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Journal ArticleDOI

A New Fluid-Chip Co-Design for Digital Microfluidic Biochips Considering Cost Drivers and Design Convergence

01 Oct 2018-Vol. 4, Iss: 4, pp 548-564
TL;DR: This paper aims to propose a fluid-chip co-design methodology in dealing with the consideration of the fluid- chip cost drivers, while reducing the design cycles in between.
Abstract: The design process for digital microfluidic biochips (DMFBs) is becoming more complex due to the growing need for essential bio-protocols. A number of significant fluid- and chip-level synthesis tools have been offered previously for designing an efficient system. Several important cost drivers like bioassay schedule length, total pin count, congestion-free wiring, total wire length, and total layer count together measure the efficiency of the DMFBs. Besides, existing design gaps among the sub-tasks of the fluid and chip level make the design process expensive delaying the time-to-market and increasing the overall cost. In this context, removal of design cycles among the sub-tasks is a prior need to obtain a low-cost and efficient platform. Hence, this paper aims to propose a fluid-chip co-design methodology in dealing with the consideration of the fluid-chip cost drivers, while reducing the design cycles in between. A simulation study considering a number of benchmarks has been presented to observe the performance.
Citations
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Proceedings ArticleDOI
01 Jan 2020
TL;DR: This paper presents a fluid-control co-design considering several important cost-driving issues like minimization of schedule length, control pin count, and wirelength, together with congestion-free and conflict-free wiring.
Abstract: Paper-based digital microfluidic biochips (PDMFBs) are becoming highly effective among the microfluidic platforms due to its low-cost and in-place fabrication. The designed electrodes and wiring can be fabricated on a piece of paper by an inkjet printer and conductive ink containing carbon nanotube particles (CNTs). However, due to induced control interference, the wires cannot pass by an arbitrary electrode. Each wire that is to be routed possesses its conflict electrode group, which must be avoided for a feasible droplet movement. This paper presents a fluid-control co-design considering several important cost-driving issues like minimization of schedule length, control pin count, and wirelength, together with congestion-free and conflict-free wiring. Observably, design gaps exist among the sub-tasks of the fluid-level, control-level, and fluid-control as a whole, due to their separate considerations. It indeed introduces many design cycles lengthening the design process, and thus increases the overall cost. In this context, this work integrates the sub-tasks as a prior need to obtain a low cost and efficient platform. Several benchmarks have been studied to evaluate the performance.

2 citations

Journal ArticleDOI
TL;DR: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the technology into the design process.
Abstract: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the ...

1 citations

Journal ArticleDOI
TL;DR: A machine learning-based model is built to predict violation in control design beforehand and accordingly guides the fluid-control codesign to tackle important cost-driving issues while attaining congestion- and conflict-free wiring and effectively eliminates the design cycles producing a low-cost platform.
Abstract: Paper-based digital microfluidic biochips (or P-DMFBs) are becoming highly impelling due to its low-cost and in-place fabrication of electrodes and control wiring on a single piece of paper having an inkjet printer and conductive ink. Despite enormous advantages, several complex design rules also subsist, such as avoidance of induced control interference, minimum separation among the control lines, and congestion-free wiring on a single layer, which is to be correlated leading toward overall feasibility of the design. Several cost raising issues, such as schedule length, control pin count, and wire length, must be considered for attaining a successful fluid-control codesign. Moreover, design gaps exist among the subtasks of the fluid level, control level, and fluid-control design as a whole, which undeniably impose expensive design cycles increasing overall cost. This article builds a machine learning-based model for the pin-constrained P-DMFBs to predict violation in control design beforehand and accordingly guides the fluid-control codesign to tackle important cost-driving issues while attaining congestion- and conflict-free wiring. This model effectively eliminates the design cycles producing a low-cost platform. The predictive model has been evaluated over a balanced data set. Several benchmarks for assessing the performance are studied.

1 citations


Cites background from "A New Fluid-Chip Co-Design for Digi..."

  • ...Like traditional DMFBs, through analyzing the activation sequences, a compatibility graph (Gcom) for a group of electrodes can be acquired [9], [15], where an edge denotes the compatibility between the electrode pairs....

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  • ...NP-hard [15], [25], [26]) is aimed to assure a higher quality solution of the fluid level, control level, and overall codesign....

