By eliminating the reliance on external post-processing environments and manual data manipulation, ACDC significantly accelerates dynamic analysis and lowers the barrier to entry for wind energy researchers and engineers.

Summerville, Brent [National Laboratory of the Roc↗
DOE OSTI2025

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle, ↗
DOE OSTI2020

Simulations and symmetries

ABSTRACT We investigate the range of applicability of a model for the real-space power spectrum based on N-body dynamics and a (quadratic) Lagrangian bias expansion. This combination uses the highly accurate particle displacements that can be efficiently achieved by modern N-body methods with a symmetries-based bias expansion which describes the clustering of any tracer on large scales. We show that at low redshifts, and for moderately biased tracers, the substitution of N-body-determined dynamics improves over an equivalent model using perturbation theory by more than a factor of two in scale, while at high redshifts and for highly biased tracers the gains are more modest. This hybrid approach lends itself well to emulation. By removing the need to identify haloes and subhaloes, and by not requiring any galaxy-formation-related parameters to be included, the emulation task is significantly simplified at the cost of modelling a more limited range in scale.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Phase evolution in two-phase alloys during severe plastic deformation

Herein, phase evolution in FCC metals with strongly interacting alloy components during severe plastic deformation is investigated using molecular dynamics simulations. Specifically, we study the alloy microstructure in steady state, nucleation and growth of precipitates in supersaturated alloys, and the decomposition of precipitates in undersaturated alloys. The results are compared to a modified effective temperature model, providing a physical understanding for the atomic processes underlying the model and a perspective on its strengths and weaknesses. Key observations in this work are nucleation and growth of precipitates during SPD at a temperature of 100 K; Gibbs-Thomson-like behavior relating solubility to precipitate size under steady-state shearing; a direct relationship between the effective temperature and the shear modulus; and the importance of cluster agglomeration during precipitate growth. The study also reveals that the mechanisms of forced chemical mixing depends on precipitate size, adding complications for effective temperature models describing inhomogeneous systems. The simulations are shown to provide good semiquantitative agreement with experimental findings reported in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2022

ParFlow-CLM model simulation files for Maina et al., Journal of Hydrology, 2022

This dataset contains the files to run a ParFlow-CLM integrated hydrologic model simulation for Maina et al., HESS, 2022. It also contains the associated daily pressure output of those simulations. Simulations are for a hillslope-similarity approach based on seasonal groundwater changes in the East River, Colorado. Comparisons are made to different clustering, or functional zonation approaches. We assess the ability of these clustering approaches to identify and categorize hillslopes with similar static characteristics, hydroclimate, land surface processes, and subsurface dynamics in a mountainous watershed. ParFlow binary files (.pfb) are model specific, and can be modified/viewed with conversion to .sa, .silo, or .vtk file formats. ParFlow input scripts are in the .tcl file format. Associated post-processing scripts are included as .f90 files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Defect cluster and nonequilibrium gas bubble associated growth in irradiated UMo fuels – a cluster dynamics and phase field model

Irradiation examination shows that gas bubble swelling kinetics is much faster after irradiation-induced recrystallization than that prior recrystallization in UMo fuels. It implies that gas bubbles in coarse grains and small recrystallized grains have different growth behavior. In this work, a phase-field model of gas bubble evolution integrating microstructure dependent cluster dynamics has been developed, for the first time, to study the gas bubble swelling behavior in the recrystallization zone of UMo fuels. Generation, diffusion, reaction, sink, emission and clustering of vacancies and interstitials are described by the cluster dynamics model while a phase-field model is used to describe the evolution of non-equilibrium gas bubbles including nucleation and growth. With the coupled model, the effect of defect generation rate, clustering rate, interstitial emission and sink rates on grain boundaries on the gas bubble evolution are systematically simulated. A set of model parameters (defect generation rate, clustering rate, interstitial emission and sink rates) is determined by comparing measured and simulated gas bubble swelling kinetics. The results demonstrate that interstitial clustering is one of the important physical mechanisms which results in a fast gas bubble swelling kinetics in the recrystallization zone. The developed model can also be extended to study the associated growth of defect and second phase precipitates often observed in irradiated materials.

Hu, Shenyang↗
DOE OSTI2023

Computational insights into the interaction of water with the UiO-66 metal–organic framework and its functionalized derivatives

The UiO-66 metal–organic framework (MOF) has been identified as a promising hydrophilic material for water harvesting. Recent studies show that its water uptake ability at low relative humidity (RH) can be improved by incorporating hydrophilic functional groups into the framework. In this work, we provide computational insights into the adsorption of water in UiO-66 and its functionalized derivatives to reveal the role played by different adsorption sites and functional groups in the adsorption mechanism. We started by developing molecular models for UiO-66, UiO-66-NH 2 , UiO-66-OH, and UiO-66-(OH) 2 compatible with the MB-pol data-driven many-body potential of water. We then benchmarked these models against ab initio data. Here we used these models to perform molecular dynamics simulations and calculate radial distribution functions, IR spectra, and two-dimensional density distribution maps for water in the MOFs. These results consistently show that the μ 3 -OH sites are the preferential interaction sites for water in UiO-66 and all its variants, and the formation of localised water clusters inside the octahedral pores is responsible for the abrupt step in the experimental adsorption isotherms. Furthermore, the presence of functional groups in the framework allows water to cluster in the octahedral pores at lower RH, thus making the MOF a more efficient water harvester. Overall, this study provides molecular-level insights into the pore filling process of UiO-66 and its functionalized derivatives, which are needed for the design of efficient water harvesting materials based on MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fisher for complements: extracting cosmology and neutrino mass from the counts-in-cells PDF

