Programmable Microfluidic Devices (PMDs) have emerged as a new architecture for next-generation flow-based biochips. These devices can be dynamically reconfigured to execute different bioassays flexibly and efficiently owing to their two-dimensional regularly-arranged valve structure. During execution of a bioassay or between the execution of multiple bioassays, some areas on the PMD, however, become contaminated and must be cleaned by washing them with a buffer flow before they are reused. In this paper, we propose a novel block-based washing technique called block flushing. In this method, contaminated areas are first collected according to given patterns and flushed as a whole to increase washing efficiency. Simulation results show that with this technique the proposed method can achieve on average 28% improvement in reducing washing time compared with two other baseline solutions.
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