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Molecular Physics
An International Journal at the Interface Between Chemistry and Physics
Volume 119, 2021 - Issue 19-20: Special Issue in honour of Michael L. Klein FRS
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Klein Special Issue

Collective variables for the study of crystallisation

Tarak Karmakara Institute of Computational Sciences, Faculty of Informatics, Universit della Svizzera italiana, Lugano, Switzerland;b Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland;c Italian Institute of Technology, Genova, ItalyORCID Iconhttps://orcid.org/0000-0002-8721-6247View further author information
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Michele Invernizzia Institute of Computational Sciences, Faculty of Informatics, Universit della Svizzera italiana, Lugano, Switzerland;c Italian Institute of Technology, Genova, Italy;d Department of Physics, ETH Zurich, Zurich, SwitzerlandORCID Iconhttps://orcid.org/0000-0002-3328-6557View further author information
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Valerio Rizzia Institute of Computational Sciences, Faculty of Informatics, Universit della Svizzera italiana, Lugano, Switzerland;b Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland;c Italian Institute of Technology, Genova, ItalyView further author information
&
Michele Parrinelloa Institute of Computational Sciences, Faculty of Informatics, Universit della Svizzera italiana, Lugano, Switzerland;b Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland;c Italian Institute of Technology, Genova, ItalyCorrespondence[email protected]
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Article: e1893848 | Received 08 Jan 2021, Accepted 17 Feb 2021, Published online: 01 Mar 2021

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Ofir Blumer, Shlomi Reuveni & Barak Hirshberg. (2024) Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations. Nature Communications 15:1.
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Paulo G. M. Mileo, Caroline M. Krauter, Jeffrey M. Sanders, Andrea R. Browning & Mathew D. Halls. (2023) Molecular-Scale Exploration of Mechanical Properties and Interactions of Poly(lactic acid) with Cellulose and Chitin. ACS Omega 8:45, pages 42417-42428.
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Taehee Ko, Joseph P. Heindel, Xingyi Guan, Teresa Head-Gordon, David B. Williams-Young & Chao Yang. (2023) Using Diffusion Maps to Analyze Reaction Dynamics for a Hydrogen Combustion Benchmark Dataset. Journal of Chemical Theory and Computation 19:17, pages 5872-5885.
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Eric R. Beyerle, Ziyue Zou & Pratyush Tiwary. (2023) Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence. Current Opinion in Solid State and Materials Science 27:4, pages 101093.
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Yuanpeng Deng, Shubin Fu, Jingran Guo, Xiang Xu & Hui Li. (2023) Anisotropic Collective Variables with Machine Learning Potential for Ab Initio Crystallization of Complex Ceramics . ACS Nano 17:14, pages 14099-14113.
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Subarna Sasmal, Martin McCullagh & Glen M. Hocky. (2023) Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions. Journal of Chemical Theory and Computation 19:14, pages 4427-4435.
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Nawavi Naleem, Charlles R. A. Abreu, Krzysztof Warmuz, Muchen Tong, Serdal Kirmizialtin & Mark E. Tuckerman. (2023) An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. The Journal of Chemical Physics 159:3.
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Luigi Bonati, Enrico Trizio, Andrea Rizzi & Michele Parrinello. (2023) A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar . The Journal of Chemical Physics 159:1.
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Dhiman Ray, Enrico Trizio & Michele Parrinello. (2023) Deep learning collective variables from transition path ensemble. The Journal of Chemical Physics 158:20.
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Federica Lodesani, Maria Cristina Menziani, Shingo Urata & Alfonso Pedone. (2023) Evidence of Multiple Crystallization Pathways in Lithium Disilicate: A Metadynamics Investigation. The Journal of Physical Chemistry Letters 14:6, pages 1411-1417.
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Ziyue Zou, Eric R. Beyerle, Sun-Ting Tsai & Pratyush Tiwary. (2023) Driving and characterizing nucleation of urea and glycine polymorphs in water. Proceedings of the National Academy of Sciences 120:7.
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Neha, Vikas Tiwari, Soumya Mondal, Nisha Kumari & Tarak Karmakar. (2022) Collective Variables for Crystallization Simulations─from Early Developments to Recent Advances. ACS Omega 8:1, pages 127-146.
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Rangsiman Ketkaew & Sandra Luber. (2022) DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space. Journal of Chemical Information and Modeling 62:24, pages 6352-6364.
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S. R. G. Balestra & R. Semino. (2022) Computer simulation of the early stages of self-assembly and thermal decomposition of ZIF-8. The Journal of Chemical Physics 157:18.
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Kristof M. Bal & Erik C. Neyts. (2022) Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory. The Journal of Chemical Physics 157:18, pages 184113.
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Narjes Ansari, Valerio Rizzi & Michele Parrinello. (2022) Water regulates the residence time of Benzamidine in Trypsin. Nature Communications 13:1.
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Sapna Sarupria, Steven W. Hall & Jutta Rogal. (2022) Machine learning for molecular simulations of crystal nucleation and growth. MRS Bulletin 47:9, pages 949-957.
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Michele Invernizzi & Michele Parrinello. (2022) Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling. Journal of Chemical Theory and Computation 18:6, pages 3988-3996.
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Umberto Raucci, Valerio Rizzi & Michele Parrinello. (2022) Discover, Sample, and Refine: Exploring Chemistry with Enhanced Sampling Techniques. The Journal of Physical Chemistry Letters 13:6, pages 1424-1430.
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Ziyue Zou, Sun-Ting Tsai & Pratyush Tiwary. (2021) Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. The Journal of Physical Chemistry B 125:47, pages 13049-13056.
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Luigi Bonati, GiovanniMaria Piccini & Michele Parrinello. (2021) Deep learning the slow modes for rare events sampling. Proceedings of the National Academy of Sciences 118:44.
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Kristof M. Bal. (2021) Nucleation rates from small scale atomistic simulations and transition state theory. The Journal of Chemical Physics 155:14.
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Enrico Trizio & Michele Parrinello. (2021) From Enhanced Sampling to Reaction Profiles. The Journal of Physical Chemistry Letters 12:35, pages 8621-8626.
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. 2021. The Crystalline States of Organic Compounds. The Crystalline States of Organic Compounds 267 287 .

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