ilp-based pin-count aware design methodology for microfluidic biochips chiung-yu lin and yao-wen...
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ILP-Based Pin-Count Aware Design Methodology for Microfluidic Biochips
Chiung-Yu Lin and Yao-Wen Chang
Department of EE, NTU
DAC 2009
Outline
Introduction Pin demand and proposed flow Stage assignment Device assignment Placement and routing guideline Experimental results Conclusions
Introduction
Digital microfluidic biochips, also referred to as lab-on-a-chip, have emerged as an alternative for conventional laboratory experiments.
A biochip consists of a 2D electrode array and peripheral devices (optical detector, dispensing ports, etc.)
Movement of the droplets are controlled by the electrodes.
Introduction
Devices and reactions Reservoirs/Dispensing ports: droplet generation Optical detector: droplet detection Mixer: mixing two droplets
Introduction
The side view of the 2D array. A droplet moves to an adjacent electrode when this electrode
is activated. A droplet can stay at one cell if its neighboring electrodes are
not activated.
Introduction
Pin demand and proposed flow
Classify the demand of pins Np into three categories:
Pin demand and proposed flow
Stage assignment: This stage minimizes Preaction by enables the synchronous
control of the reactions.
Pin demand and proposed flow
Device assignment: This stage minimizes Pbranching by matching the reactions
to specific devices.
Stage assignment
Advantage of Synchronous Reactions
(a) Asynchronous: Mixers 1 and 2 are controlled separately and do not share a control pin. A shorter completion time is achieved.
(b) Synchronous: Mixers 1 and 2 are controlled together, the mixers must begin and cease their mixing reactions synchronously. Mixers 1 and 2 can share their control pins.
Stage assignment
The Stage Assignment Problem
Given a bioassay, stage assignment divides the reactions into a set of execution stages, and each stage is dedicated to a single category of reactions.
e.g., generation of certain sample/reagent, mixing, optical detection, etc.
Stage assignment
Following are the constraints for the stage assignment:
Capacity constraints: The number of reactions in a stage is upper-bounded by the
number of the devices belonging to the category of the stage.
Uniqueness constraints: A reaction exists in exactly one stage.
Duration constraints: The duration of a stage is the duration of the slowest reaction.
Stage assignment
Sequence constraints: Stages that belong to the same category are sorted and e
xecuted sequentially without overlapping.
Precedence constraints: If reaction Ri must happen before reaction Rj, then the sta
ge that includes Rj can begin only after the stage of Ri ends.
Problem Formulation for Stage Assignment
Given:
Problem Formulation for Stage Assignment
Find: A partitioning of Sr into independent stages Sm,1, Sm,2, …,
Sm,Im, where Sm,i represents the i-th stage for Dm, and Im represents the max number of stages for Dm.
Corresponding start time Bm,i and finish time Em,i for these stages.
Minimize:
ILP Formulation for Stage Assignment
ILP Formulation for Stage Assignment
Solution Space Reduction
Reaction Category Mapping All gn,m,i with m≠Vn can be removed.
Upper Bound for the Stage Number Bound the number of stages used by each device categor
y.
Lower Bound for Assay Completion Time Add a lower bound for the assay completion time into the I
LP formulation to speed up the runtime.
Device Assignment
Effect of Device Permutation Device assignment can affect the number of branchings. In (b), {1-1, 1-2, 2-1} three paths are used. In (c), {1-1, 2-1} only two paths are used and thus fewer el
ectrodes are needed for controlling the branchings.
Problem Formulation for Device Assignment
Given: Sr, Sd, Vn, Cm, Sp, Sm,i same as that from stage assignme
nt.
Find:
xn,z is the occurrence of that Rn is assigned to the z-th device of the category.
Minimize:
pm1,z1,m2,z2 denotes the existence of a path from the z1-th device of Dm1 to the z2-th device of Dm2.
ILP Formulation for Device Assignment
Solution-Space Reduction
Redundancy Pruning Reduce the solution space by removing the path
around universal peripheral reactions.
R1
R2
R3 R4
Placement and Routing Guideline
Pin-Count Saving Guidelines Provide guarding cells between two electrodes that work
in separate time spans. Electrodes E1 and E2 are turned on for different routing
paths in separate time slots, but they still cannot be controlled by the same pin because they are neighbors.
Placement and Routing Guideline
Propose the following placement and routing guidelines:
The placement and routing for the entire bioassay should be decided simultaneously on a 2D plane.
Routing paths should not touch each other, except for necessary crossings or branchings.
Guarding electrodes should be placed between devices and devices.
Experimental Results
Experimental Results
Experimental Results
Experimental Results
Conclusions
ILP-based algorithms have been proposed for the stage and device assignments with effective solution-space reductions.
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