Dynamic ion channel activation scheduling in patch clamp on a chip

TitleDynamic ion channel activation scheduling in patch clamp on a chip
Publication TypeJournal Article
Year of Publication2004
AuthorsKrishnamurthy, V.
JournalNanoBioscience, IEEE Transactions on
Pagination217 -224
Date Publishedsep.
KeywordsAlgorithms, Artificial Intelligence, bioelectric phenomena, Biological, biological techniques, biomembrane transport, computer simulation, Decision Support Techniques, drug discovery efforts, dynamic ion channel activation scheduling, Ion Channel Gating, ion channels, Markov Chains, Markov decision process, Markov processes, Microchip Analytical Procedures, Models, multiarmed bandit structure, near-optimal dynamic scheduling near-optimal dynamic scheduling, operations research, patch clamp chip, Patch-Clamp Techniques, physiological models, planar quartz-based biological chip, scheduling, Statistical

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.


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