An efficient method for the coordinate transformation problem of massively three-dimensional networks | Zendy

Károly Németh | Zendy; Olivier Coulaud | Zendy; Gérald Monard | Zendy; János G. Ángyán | Zendy

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An efficient method for the coordinate transformation problem of massively three-dimensional networks

Author(s) -

Károly Németh,

Olivier Coulaud,

Gérald Monard,

János G. Ángyán

Publication year - 2001

Publication title -

the journal of chemical physics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.071

H-Index - 357

eISSN - 1089-7690

pISSN - 0021-9606

DOI - 10.1063/1.1370534

Subject(s) - massively parallel , coordinate system , transformation (genetics) , computer science , scaling , diamond , parallel computing , computational science , algorithm , mathematics , geometry , materials science , chemistry , artificial intelligence , biochemistry , composite material , gene

A new and efficient algorithm is presented for the coordinate transformation problem of massively three-dimensional networks formed, e.g., by the atoms of crystal fragments or molecular clusters. The new algorithm is based on a divide-and-conquer technique to perform iterative coordinate transformation, applicable even for three-dimensional networks, with linear scaling memory and near linear scaling CPU time requirements. The new algorithm proved to be very fast in the coordinate transformation problems and geometry optimization of diamond fragments, water clusters, globular proteins, and proteins in solvent.

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