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  • ...If the associated goals for fluid- and control-level tasks are viewed in isolation, a “good” result from a phase may guide to an “unsatisfactory” outcome for the succeeding phases [15]–[17]....

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  • ...wiring in a microfluidic platform [8], [15], [16]....

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Journal ArticleDOI
TL;DR: In this article , an attack-tolerant synthesis is proposed with two-way security through integrating attack-detection and attack-recovery from various Denial of Service attacks.
Abstract: A digital microfluidic biochip (DMFB) with cyber-physical adaptation implements complex bio-protocols with high precision and high throughput dealing with safety-critical applications including point-of-care diagnosis, personalized medicine, and drug development. Having integrated sensors with network connectivity, a cyber-physical DMFB is undeniably susceptible to attacks. A number of leading research works are carried out to assess various attacks and their impacts. Several defense mechanisms are developed by arranging on-chip monitoring systems through deployment of checkpoints. As checkpoints are external resources imposing a cost-overhead to the system, a cost-effective detection mechanism is of utmost importance. Moreover, after detecting an attack, an efficient recovery process is imperative to execute the associated bioassay in a vulnerable environment. Here, an attack-tolerant synthesis is proposed with two-way security through integrating attack-detection and attack-recovery from various Denial of Service attacks. Moreover, a selective re-synthesis approach has been introduced to allow multiple recovery steps to be executed simultaneously on the biochip. The recovery strategy is closely coupled with the detection process which makes the system adaptive towards attack-tolerance. Experimental results on several benchmarks demonstrate the efficacy of the proposed two-way attack-tolerance strategy.
References
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Journal ArticleDOI
TL;DR: This work provides a comprehensive integration throughout fluidic-operation scheduling, chip layout generation, control pin assignment, and wiring solution to achieve higher design performance and feasibility in digital microfluidic biochips.
Abstract: Recently, digital microfluidic biochips (DMFBs) have revolutionized many biochemical laboratory procedures and received much attention due to their many advantages, such as high throughput, automatic control, and low cost. To meet the challenges of increasing design complexity, computer-aided-design (CAD) tools have been used to build DMFBs efficiently. Current CAD tools generally conduct a two-stage based design flow of fluidic-level synthesis followed by chip-level design to optimize fluidic behaviors and chip architecture separately. Nevertheless, existing fluidic-chip design gap will become even wider with a rapid escalation in the number of assay operations incorporated into a single DMFB. As more and more large-scale assay protocols are delivered in the current emerging marketplace, this problem may potentially restrict the effectiveness and feasibility of the entire DMFB realization and thus needs to be solved quickly. In this paper, we propose the first fluidic-chip co-design methodology for DMFBs to effectively bridge the fluidic-chip design gap. Our work provides a comprehensive integration throughout fluidic-operation scheduling, chip layout generation, control pin assignment, and wiring solution to achieve higher design performance and feasibility. Experimental results show the effectiveness, robustness, and scalability of our co-design methodology on a set of real-life assay applications.

11 citations

Journal ArticleDOI
01 Oct 2018
TL;DR: Simulation results demonstrate that the first operation-variation-aware placement algorithm that fully utilizes the real-time detection since completion-time uncertainties have been considered leads to reduced time-to-result and minimizes the chip size while not exceeding completion time compared to the benchmarks.
Abstract: Digital microfluidic biochips (DMFBs) are an emerging technology that are replacing traditional laboratory procedures. With the integrated functions which are necessary for biochemical experiments, DMFBs are able to achieve automatic experiments. Recently, DMFBs based on a new architecture called micro-electrode-dot-array (MEDA) have been demonstrated. Compared with conventional DMFBs which sensors are specifically located, each microelectrode is integrated with a sensor on MEDA-based biochips. Benefiting from the advantage of MEDA-based biochips, real-time reaction-outcome detection is attainable. However, to the best of our knowledge, synthesis algorithms proposed in the literature for MEDA-based biochips do not fully utilize the real-time detection since completion-time uncertainties have not yet been considered. During the execution of a biochemical experiment, operations may finish earlier or delay due to variability and randomness in biochemical reactions. Such uncertainties also have effects when allocating modules for each fluidic operation and placing them on a biochip since a biochip with a fixed size area restricts the number and the size of these modules. Thus, in this paper, we proposed the first operation-variation-aware placement algorithm that fully utilizes the real-time detection since completion-time uncertainties have been considered. Simulation results demonstrate that with the proposed approach, it leads to reduced time-to-result and minimizes the chip size while not exceeding completion time compared to the benchmarks.

