Article

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

Design Automation for Embedded Systems (Impact Factor: 0.29). 01/2010; 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.

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    ABSTRACT: Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the basic functions for biochemical analysis. The "digital" microfluidic biochips are manipulating liquids not as a continuous flow, but as discrete droplets on a two-dimensional array of electrodes. Basic microfluidic operations, such as mixing and dilution, are performed on the array, by routing the corresponding droplets on a series of electrodes. So far, researchers have assumed that these operations are executed on rectangular virtual devices, formed by grouping several adjacent electrodes. One drawback is that all electrodes are considered occupied during the operation execution, although the droplet uses only one electrode at a time. Moreover, the operations can actually execute by routing the droplets on any sequence of electrodes on the array. Hence, in this paper, we eliminate the concept of virtual modules and allow the droplets to move on the chip on any route during operation execution. Thus, the synthesis problem is transformed into a routing problem. We propose an approach derived from a Greedy Randomized Adaptive Search Procedure (GRASP) and we show that by considering routing-based synthesis, significant improvements can be obtained in the application completion time. The proposed heuristic has been evaluated using two real-life case studies and ten synthetic benchmarks.
    Proceedings of the 2010 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems, CASES 2010, Scottsdale, AZ, USA, October 24-29, 2010; 01/2010
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