A variational approach to assess reaction coordinates for two-step crystallization

LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

(2021) Aidan P. Thompson et al.   COMPUTER PHYSICS COMMUNICATIONS

The seven deadly sins: When computing crystal nucleation rates, the devil is in the details

(2021) Katarina E. Blow et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

(2020) Nicholas F. Francia et al.   CRYSTAL GROWTH & DESIGN

Nucleation in aqueous NaCl solutions shifts from 1-step to 2-step mechanism on crossing the spinodal

(2019) Hao Jiang et al.   JOURNAL OF CHEMICAL PHYSICS

Improving collective variables: The case of crystallization

(2019) Yue-Yu Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

Variational Approach for Learning Markov Processes from Time Series Data

(2019) Hao Wu et al.   JOURNAL OF NONLINEAR SCIENCE

Size-dependent thermodynamic structural selection in colloidal crystallization

(2019) Evan Pretti et al.   Science Advances

Classical nucleation theory approach to two-step nucleation of crystals

(2019) Dimo Kashchiev   JOURNAL OF CRYSTAL GROWTH

NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates

(2018) Nils. E. R. Zimmermann et al.   JOURNAL OF CHEMICAL PHYSICS

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Analyzing and Driving Cluster Formation in Atomistic Simulations

(2017) Gareth A. Tribello et al.   Journal of Chemical Theory and Computation

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

(2017) Pablo M. Piaggi et al.   PHYSICAL REVIEW LETTERS

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

(2016) Gabriele C. Sosso et al.   CHEMICAL REVIEWS

Robust structural identification via polyhedral template matching

(2016) Peter Mahler Larsen et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Urea homogeneous nucleation mechanism is solvent dependent

(2015) Matteo Salvalaglio et al.   FARADAY DISCUSSIONS

Variational cross-validation of slow dynamical modes in molecular kinetics

(2015) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates

(2015) Nils E. R. Zimmermann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Urea homogeneous nucleation mechanism is solvent dependent

(2015) Matteo Salvalaglio et al.   FARADAY DISCUSSIONS

Molecular-dynamics simulations of urea nucleation from aqueous solution

(2014) Matteo Salvalaglio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

Homogeneous Ice Nucleation at Moderate Supercooling from Molecular Simulation

(2013) E. Sanz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Homogeneous Nucleation of Methane Hydrates: Unrealistic under Realistic Conditions

(2012) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing Nucleus Size Metrics for Liquid–Solid Nucleation from Transition Paths of Near-Nanosecond Duration

(2011) Gregg T. Beckham et al.   Journal of Physical Chemistry Letters

The two-step mechanism of nucleation of crystals in solution

(2010) Peter G. Vekilov   Nanoscale

Experimental Evidence for Two-Step Nucleation in Colloidal Crystallization

(2009) J. R. Savage et al.   PHYSICAL REVIEW LETTERS

Accurate determination of crystal structures based on averaged local bond order parameters

(2008) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS