Literature DB >> 24907992

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

Tang-Qing Yu1, Pei-Yang Chen2, Ming Chen2, Amit Samanta3, Eric Vanden-Eijnden1, Mark Tuckerman1.   

Abstract

The problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampling approaches can be brought to bear on the problem. In this paper, we build on a scheme previously introduced by two of the authors in which the lengths and angles of the supercell are targeted for enhanced sampling via temperature accelerated adiabatic free energy dynamics [T. Q. Yu and M. E. Tuckerman, Phys. Rev. Lett. 107, 015701 (2011)]. Here, that framework is expanded to include general order parameters that distinguish different crystalline arrangements as target collective variables for enhanced sampling. The resulting free energy surface, being of quite high dimension, is nontrivial to reconstruct, and we discuss one particular strategy for performing the free energy analysis. The method is applied to the study of polymorphism in xenon crystals at high pressure and temperature using the Steinhardt order parameters without and with the supercell included in the set of collective variables. The expected fcc and bcc structures are obtained, and when the supercell parameters are included as collective variables, we also find several new structures, including fcc states with hcp stacking faults. We also apply the new method to the solid-liquid phase transition in copper at 1300 K using the same Steinhardt order parameters. Our method is able to melt and refreeze the system repeatedly, and the free energy profile can be obtained with high efficiency.

Entities:  

Mesh:

Year:  2014        PMID: 24907992      PMCID: PMC4048450          DOI: 10.1063/1.4878665

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  37 in total

1.  Exercises in prognostication: crystal structures and protein folding.

Authors:  Jack D Dunitz; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-27       Impact factor: 11.205

2.  Blind crystal structure prediction of a novel second polymorph of 1-hydroxy-7-azabenzotriazole.

Authors:  Harriott Nowell; Christopher S Frampton; Julie Waite; Sarah L Price
Journal:  Acta Crystallogr B       Date:  2006-07-12

3.  Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.

Authors:  Jerry B Abrams; Mark E Tuckerman
Journal:  J Phys Chem B       Date:  2008-12-11       Impact factor: 2.991

4.  Graph representation of protein free energy landscape.

Authors:  Minghai Li; Mojie Duan; Jue Fan; Li Han; Shuanghong Huo
Journal:  J Chem Phys       Date:  2013-11-14       Impact factor: 3.488

5.  Neural networks for local structure detection in polymorphic systems.

Authors:  Philipp Geiger; Christoph Dellago
Journal:  J Chem Phys       Date:  2013-10-28       Impact factor: 3.488

6.  Metadynamics simulations of ice nucleation and growth.

Authors:  D Quigley; P M Rodger
Journal:  J Chem Phys       Date:  2008-04-21       Impact factor: 3.488

7.  Three-body-exchange interaction in dense rare gases.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1988-04-01

8.  Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction.

Authors:  Andrei V Kazantsev; Panagiotis G Karamertzanis; Claire S Adjiman; Constantinos C Pantelides; Sarah L Price; Peter T A Galek; Graeme M Day; Aurora J Cruz-Cabeza
Journal:  Int J Pharm       Date:  2011-04-08       Impact factor: 5.875

9.  Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

Authors:  Aleks Reinhardt; Jonathan P K Doye; Eva G Noya; Carlos Vega
Journal:  J Chem Phys       Date:  2012-11-21       Impact factor: 3.488

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

Authors:  Nathan Duff; Baron Peters
Journal:  J Chem Phys       Date:  2011-10-07       Impact factor: 3.488

View more
  4 in total

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

Authors:  Gabriele C Sosso; Ji Chen; Stephen J Cox; Martin Fitzner; Philipp Pedevilla; Andrea Zen; Angelos Michaelides
Journal:  Chem Rev       Date:  2016-05-26       Impact factor: 60.622

2.  Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.

Authors:  Alexander G Shtukenberg; Qiang Zhu; Damien J Carter; Leslie Vogt; Johannes Hoja; Elia Schneider; Hongxing Song; Boaz Pokroy; Iryna Polishchuk; Alexandre Tkatchenko; Artem R Oganov; Andrew L Rohl; Mark E Tuckerman; Bart Kahr
Journal:  Chem Sci       Date:  2017-05-15       Impact factor: 9.825

3.  Screening toward the Development of Fingerprints of Atomic Environments Using Bond-Orientational Order Parameters.

Authors:  Hideo Doi; Kazuaki Z Takahashi; Takeshi Aoyagi
Journal:  ACS Omega       Date:  2022-01-24

Review 4.  Collective variable-based enhanced sampling and machine learning.

Authors:  Ming Chen
Journal:  Eur Phys J B       Date:  2021-10-20       Impact factor: 1.500

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.