PROJECT TITLE :

Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms

ABSTRACT:

Biological systems encompass complexity that so much surpasses many artificial systems. Modeling and simulation of enormous and complicated biochemical pathways may be a computationally intensive challenge. Ancient tools, such as standard differential equations, partial differential equations, stochastic master equations, and Gillespie type ways, are all limited either by their modeling fidelity or computational potency or both. In this work, we tend to present a scalable computational framework based on modeling biochemical reactions in express 3D house, that's suitable for studying the behavior of enormous and complex biological pathways. The framework is designed to take advantage of parallelism and scalability offered by commodity massively parallel processors such as the graphics processing units (GPUs) and alternative parallel computing platforms. The reaction modeling in 3D space is aimed toward enhancing the realism of the model compared to ancient modeling tools and framework. We introduce the Parallel Select algorithm that is key to breaking the sequential bottleneck limiting the performance of most other tools designed to review biochemical interactions. The algorithm is meant to be computationally tractable, handle hundreds of interacting chemical species and countless independent agents by considering all-particle interactions among the system. We have a tendency to additionally gift an implementation of the framework on the favored graphics processing units and apply it to the simulation study of JAK-STAT Signal Transduction Pathway. The computational framework will supply a deeper insight into numerous biological processes at intervals the cell and help us observe key events as they unfold in area and time. This will advance the present state-of-the-art in simulation study of large scale biological systems and also enable the realistic simulation study of macro-biological cultures, where inter-cellular interactions are prevalent.