Exact routing for digital microfluidic biochips with temporary blockages

Abstract

Abstract-Digital microfluidic biochips enable a higher degree of automation in laboratory procedures in biochemistry and molecular biology and have received significant attention in the recent past. Their design is usually conducted in several stages with routing being a particularly critical challenge. Previously proposed solutions for this design step suffer from two issues: They are mainly of heuristic nature and usually assume that the blockages to be bypassed are present the entire time. In contrast, we present a methodology which exploits the fact that blockages are often only present at certain intervals. At the same time, our approach guarantees exact solutions, i.e. always determines a routing with a minimal number of time steps. Experimental results show that, despite the huge complexity, optimal results can be achieved in reasonable run-time and that the consideration of temporary blockages indeed significantly improves the routing results.

A general and exact routing methodology for Digital Microfluidic Biochips

“…Finally, the required run-time (in CPU seconds) needed to obtain both the routing as well as the pin mapping is listed (denoted by CPU time). As can clearly be seen, for a variety of pin-aware routing tasks which similarly have also been considered in related work (such as [14], [20]), (minimal) solutions can be obtained in a rather efficient fashion.…”

“…This includes greedy approaches [5], [10] as well methods based on network-flows [9] or the concept of entropy [17] together with clever heuristics or solving schemes such as dynamic programming. While these solutions lead to heuristic results, also exact methods aiming for minimal routings have been considered e.g., in [18] (based on Integer Linear Programming, ILP) or [19], [20] (based on Boolean satisfiability, i.e. SAT).…”

“…By this, the precise pin mapping becomes irrelevant and the solver only has to determine the actual movements of the droplets in order to realize the routing. In doing so, all problems as considered in [9], [10], [17], [20] can easily be addressed without the need for the specific suboptimal solutions proposed in previous work.…”

Advances in Design Automation Techniques for Digital-Microfluidic Biochips

“…It creates the final layout of the biochip, consisting of the placement of microfluidic modules such as mixers and storage units [22][23][24], the routes that droplets take between different modules [28][29][30], and other geometrical details [20]. This is the reason why this step is also known as geometry-level synthesis.…”

“…Therefore, Keszocze et al provide a droplet routing solution that considers temporality of blockages in [30]. In addition, to tackle the complexity of droplet routing, they exploit the power of Satisfiability Modulo Theory (SMT) solvers to obtain an exact routing solution.…”