𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Tracking Explicit Chain Sequence in Kinetic Monte Carlo Simulations

✍ Scribed by Lin Wang; Linda J. Broadbelt

Publisher
John Wiley and Sons
Year
2010
Tongue
English
Weight
408 KB
Volume
20
Category
Article
ISSN
1022-1344

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

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.
magnified image

πŸ“œ SIMILAR VOLUMES

Mixed monte carlo/molecular dynamics sim
Mixed monte carlo/molecular dynamics simulations in explicit solvent
✍ AndrΓ© A. S. T. Ribeiro; Ricardo B. de Alencastro πŸ“‚ Article πŸ“… 2012 πŸ› John Wiley and Sons 🌐 English βš– 953 KB

## Abstract A mixed Monte Carlo/Molecular Dynamics method using the trial moves for peptide backbone sampling known as Concerted Rotations with Angles was implemented. The algorithm was used to study polyalanine systems. Equivalent results to conventional Molecular Dynamics were obtained for simula

Monte Carlo simulation of kinetics and c
Monte Carlo simulation of kinetics and chain-length distribution in radical polymerization
✍ Lu, Jianming ;Zhang, Hongdong ;Yang, Yuliang πŸ“‚ Article πŸ“… 1993 πŸ› Wiley (John Wiley & Sons) βš– 587 KB

## Abstract In this paper, the Monte Carlo method for numerically simulating the kinetics and chain‐length distribution in radical polymerization is described. Because the Monte Carlo method is not subject to the assumption of steady‐state, it is particularly suitable for studying the kinetic behav

Bayesian Modeling and Markov Chain Monte
Bayesian Modeling and Markov Chain Monte Carlo Simulations for a Kinetic Study of Homo- and Co- Polymerization Systems
✍ Ali Habibi; Ebrahim Vasheghani-Farahani πŸ“‚ Article πŸ“… 2007 πŸ› John Wiley and Sons 🌐 English βš– 695 KB

## Abstract A Bayesian modeling and Markov Chain Monte Carlo simulation was developed for a kinetic study of homopolymerization and copolymerization systems at the molecular scale. Two copolymerization models – the terminal unit model and the penultimate unit model – were considered. Prior estimate