Collective Variables for Crystallization Simulations─from Early Developments to Recent Advances

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters

(2022) Federica Lodesani et al.   JOURNAL OF CHEMICAL PHYSICS

Relationship of structure and mechanical property of silica with enhanced sampling and machine learning

(2021) Yuanpeng Deng et al.   JOURNAL OF THE AMERICAN CERAMIC SOCIETY

Collective variables for the study of crystallisation

(2021) Tarak Karmakar et al.   MOLECULAR PHYSICS

A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3

(2021) Paramvir Ahlawat et al.   Science Advances

Solubility Prediction of Organic Molecules with Molecular Dynamics Simulations

(2021) Zoran Bjelobrk et al.   CRYSTAL GROWTH & DESIGN

Nucleating a Different Coordination in a Crystal under Pressure: A Study of the B1−B2 Transition in NaCl by Metadynamics

(2021) Matej Badin et al.   PHYSICAL REVIEW LETTERS

Exploring the crystallization path of lithium disilicate through metadynamics simulations

(2021) Federica Lodesani et al.   Physical Review Materials

Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics

(2021) Ziyue Zou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Deep learning the slow modes for rare events sampling

(2021) Luigi Bonati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Data-Driven Collective Variables for Enhanced Sampling

(2020) Luigi Bonati et al.   Journal of Physical Chemistry Letters

Rethinking Metadynamics: From Bias Potentials to Probability Distributions

(2020) Michele Invernizzi et al.   Journal of Physical Chemistry Letters

Ab initio phase diagram and nucleation of gallium

(2020) Haiyang Niu et al.   Nature Communications

Pathways for the formation of ice polymorphs from water predicted by a metadynamics method

(2020) Hiroki Nada   Scientific Reports

Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics

(2020) Jayashrita Debnath et al.   Journal of Physical Chemistry Letters

Out-of-Equilibrium Polymorph Selection in Nanoparticle Freezing

(2020) Jonathan Amodeo et al.   Journal of Physical Chemistry Letters

Unified Approach to Enhanced Sampling

(2020) Michele Invernizzi et al.   Physical Review X

Improving collective variables: The case of crystallization

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

DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules

(2019) Maxwell Fulford et al.   Journal of Chemical Information and Modeling

Calculation of phase diagrams in the multithermal-multibaric ensemble

(2019) Pablo M. Piaggi et al.   JOURNAL OF CHEMICAL PHYSICS

Temperature Dependence of Homogeneous Nucleation in Ice

(2019) Haiyang Niu et al.   PHYSICAL REVIEW LETTERS

Entropic colloidal crystallization pathways via fluid–fluid transitions and multidimensional prenucleation motifs

(2019) Sangmin Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Dynamics Simulations of Crystal Nucleation from Solution at Constant Chemical Potential

(2019) Tarak Karmakar et al.   Journal of Chemical Theory and Computation

Neural-Network-Based Path Collective Variables for Enhanced Sampling of Phase Transformations

(2019) Jutta Rogal et al.   PHYSICAL REVIEW LETTERS

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

(2018) Wei Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation of Molecular Crystals Driven by Relative Information Entropy

(2018) Gianpaolo Gobbo et al.   Journal of Chemical Theory and Computation

Searching for Entropically Stabilized Phases: The Case of Silver Iodide

(2018) Dan Mendels et al.   Journal of Physical Chemistry C

Molecular dynamics simulations of liquid silica crystallization

(2018) Haiyang Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated design of collective variables using supervised machine learning

(2018) Mohammad M. Sultan et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics with Discriminants: A Tool for Understanding Chemistry

(2018) GiovanniMaria Piccini et al.   Journal of Chemical Theory and Computation

Predicting polymorphism in molecular crystals using orientational entropy

(2018) Pablo M. Piaggi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding a small protein using harmonic linear discriminant analysis

(2018) Dan Mendels et al.   JOURNAL OF CHEMICAL PHYSICS

Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics

(2018) Luigi Bonati et al.   PHYSICAL REVIEW LETTERS

A variational conformational dynamics approach to the selection of collective variables in metadynamics

(2017) James McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

(2017) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

A Local Order Parameter-Based Method for Simulation of Free Energy Barriers in Crystal Nucleation

(2017) Hossein Eslami 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

Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

(2017) Michele Invernizzi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Crystal nucleation as the ordering of multiple order parameters

(2016) John Russo et al.   JOURNAL OF CHEMICAL PHYSICS

Comparing molecules and solids across structural and alchemical space

(2016) Sandip De et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Insight into the nucleation of urea crystals from the melt

(2015) Federico Giberti et al.   CHEMICAL ENGINEERING SCIENCE

Solid-liquid interfacial free energy out of equilibrium

(2015) Bingqing Cheng et al.   PHYSICAL REVIEW B

Metadynamics studies of crystal nucleation

(2015) Federico Giberti et al.   IUCrJ

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

(2014) Tang-Qing Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms

(2014) Andrew W. Long et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

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

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Neural networks for local structure detection in polymorphic systems

(2013) Philipp Geiger et al.   JOURNAL OF CHEMICAL PHYSICS

Shortcomings of the bond orientational order parameters for the analysis of disordered particulate matter

(2013) Walter Mickel et al.   JOURNAL OF CHEMICAL PHYSICS

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

On representing chemical environments

(2013) Albert P. Bartók et al.   PHYSICAL REVIEW B

Uncovering Molecular Details of Urea Crystal Growth in the Presence of Additives

(2012) Matteo Salvalaglio et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of ice crystallized from supercooled water

(2012) T. L. Malkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine

(2011) Nathan Duff et al.   JOURNAL OF CHEMICAL PHYSICS

A general set of order parameters for molecular crystals

(2011) Erik E. Santiso et al.   JOURNAL OF CHEMICAL PHYSICS

Atom-centered symmetry functions for constructing high-dimensional neural network potentials

(2011) Jörg Behler   JOURNAL OF CHEMICAL PHYSICS

Computer Simulations of Homogeneous Nucleation of Benzene from the Melt

(2011) Manas Shah et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterizing Structure Through Shape Matching and Applications to Self-Assembly

(2011) Aaron S. Keys et al.   Annual Review of Condensed Matter Physics

Solid-liquid interface free energy through metadynamics simulations

(2010) Stefano Angioletti-Uberti et al.   PHYSICAL REVIEW B

Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited

(2009) Baron Peters   JOURNAL OF CHEMICAL PHYSICS

An integrate-over-temperature approach for enhanced sampling

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS

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

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

Gas hydrate nucleation and cage formation at a water/methane interface

(2008) Robert W. Hawtin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS