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Tracking Explicit Chain Sequence in Kinetic Monte Carlo Simulations
Author(s) -
Wang Lin,
Broadbelt Linda J.
Publication year - 2011
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/mats.201000041
Subject(s) - bottleneck , sequence (biology) , computer science , scheme (mathematics) , algorithm , kinetic monte carlo , event (particle physics) , transformation (genetics) , tracking (education) , monte carlo method , chemistry , mathematics , physics , psychology , mathematical analysis , pedagogy , biochemistry , statistics , quantum mechanics , gene , embedded system
The execution of individual KMC events can become a major computational bottleneck in the simulation of sequences along chains using KMC because of complex data storage schemes required to record the sequence of each chain. The execution of a KMC event can be very time‐consuming because searching, moving, and modifying all the data detailing a chain to reflect the transformation as a result of a chemical reaction event can be computationally expensive. To address this issue, we developed a new data storage scheme for recording sequence, which can significantly improve calculation speed without affecting the information content of the calculations. By using the proposed data storage scheme, the computational time can be reduced significantly from 12 h to 4 min for our test reaction system.