Preparing Fluid Samples Under Retention Time Constraints Using Flow-Based Microfluidic Biochips

Abstract

Sample preparation is an essential step in almost all bioprotocols, which can be efficiently achieved via sequence of mixing steps called mixing graph. In literature, several techniques have been reported to determine a mixing graph with the minimal number of mixing steps, or the minimal usage of reagent fluids, or the minimal wastage, or sometime a combination of them. The retention time of an flow-based microfluidic biochip (FMB) is defined as the maximum duration for which a fluid can be stored within a microchannel without any fluid leakage. However, the retention time has not yet been considered as a scheduling constraint during automation of the sample preparation using an FMB in order to obtain the scheduled mixing graphs. In this paper, we propose a retention time aware scheduling method called time aware list scheduling ( TALS), which can be used with the state-of-the-art methods, and a new satisfiability based mixing algorithm called time aware sample preparation ( TASP) to obtain the scheduled mixing graph for a target ratio satisfying the retention time constraint and the number of available on-chip mixers in an FMB. Simulation results suggest that on an average TALS always outperforms a baseline scheduling method, while scheduling any mixing graph. Whereas, TASP can determine the optimal and scheduled mixing graphs compared to the existing mixing methods combined with TALS.