10 citations


"A New Fluid-Chip Co-Design for Digi..." refers background in this paper

  • ...able sized droplets on a chip [7], [8], [9]....

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Journal ArticleDOI
TL;DR: This paper presents a comprehensive survey on design automation for biochip, highlighting some recent works on bioassay analysis, resource binding, and scheduling in geometry level, and some possible future research directions.

9 citations


"A New Fluid-Chip Co-Design for Digi..." refers background in this paper

  • ...tion of an optimal bioassay schedule length is NP-hard, implying unless P = NP, there is no algorithm solving the problem in polynomial time [28]....

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Proceedings ArticleDOI
01 Jan 2017
TL;DR: A new scheduling scheme namely Reservoir and Mixer constrained Scheduling (RMS) is proposed that can schedule a mixing tree obtained by a mixing algorithm, while minimizing the number of switching such that the total completion time can be minimized.
Abstract: In recent years, digital microfluidic biochips are being dominantly used for implementing a wide range of biochemical laboratory protocols (bioprotocols) on hand-held devices. Accurate preparation of fluid-samples is a fundamental preprocessing step that is needed in many bioprotocols. Oftentimes, the number of reservoirs built on-chip may be far less than that of the reactant fluids to be mixed. Hence, during the execution of an assay, several fluids are to be unloaded from the reservoirs to make room for loading new fluids stored off-line. Such unload-wash-load steps (switching) may be required several times, and these steps, being manual, significantly impact assay-completion time. In this paper, we propose a new scheduling scheme namely Reservoir and Mixer constrained Scheduling (RMS) that can schedule a mixing tree obtained by a mixing algorithm, while minimizing the number of switching such that the total completion time can be minimized. Simulation results over a large number of target ratios show that given the mixing trees obtained by standard mixing algorithms such as MinMix/RMA/CoDOS, RMS reduces switching steps (on average by 40.3%/41.9%/33%) at the cost of increasing mixing time (by only 3.5%/6.2%/4.8%), compared to an existing scheduling scheme invoked with reservoir constraints.

9 citations


"A New Fluid-Chip Co-Design for Digi..." refers background in this paper

  • ...With the increase of required storages, a lesser number of mixers could be placed on the chip floor reducing chip throughput and hence delays the completion time [27]....

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Journal ArticleDOI
TL;DR: An orientation strategy for layout of a multichip that reduces routing congestion and consequently facilitates wire routing for the electrode array and supports a hierarchical approach to wire routing that ensures scalability is presented.
Abstract: Potential applications of digital microfluidic (DMF) biochips now include several areas of real-life applications like environmental monitoring, water and air pollutant detection, and food processing to name a few. In order to achieve sufficiently high throughput for these applications, several instances of the same bioassay may be required to be executed concurrently on different samples. As a straightforward implementation, several identical biochips can be integrated on a single substrate as a multichip to execute the assay for various samples concurrently. Controlling individual electrodes of such a chip by independent pins may not be acceptable since it increases the cost of fabrication. Thus, in order to keep the overall pin-count within an acceptable bound, all the respective electrodes of these individual pieces are connected internally underneath the chip so that they can be controlled with a single external control pin. In this article, we present an orientation strategy for layout of a multichip that reduces routing congestion and consequently facilitates wire routing for the electrode array. The electrode structure of the individual pieces of the multichip may be either direct-addressable or pin-constrained. The method also supports a hierarchical approach to wire routing that ensures scalability. In this scheme, the size of the biochip in terms of the total number of electrodes may be increased by a factor of four by increasing the number of routing layers by only one. In general, for a multichip with 4n identical blocks, (n p 1) layers are sufficient for wire routing.

8 citations


"A New Fluid-Chip Co-Design for Digi..." refers background in this paper

  • ...After obtaining a minimized schedule, a congestion-free wire routing is to be realized maintaining the permissible total wire length [14], [15]....

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