A progressive-ILP based routing algorithm for cross-referencing biochips

Abstract

Due to recent advances in microfluidics technology, digital microfluidic biochips and their associated CAD problems have gained much attention, most of which has been devoted to direct-addressing biochips. In this paper, we solve the droplet routing problem under the more scalable crossreferencing biochip paradigm, which uses row/column addressing scheme to activate electrodes. We propose the first droplet routing algorithm that directly solves the problem of routing in cross-referencing biochips. The main challenge of this type of biochips is the electrode interference which prevents simultaneous movement of multiple droplets. We first present a basic integer linear programming (ILP) formulation to optimally solve the droplet routing problem. Due to its complexity, we also propose a progressive ILP scheme to determine the locations of droplets at each time step. Experimental results demonstrate the efficiency and effectiveness of our progressive ILP scheme on a set of practical bioassays.

Droplet-routing-aware module placement for cross-referencing biochips

“…Another more promising method is called cross-referencing, which applies high and low voltages to a row (column) and a column (row) electrode so as to activate the cell at the corresponding intersection point. Figure 1(b) gives an illustration of a cross-referencing biochip [6].…”

“…Nevertheless, one can maximize the parallelism by carefully arranging voltages, and achieves routing result as good as routing in direct-addressing DMFB. In paper [6] and [7] it is shown that all the benchmarks can be routed by both proposed cross-referencing router. These routers are designed dedicatedly for routing in cross-referencing biochip.…”

“…marks including the protein bioassay, and more contemporary routers will be tested, e.g., router in [18] and in [6]. In the future, this work is expected to be expanded and included into the automated design tool chain for crossreferencing biochips, which will facilitate scheduler and router to provide dedicate effort in designing cross-referencing biochip.…”

Tabu search-based synthesis of dynamically reconfigurable digital microfluidic biochips

“…Su and Chakrabarty [16] have proposed an integer linear programming (ILP) model for scheduling and binding, considering a given allocation, but without addressing placement and routing. During the physical-level synthesis, the placement [18,25] of each module on the microfluidic array and the droplets routes [6,23,28] have to be determined.…”

“…Two approaches have been considered for solving this problem. The first approach, used in [17,23], consists in having a one-cell distance between any two adjacent modules, which is sufficient for isolating the functional regions on which operations are executing. However, if routing is not considered at the same time with placement, the resulted solution will require significant modifications for accomodating the necessary routes.…”