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Title: Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

Abstract

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [2]; ORCiD logo [2]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Xiamen Univ. (China)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Xiamen Univ. (China)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE)
OSTI Identifier:
1463546
Alternate Identifier(s):
OSTI ID: 1375255
Report Number(s):
LA-UR-17-23766
Journal ID: ISSN 0021-9606
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 147; Journal Issue: 15; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; Material Science

Citation Formats

Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., and Perez, Danny. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles. United States: N. p., 2017. Web. doi:10.1063/1.4996922.
Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., & Perez, Danny. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles. United States. https://doi.org/10.1063/1.4996922
Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., and Perez, Danny. Wed . "Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles". United States. https://doi.org/10.1063/1.4996922. https://www.osti.gov/servlets/purl/1463546.
@article{osti_1463546,
title = {Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles},
author = {Huang, Rao and Lo, Li-Ta and Wen, Yuhua and Voter, Arthur F. and Perez, Danny},
abstractNote = {Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.},
doi = {10.1063/1.4996922},
journal = {Journal of Chemical Physics},
number = 15,
volume = 147,
place = {United States},
year = {Wed Aug 16 00:00:00 EDT 2017},
month = {Wed Aug 16 00:00:00 EDT 2017}
}

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Works referenced in this record:

Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level
journal, January 2010

  • Zhou, Xiaochun; Xu, Weilin; Liu, Guokun
  • Journal of the American Chemical Society, Vol. 132, Issue 1
  • DOI: 10.1021/ja904307n

Structural Dynamics of Low-Symmetry Au Nanoparticles Stimulated by Electron Irradiation
journal, October 2011

  • Zhang, Bingsen; Wang, Di; Zhang, Wei
  • Chemistry - A European Journal, Vol. 17, Issue 46
  • DOI: 10.1002/chem.201102092

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
journal, May 2008


Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
journal, February 2012

  • Vitalis, Andreas; Caflisch, Amedeo
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 3
  • DOI: 10.1021/ct200801b

Determination of reaction coordinates via locally scaled diffusion map
journal, March 2011

  • Rohrdanz, Mary A.; Zheng, Wenwei; Maggioni, Mauro
  • The Journal of Chemical Physics, Vol. 134, Issue 12
  • DOI: 10.1063/1.3569857

Structural instability of ultrafine particles of metals
journal, February 1986


Accurate Interatomic Potentials for Ni, Al and Ni3Al
journal, January 1986


Melting of gold clusters
journal, August 1999


Time-Dependent Density Functional Theory Studies of Optical Properties of Au Nanoparticles: Octahedra, Truncated Octahedra, and Icosahedra
journal, September 2015

  • Bae, Gyun-Tack; Aikens, Christine M.
  • The Journal of Physical Chemistry C, Vol. 119, Issue 40
  • DOI: 10.1021/acs.jpcc.5b05978

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
journal, October 2007

  • Shao, Jianyin; Tanner, Stephen W.; Thompson, Nephi
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 6
  • DOI: 10.1021/ct700119m

A coarse graining method for the identification of transition rates between molecular conformations
journal, January 2007

  • Kube, Susanna; Weber, Marcus
  • The Journal of Chemical Physics, Vol. 126, Issue 2
  • DOI: 10.1063/1.2404953

Hybrid atomistic simulation methods for materials systems
journal, January 2009


Robust Perron cluster analysis in conformation dynamics
journal, March 2005


A mathematical formalization of the parallel replica dynamics
journal, January 2012

  • Le Bris, Claude; Lelièvre, Tony; Luskin, Mitchell
  • Monte Carlo Methods and Applications, Vol. 18, Issue 2
  • DOI: 10.1515/mcma-2012-0003

Dynamic Atomic-Level Rearrangements in Small Gold Particles
journal, August 1986


Long-Time Dynamics through Parallel Trajectory Splicing
journal, December 2015

  • Perez, Danny; Cubuk, Ekin D.; Waterland, Amos
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 1
  • DOI: 10.1021/acs.jctc.5b00916

