title: Agent based modeling of blood coagulation system: implementation using a GPU based high speed framework.
abstract: The coagulation and fibrinolytic systems are complex, inter-connected biological systems with major physiological roles. The complex, nonlinear multi-point relationships between the molecular and cellular constituents of two systems render a comprehensive and simultaneous study of the system at the microscopic and macroscopic level a significant challenge. We have created an Agent Based Modeling and Simulation (ABMS) approach for simulating these complex interactions. As the scale of agents increase, the time complexity and cost of the resulting simulations presents a significant challenge. As such, in this paper, we also present a high-speed framework for the coagulation simulation utilizing the computing power of graphics processing units (GPU). For comparison, we also implemented the simulations in NetLogo, Repast, and a direct C version. As our experiments demonstrate, the computational speed of the GPU implementation of the million-level scale of agents is over 10 times faster versus the C version, over 100 times faster versus the Repast version and over 300 times faster versus the NetLogo simulation.
authors.affiliation: Department of Biostatistics, Virginia Commonwealth University, USA. chenw6@vcu.edu
authors.forename: Wenan
authors.initials: W
authors.lastname: Chen
authors.forename: Kevin
authors.initials: K
authors.lastname: Ward
authors.forename: Qi
authors.initials: Q
authors.lastname: Li
authors.forename: Vojislav
authors.initials: V
authors.lastname: Kecman
authors.forename: Kayvan
authors.initials: K
authors.lastname: Najarian
authors.forename: Nathan
authors.initials: N
authors.lastname: Menke
mesh_terms: D000818:Animals; D001777:Blood Coagulation / Q000502:physiology*; D001779:Blood Coagulation Factors / Q000378:metabolism*; D003196:Computer Graphics / Q000295:instrumentation*; D003198:Computer Simulation; D004867:Equipment Design; D019544:Equipment Failure Analysis; D006801:Humans; D008955:Models, Cardiovascular; D012815:Signal Processing, Computer-Assisted / Q000295:instrumentation*
chemical_list: D001779:Blood Coagulation Factors