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

Journal Article · · Journal of Chemical Physics
DOI: https://doi.org/10.1063/1.4996922 · OSTI ID:1463546
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)
+ Show Author Affiliations

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.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE Office of Nuclear Energy (NE); USDOE
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1463546
Alternate ID(s):
OSTI ID: 1375255
Report Number(s):
LA-UR-17-23766
Journal Information:
Journal of Chemical Physics, Vol. 147, Issue 15; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English

References (40)

Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level journal January 2010
Structural Dynamics of Low-Symmetry Au Nanoparticles Stimulated by Electron Irradiation journal October 2011
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
Determination of reaction coordinates via locally scaled diffusion map journal March 2011
Adaptive Spectral Clustering in Molecular Simulation book September 2012
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
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms journal October 2007
A coarse graining method for the identification of transition rates between molecular conformations journal January 2007
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
Dynamic Atomic-Level Rearrangements in Small Gold Particles journal August 1986
Long-Time Dynamics through Parallel Trajectory Splicing journal December 2015
Comparing geometric and kinetic cluster algorithms for molecular simulation data journal February 2010
Network models for molecular kinetics and their initial applications to human health journal April 2010
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
Robust Perron Cluster Analysis for Various Applications in Computational Life Science book January 2005
Shape- and Symmetry-Dependent Mechanical Properties of Metallic Gold and Silver on the Nanoscale journal January 2014
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
Adaptive spectral clustering with application to tripeptide conformation analysis journal November 2013
Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems journal January 2008
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
Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge journal November 2016
Algorithms for clustering molecular dynamics configurations journal December 1994
Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories text January 2012
Time-Dependent Density Functional Theory Studies of Optical Properties of Ag Nanoparticles: Octahedra, Truncated Octahedra, and Icosahedra journal May 2012
Entropic Effects on the Size Dependence of Cluster Structure text January 2001
A mathematical formalization of the parallel replica dynamics preprint January 2011

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

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