title: Improved delay-leaping simulation algorithm for biochemical reaction systems with delays.
abstract: In biochemical reaction systems dominated by delays, the simulation speed of the stochastic simulation algorithm depends on the size of the wait queue. As a result, it is important to control the size of the wait queue to improve the efficiency of the simulation. An improved accelerated delay stochastic simulation algorithm for biochemical reaction systems with delays, termed the improved delay-leaping algorithm, is proposed in this paper. The update method for the wait queue is effective in reducing the size of the queue as well as shortening the storage and access time, thereby accelerating the simulation speed. Numerical simulation on two examples indicates that this method not only obtains a more significant efficiency compared with the existing methods, but also can be widely applied in biochemical reaction systems with delays.
authors.affiliation: Department of Mathematics, Shanghai University, Shanghai 200444, People's Republic of China. wzhshyina@shu.edu.cn
authors.forename: Na
authors.initials: N
authors.lastname: Yi
authors.forename: Gang
authors.initials: G
authors.lastname: Zhuang
authors.forename: Liang
authors.initials: L
authors.lastname: Da
authors.forename: Yifei
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D018398:Homeodomain Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008954:Models, Biological; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D018398:Homeodomain Proteins; D012333:RNA, Messenger