Comparing geometric and kinetic cluster algorithms for molecular simulation data
journal, February 2010

  • Keller, Bettina; Daura, Xavier; van Gunsteren, Wilfred F.
  • The Journal of Chemical Physics, Vol. 132, Issue 7
  • DOI: 10.1063/1.3301140

Network models for molecular kinetics and their initial applications to human health
journal, April 2010

  • Bowman, Gregory R.; Huang, Xuhui; Pande, Vijay S.
  • Cell Research, Vol. 20, Issue 6
  • DOI: 10.1038/cr.2010.57

Extending the Time Scale in Atomistic Simulation of Materials
journal, August 2002


Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects
journal, May 2005


The parallel replica dynamics method – Coming of age
journal, April 2015


Systematic analysis of local atomic structure combined with 3D computer graphics
journal, March 1994


Formation of an Icosahedral Structure during the Freezing of Gold Nanoclusters: Surface-Induced Mechanism
journal, December 2002


Shape- and Symmetry-Dependent Mechanical Properties of Metallic Gold and Silver on the Nanoscale
journal, January 2014

  • Mahmoud, Mahmoud A.; O’Neil, Daniel; El-Sayed, Mostafa A.
  • Nano Letters, Vol. 14, Issue 2
  • DOI: 10.1021/nl4040362

Experimental studies of small particle structures
journal, June 1994


Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
journal, May 2005

  • Coifman, R. R.; Lafon, S.; Lee, A. B.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 21
  • DOI: 10.1073/pnas.0500334102

Adaptive spectral clustering with application to tripeptide conformation analysis
journal, November 2013

  • Haack, Fiete; Fackeldey, Konstantin; Röblitz, Susanna
  • The Journal of Chemical Physics, Vol. 139, Issue 19
  • DOI: 10.1063/1.4830409

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems
journal, January 2008

  • Coifman, R. R.; Kevrekidis, I. G.; Lafon, S.
  • Multiscale Modeling & Simulation, Vol. 7, Issue 2
  • DOI: 10.1137/070696325

Correlated Orientations in Nanocrystal Fluctuations
journal, March 1997


Entropic Effects on the Size Dependence of Cluster Structure
journal, April 2001


Accelerated Molecular Dynamics Methods: Introduction and Recent Developments
book, January 2009


Structural stability of icosahedral FePt nanoparticles
journal, January 2009

  • Wang, Rongming; Zhang, Hongzhou; Farle, Michael
  • Nanoscale, Vol. 1, Issue 2
  • DOI: 10.1039/b9nr00096h

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge
journal, November 2016

  • Melvin, Ryan L.; Godwin, Ryan C.; Xiao, Jiajie
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 12
  • DOI: 10.1021/acs.jctc.6b00757

Algorithms for clustering molecular dynamics configurations
journal, December 1994

  • Torda, Andrew E.; van Gunsteren, Wilfred F.
  • Journal of Computational Chemistry, Vol. 15, Issue 12
  • DOI: 10.1002/jcc.540151203

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
text, January 2012

  • Vitalis, Andreas; Caflisch, Amedeo
  • American Chemical Society
  • DOI: 10.5167/uzh-65066

Time-Dependent Density Functional Theory Studies of Optical Properties of Ag Nanoparticles: Octahedra, Truncated Octahedra, and Icosahedra
journal, May 2012

  • Bae, Gyun-Tack; Aikens, Christine M.
  • The Journal of Physical Chemistry C, Vol. 116, Issue 18
  • DOI: 10.1021/jp300789x

Entropic Effects on the Size Dependence of Cluster Structure
text, January 2001


A mathematical formalization of the parallel replica dynamics
preprint, January 2011


Works referencing / citing this record:

Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
journal, December 2017

  • Perez, Danny; Huang, Rao; Voter, Arthur F.
  • Journal of Materials Research, Vol. 33, Issue 7
  • DOI: 10.1557/jmr.2017.456