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

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

(2016) Ryan L. Melvin et al.   Journal of Chemical Theory and Computation

The parallel replica dynamics method – Coming of age

(2015) Danny Perez et al.   COMPUTATIONAL MATERIALS SCIENCE

Long-Time Dynamics through Parallel Trajectory Splicing

(2015) Danny Perez et al.   Journal of Chemical Theory and Computation

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

(2015) Gyun-Tack Bae et al.   Journal of Physical Chemistry C

A Survey of Clustering Algorithms for Big Data: Taxonomy and Empirical Analysis

(2014) Adil Fahad et al.   IEEE Transactions on Emerging Topics in Computing

Adaptive spectral clustering with application to tripeptide conformation analysis

(2013) Fiete Haack et al.   JOURNAL OF CHEMICAL PHYSICS

Shape- and Symmetry-Dependent Mechanical Properties of Metallic Gold and Silver on the Nanoscale

(2013) Mahmoud A. Mahmoud et al.   NANO LETTERS

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

(2012) Andreas Vitalis et al.   Journal of Chemical Theory and Computation

Structural Dynamics of Low-Symmetry Au Nanoparticles Stimulated by Electron Irradiation

(2011) Bingsen Zhang et al.   CHEMISTRY-A EUROPEAN JOURNAL

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Network models for molecular kinetics and their initial applications to human health

(2010) Gregory R Bowman et al.   CELL RESEARCH

Comparing geometric and kinetic cluster algorithms for molecular simulation data

(2010) Bettina Keller et al.   JOURNAL OF CHEMICAL PHYSICS

Size-Dependent Catalytic Activity and Dynamics of Gold Nanoparticles at the Single-Molecule Level

(2009) Xiaochun Zhou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural stability of icosahedral FePt nanoparticles

(2009) Rongming Wang et al.   Nanoscale

Hybrid atomistic simulation methods for materials systems

(2009) N Bernstein et al.   REPORTS ON PROGRESS IN PHYSICS

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

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

Kinetic activation-relaxation technique: An off-lattice self-learning kinetic Monte Carlo algorithm

(2008) Fedwa El-Mellouhi et al.   PHYSICAL REVIEW B

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry