Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable non-rectangular devices.

Design Automation for Embedded Systems (Impact Factor: 0.24). 09/2010; 14:287-307. DOI: 10.1007/s10617-010-9059-x
Source: DBLP

ABSTRACT Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary
functions for biochemical analysis. The “digital” microfluidic biochips are manipulating liquids not as a continuous flow,
but as discrete droplets, and hence they are highly reconfigurable and scalable. A digital biochip is composed of a two-dimensional
array of cells, together with reservoirs for storing the samples and reagents. Several adjacent cells are dynamically grouped
to form a virtual device, on which operations are performed. So far, researchers have assumed that throughout its execution,
an operation is performed on a rectangular virtual device, whose position remains fixed. However, during the execution of
an operation, the virtual device can be reconfigured to occupy a different group of cells on the array, forming any shape,
not necessarily rectangular. In this paper, we present a Tabu Search metaheuristic for the synthesis of digital microfluidic
biochips, which, starting from a biochemical application and a given biochip architecture, determines the allocation, resource
binding, scheduling and placement of the operations in the application. In our approach, we consider changing the device to
which an operation is bound during its execution, to improve the completion time of the biochemical application. Moreover,
we devise an analytical method for determining the completion time of an operation on a device of any given shape. The proposed
heuristic has been evaluated using a real-life case study and ten synthetic benchmarks.

  • Design Automation for Embedded Systems 01/2015; DOI:10.1007/s10617-014-9157-2 · 0.24 Impact Factor
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    ABSTRACT: Microfluidic biochips represent an alternative to conventional biochemical analyzers. A digital biochip manipulates liquids not as continuous flow, but as discrete droplets on a two-dimensional array of electrodes. Several electrodes are dynamically grouped to form a virtual device, on which operations are executed by moving the droplets. So far, researchers have ignored the locations of droplets inside devices, considering that all the electrodes forming the device are occupied throughout the operation execution. In this article, we consider a droplet-aware execution of microfluidic operations, which means that we know the exact position of droplets inside the modules at each time-step. We propose a Tabu Search-based metaheuristic for the synthesis of digital biochips with droplet-aware operation execution. Experimental results show that our approach can significantly reduce the application completion time, allowing us to use smaller area biochips and thus reduce costs.
    ACM Journal on Emerging Technologies in Computing Systems 02/2013; 9(1). DOI:10.1145/2422094.2422096 · 0.83 Impact Factor
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    ABSTRACT: With the advances of the microfluidic technology, the design of digital microfluidic biochips recently received significant attention. But thus far, the corresponding design tasks such as binding, scheduling, placement, and routing have usually been considered separately. Furthermore, often just heuristic results have been obtained. In this work, we present a one-pass synthesis scheme which directly realizes the desired functionality onto the chip and, at the same time, guarantees minimality with respect to area and/or timing. For this purpose, the deductive power of solvers for Boolean satisfiability is exploited. Experiments show how the approach leverages the design of the respective devices.