Dynamic ion channel activation scheduling in patch clamp on a chip.
In 2002, Fertig et al. made a remarkable invention: the first successful demonstration of a patch clamp on a chip--a planar quartz-based biological chip that contains up to several hundred ion channels. This patch-clamp chip can be used in massively parallel screens for ion channel activity, thereby providing a high-throughput screening tool for drug discovery efforts. In this paper, we propose computationally efficient dynamic stochastic scheduling algorithms for activating individual ion channels in the patch-clamp chip. By formulating the ion channel activation scheduling problem as a partially observed Markov decision process with a multiarmed bandit structure, near-optimal dynamic scheduling for activation of the individual channels is achieved to optimize the information gained from the patch-clamp chip. Numerical examples using state-of-the-art algorithms developed recently in artificial intelligence and operations research are presented to illustrate these dynamic ion channel (macromolecule) activation scheduling algorithms.
Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. vikramk@ece.ubc.ca
Vikram
V
Krishnamurthy
D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D003661:Decision Support Techniques; D015640:Ion Channel Gating / Q000502:physiology*; D007473:Ion Channels / Q000502:physiology*; D008390:Markov Chains; D046208:Microchip Analytical Procedures / Q000379:methods*; D008954:Models, Biological; D015233:Models, Statistical; D018408:Patch-Clamp Techniques / Q000379:methods*
D007473:Ion Channels