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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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
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
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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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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08 Jun 2008
TL;DR: A broadcast-addressing-based design technique for pin-constrained multi-functional biochips that provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with "compatible" actuation sequences.
Abstract: Recent advances in digital microfluidics have enabled lab-on-a-chip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Basic operations such as droplet dispensing, mixing, dilution, localized heating, and incubation can be carried out using a two-dimensional array of electrodes and nanoliter volumes of liquid. The number of independent input pins used to control the electrodes in such microfluidic "biochips" is an important cost-driver, especially for disposable PCB devices that are being developed for clinical and point-of-care diagnostics. However, most prior work on biochip design-automation has assumed independent control of the electrodes using a large number of input pins. Another limitation of prior work is that the mapping of control pins to electrodes is only applicable for a specific bioassay. We present a broadcast-addressing-based design technique for pin-constrained multi-functional biochips. The proposed method provides high throughput for bioassays and it reduces the number of control pins by identifying and connecting control pins with "compatible" actuation sequences. The proposed method is evaluated using a multifunctional chip designed to execute a set of multiplexed bioassays, the polymerase chain reaction, and a protein dilution assay.
137 citations
"A New Fluid-Chip Co-Design for Digi..." refers methods in this paper
...For the evaluation purpose, benchmark bioassays, namely, Polymerase Chain Reactions (PCR), Multiplexed bioassay, DNA Sequencing, In Vitro Diagnostics, and Protein Assay as reported in [36], [37], [38] are considered....
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07 Jun 2004
TL;DR: A simulated annealing-based technique for module placement in “digital” droplet-based microfluidic biochips is presented, which not only addresses chip area, but also considers fault tolerance, which allows a micro fluidic module to be relocated elsewhere in the system when a single cell is detected to be faulty.
Abstract: Microfluidics-based biochips are soon expected to revolutionize clinical diagnosis, DNA sequencing, and other laboratory procedures involving molecular biology. Most microfluidic biochips today are based on the principle of continuous fluid flow and they rely on permanently etched microchannels, micropumps, and microvalves. We focus here on the automated design of “digital” droplet-based microfluidic biochips. In contrast to conventional continuous-flow systems, digital microfluidics offers dynamic reconfigurability; groups of cells in a microfluidics array can be reconfigured to change their functionality during the concurrent execution of a set of bioassays. We present a simulated annealing-based technique for module placement in such biochips. The placement procedure not only addresses chip area, but also considers fault tolerance, which allows a microfluidic module to be relocated elsewhere in the system when a single cell is detected to be faulty. Simulation results are presented for case studies involving the polymerase chain reaction and multiplexed in vitro clinical diagnostics.
111 citations
Additional excerpts
..., scheduling, placement, droplet routing, pin mapping, and wire routing [36], [39], [40], [41]....
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TL;DR: A droplet-routing method that avoids cross-contamination in the optimization of droplet flow paths and targets disjoint droplet routes and minimizes the number of cells used for droplet routing is proposed.
Abstract: Recent advances in digital microfluidics have enabled droplet-based biochip devices for DNA sequencing, immunoassays, clinical chemistry, and protein crystallization. Since cross-contamination between droplets of different biomolecules can lead to erroneous outcomes for bioassays, the avoidance of cross-contamination during droplet routing is a key design challenge for biochips. We propose a droplet-routing method that avoids cross-contamination in the optimization of droplet flow paths. The proposed approach targets disjoint droplet routes and synchronizes wash-droplet routing with functional droplet routing, in order to reduce the duration of droplet routing while avoiding the cross-contamination between different droplet routes. In order to avoid cross-contamination between successive routing steps, an optimization technique is used to minimize the number of wash operations that must be used between successive routing steps. Two real-life biochemical applications are used to evaluate the proposed droplet-routing methods.
100 citations
"A New Fluid-Chip Co-Design for Digi..." refers methods in this paper
...The Lee’s algorithm [30] can be applied here, effectively....
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TL;DR: In this paper, the authors considered the case of the weight constrained shortest path problem (WCSPP) defined on a graph without cycles and presented a new exact algorithm, based on scaling and rounding of weights.
78 citations
TL;DR: A branch and bound method which finds a maximum weight clique in an arbitrary weighted graph using a weighted coloring heuristic which simultaneously produces lower and upper bounds and a branching rule that uses the information obtained in the coloring.
Abstract: We present a branch and bound method which finds a maximum weight clique in an arbitrary weighted graph. The main ingredients are a weighted coloring heuristic which simultaneously produces lower and upper bounds and a branching rule that uses the information obtained in the coloring. The algorithm performs comparable to the fastest method known so far but is much easier to implement.
76 citations
"A New Fluid-Chip Co-Design for Digi..." refers methods in this paper
...From Theorem 2, as it follows that an instance of MWCP is equivalent to that of MCWR, the algorithms [33], [34], [35] solving MWCP can be preferably tailored in solving MCWR....
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