Scheduling and Fluid Routing for Flow-Based Microfluidic Laboratories-on-a-Chip

Abstract

Abstract-Microfluidic laboratories-on-chip (LoCs) are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis onchip. There are several types of LoCs, each having its advantages and limitations. In this paper we are interested in flow-based LoCs, in which a continuous flow of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex units, such as micropumps, switches, mixers and multiplexers, can be built. We consider that the architecture of the LoC is given, and we are interested in synthesizing an implementation, consisting of the binding of operations in the application to the functional units of the architecture, the scheduling of operations and the routing and scheduling of the fluid flows, such that the application completion time is minimized. To solve this problem, we propose a List Schedulingbased Application Mapping (LSAM) framework and evaluate it by using real-life as well as synthetic benchmarks. When biochemical applications contain fluids that may adsorb on the substrate on which they are transported, the solution is to use rinsing operations for contamination avoidance. Hence, we also propose a rinsing heuristic, which has been integrated in the LSAM framework.

Unified Contamination-Aware Routing Method Considering Realistic Washing Capacity Constraint in Digital Microfluidic Biochips

“…Objective: All functional droplets are routed from their sources to their targets without violating any constraints, such that the number of contamination spots, the number of used cells 1 , and the execution time of a bioassay are minimized.…”

“…Microfluidic laboratories-on-chip (LoCs) are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on chip [1]. In the automation and miniaturization applications of biochemical laboratories, the digital microfluidic biochips (DMFBs) are being widely used as a revolutionary technique to realize the lab-on-a-chip (LoC) [2], [3].…”

PathDriver

“…In recent years, a number of methods have been proposed to deal with the architecture design of biochips [11][12][13][14][15][16]. In [11] a top-down design flow is proposed to generate an optimized chip architecture while minimizing the completion time of bioassays.…”

“…In recent years, a number of methods have been proposed to deal with the architecture design of biochips [11][12][13][14][15][16]. In [11] a top-down design flow is proposed to generate an optimized chip architecture while minimizing the completion time of bioassays. In [12] physical design of biochips is investigated using a sequence-pair-based method, and it is formulated as a SAT problem in [13] to generate a close-tooptimal solution.…”

Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening

“…Advances in fabrication techniques have motivated design automation ("synthesis") research [6]. Objectives of synthesis methods thus far have included: physical design of biochips [7]- [10], bioassay mapping and scheduling [11], efficient control mechanisms for on-chip valves [12]- [15], and reduction of the number of interfacing pins [16], [17]. However, these methods cannot tackle the complexities of RFBs designed for high-throughput single-cell screening because of the following challenges: M. Ibrahim, A. Sridhar, and K. Chakrabarty are with the Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA (e-mail: {mohamed.s.ibrahim, aditya.sridhar, krishnendu.chakrabarty}@duke.edu).…”