Literature DB >> 17155444

Structural relaxation made simple.

Erik Bitzek1, Pekka Koskinen, Franz Gähler, Michael Moseler, Peter Gumbsch.   

Abstract

We introduce a simple local atomic structure optimization algorithm which is significantly faster than standard implementations of the conjugate gradient method and often competitive with more sophisticated quasi-Newton schemes typically used in ab initio calculations. It is based on conventional molecular dynamics with additional velocity modifications and adaptive time steps. The surprising efficiency and especially the robustness and versatility of the method is illustrated using a variety of test cases from nanoscience, solid state physics, materials research, and biochemistry.

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Year:  2006        PMID: 17155444     DOI: 10.1103/PhysRevLett.97.170201

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


  79 in total

1.  Void distributions reveal structural link between jammed packings and protein cores.

Authors:  John D Treado; Zhe Mei; Lynne Regan; Corey S O'Hern
Journal:  Phys Rev E       Date:  2019-02       Impact factor: 2.529

2.  Linear and nonlinear mechanical responses can be quite different in models for biological tissues.

Authors:  Preeti Sahu; Janice Kang; Gonca Erdemci-Tandogan; M Lisa Manning
Journal:  Soft Matter       Date:  2020-01-27       Impact factor: 3.679

3.  ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.

Authors:  Minh Khoa Nguyen; Léonard Jaillet; Stéphane Redon
Journal:  J Comput Aided Mol Des       Date:  2019-08-21       Impact factor: 3.686

4.  Structural hierarchy confers error tolerance in biological materials.

Authors:  Jonathan A Michel; Peter J Yunker
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-05       Impact factor: 11.205

5.  Relationship between local structure and relaxation in out-of-equilibrium glassy systems.

Authors:  Samuel S Schoenholz; Ekin D Cubuk; Efthimios Kaxiras; Andrea J Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2016-12-27       Impact factor: 11.205

6.  Periodic training of creeping solids.

Authors:  Daniel Hexner; Andrea J Liu; Sidney R Nagel
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-30       Impact factor: 11.205

7.  Generating conformational transition paths with low potential-energy barriers for proteins.

Authors:  Minh Khoa Nguyen; Léonard Jaillet; Stéphane Redon
Journal:  J Comput Aided Mol Des       Date:  2018-08-01       Impact factor: 3.686

8.  Ultrastable glasses from in silico vapour deposition.

Authors:  Sadanand Singh; M D Ediger; Juan J de Pablo
Journal:  Nat Mater       Date:  2013-01-06       Impact factor: 43.841

9.  Scaling ansatz for the jamming transition.

Authors:  Carl P Goodrich; Andrea J Liu; James P Sethna
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-10       Impact factor: 11.205

10.  Understanding soft glassy materials using an energy landscape approach.

Authors:  Hyun Joo Hwang; Robert A Riggleman; John C Crocker
Journal:  Nat Mater       Date:  2016-06-20       Impact factor: 43.841

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