Literature DB >> 12633242

Predicting crystal structures: the Parrinello-Rahman method revisited.

R Martonák1, A Laio, M Parrinello.   

Abstract

By suitably adapting a recent approach [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12 562 (2002)]] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables and define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method, our approach shows no hysteresis, and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.

Entities:  

Year:  2003        PMID: 12633242     DOI: 10.1103/PhysRevLett.90.075503

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  62 in total

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3.  Structural phase transition of BeTe: an ab initio molecular dynamics study.

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Journal:  J Mol Model       Date:  2017-08-11       Impact factor: 1.810

4.  Molecular modeling and simulation of the human eNOS reductase domain, an enzyme involved in the release of vascular nitric oxide.

Authors:  N T Devika; Prakash Amresh; Md Imtiyaz Hassan; B M Jaffar Ali
Journal:  J Mol Model       Date:  2014-10-07       Impact factor: 1.810

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

Authors:  Tang-Qing Yu; Pei-Yang Chen; Ming Chen; Amit Samanta; Eric Vanden-Eijnden; Mark Tuckerman
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

6.  Molecular dynamics simulation of the Staphylococcus aureus YsxC protein: molecular insights into ribosome assembly and allosteric inhibition of the protein.

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Journal:  J Mol Model       Date:  2011-03-02       Impact factor: 1.810

7.  Pressure-induced phase transition in wurtzite ZnTe: an ab initio study.

Authors:  Sebahaddin Alptekin
Journal:  J Mol Model       Date:  2011-06-18       Impact factor: 1.810

8.  Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies.

Authors:  Kannan Muthu; Manivel Panneerselvam; Muthukumaran Jayaraman; Nishith Saurav Topno; Arindam Atanu Das; Krishna Ramadas
Journal:  J Mol Model       Date:  2012-06-20       Impact factor: 1.810

9.  High Tensile Strength of Engineered β-Solenoid Fibrils via Sonication and Pulling.

Authors:  Zeyu Peng; Amanda S Parker; Maria D R Peralta; Krishnakumar M Ravikumar; Daniel L Cox; Michael D Toney
Journal:  Biophys J       Date:  2017-11-07       Impact factor: 4.033

10.  High-pressure polymeric phases of carbon dioxide.

Authors:  Jian Sun; Dennis D Klug; Roman Martonák; Javier Antonio Montoya; Mal-Soon Lee; Sandro Scandolo; Erio Tosatti
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-30       Impact factor: 11.205

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