In this work, we comprehensively analyse the cosmology dependence of counts-in-cells statistics. Furthermore, we focus on the shape of the one-point probability distribution function (PDF) of the matter density field at mildly non-linear scales. Based on large-deviation statistics, we parametrize the cosmology dependence of the matter PDF in terms of the linear power spectrum, the growth factor, the spherical collapse dynamics, and the non-linear variance. We extend our formalism to include massive neutrinos, finding that the total matter PDF is highly sensitive to the total neutrino mass Mν and can disentangle it from the clustering amplitude σ 8 . Additionally, using more than a million PDFs extracted from the Quijote simulations, we determine the response of the matter PDF to changing parameters in the νΛCDM model and successfully cross-validate the theoretical model and the simulation measurements. We present the first νΛCDM Fisher forecast for the matter PDF at multiple scales and redshifts, and its combination with the matter power spectrum. We establish that the matter PDF and the matter power spectrum are highly complementary at mildly non-linear scales. The matter PDF is particularly powerful for constraining the matter density Ωm, clustering amplitude σ 8 and the total neutrino mass Mν. Adding the mildly non-linear matter PDF to the mildly non-linear matter power spectrum improves constraints on Ω m by a factor of 5 and σ 8 by a factor of 2 when considering the three lowest redshifts. In our joint analysis of the matter PDF and matter power spectrum at three redshifts, the total neutrino mass is constrained to better than 0.01 eV with a total volume of 6 (Gpc h -1 ) 3 . We discuss how density-split statistics can be used to translate those encouraging results for the matter PDF into realistic observables in galaxy surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1993

Gas dynamic simulations of galaxy formation

Results are presented from a simulation modeling the formation of a group of galaxies in a 'standard' cold, dark matter universe with delta = 1, h sub 0 = 50 km/(s(Mpc)), baryon fraction omega sub b = 0.1 and spectrum normalization sigma sub 8 = 0.6 (bias parameter b = 1.7). Initial conditions are generated within a periodic box with comoving length 16 Mpc in a manner constrained to produce a small cluster of total mass approximately 10 exp 14 solar mass. Two sets of 643 particles are used to model the dark matter and baryon fluids. Each gas particle represents 1.08 x 10 exp -8 solar mass, implying an L* galaxy is resolved by approximately 1000 particles. The system is evolved self-consistently in three dimensions using the combined N-body/hydrodynamic scheme P3MSPH up to a final redshift z = 1. Evolving to the present is prohibited by the fact that the mean density in the simulated volume is above critical and the entire volume would be going nonlinear beyond this point, We are currently analyzing another run with somewhat poorer mass resolution which was evolved to the present.

Evrard, August E.↗
DOE OSTI2025

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗
DOE OSTI2020

Distributed heterogeneous compute infrastructure for the study of additive manufacturing systems

We present the current status of a large-scale computing framework to address the need of the multidisciplinary effort to study chemical dynamics. Specifically, we are enabling scientists to process and store experimental data, run large-scale computationally expensive high-fidelity physical simulation, and analyze these results using the state-of-the-art data analytics tools, machine learning, and uncertainty quantification methods using heterogeneous computing resources, such as CPU and GPU cluster. The framework can integrate or abstract out multiple domains based on roles. In order to develop this framework, we have leveraged an existing framework coupled with in-house heterogeneous computing resources. We present the results of using this framework on a single metadata triggered workflow to accelerate an additive manufacturing use case.

heterogeneous computing, hpc, workflows, reproduci↗
DOE OSTI2021

Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement

Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed fractional Brownian motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Stellar and Binary Evolution in Star Clusters

This paper presents a final report on research activities covered on Stellar and Binary Evolution in Star Clusters. Substantial progress was made in the development and dissemination of the "Starlab" software environment. Significant improvements were made to "kira," an N-body simulation program tailored to the study of dense stellar systems such as star clusters and galactic nuclei. Key advances include (1) the inclusion of stellar and binary evolution in a self-consistent manner, (2) proper treatment of the anisotropic Galactic tidal field, (3) numerous technical enhancements in the treatment of binary dynamics and interactions, and (4) full support for the special-purpose GRAPE-4 hardware, boosting the program's performance by a factor of 10-100 over the accelerated version. The data-reduction and analysis tools in Starlab were also substantially expanded. A Starlab Web site (http://www.sns.ias.edu/-starlab) was created and developed. The site contains detailed information on the structure and function of the various tools that comprise the package, as well as download information, "how to" tips and examples of common operations, demonstration programs, animations, etc. All versions of the software are freely distributed to all interested users, along with detailed installation instructions.

McMillan, Stephen L. W.↗
DOE OSTI2025

Experimental and theoretical investigation into the high pressure deflagration products of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105)

Diamond anvil cell (DAC) laser ignition experiments and reactive ab initio molecular dynamics (AIMD) simulations were performed on the high explosive (HE) LLM-105 to investigate its high pressure (HP) deflagration chemistry. Raman and optical spectroscopy measurements reveal LLM-105 reacts into an opaque carbonaceous product at 4–25 GPa. At pressures >~ 27 GPa, the reaction product consists of an amorphous optically transparent solid and nitrogen (N 2 ) in the solid phase. While not a one-to-one comparison due to the small time and length scales, the HP AIMD simulations show that some of the product is molecular N 2 , in qualitative agreement with experiment, while above 20 GPa most of the product consists of large amorphous C x H y N z O k clusters. Clustering is enhanced with pressure and reduces with temperature. In the experiments with initial sample pressure >~ 25 GPa, the pressure within the DAC decreases with minimal change in DAC cavity area. At initial sample pressures of 43.9 GPa, when quenched to 0 K, simulations predict a product experiencing a lower pressure consistent with the experimental measurement at lower load pressures. In conclusion, the results are important for understanding the HP deflagration chemistry of LLM-105.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