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Towards droplet size-aware biochemical application compilation for AM-EWOD biochips

Mirela Alistar, Paul Pop
2015 2015 Symposium on Design, Test, Integration and Packaging of MEMS/MOEMS (DTIP)  
Our routing algorithm is developed for a novel digital microfluidic biochip architecture based on Active Matrix Electrowetting on Dielectric, which uses a thin film transistor array for the electrodes.  ...  Several approaches have been proposed for the compilation of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource  ...  However, recently, a novel digital microfluidic biochip architecture has been developed based on Active Matrix Electrowetting on Dielectric (AM-EWOD), which uses a thin film transistor (TFT) array for  ... 
doi:10.1109/dtip.2015.7161024 fatcat:yxbzpyddvfdv7ehsvod6ogtdna

Drug Discovery Acceleration Using Digital Microfluidic Biochip Architecture and Computer-aided-design Flow

2019 International Journal of Engineering  
A Digital Microfluidic Biochip (DMFB) offers a promising platform for medical diagnostics, DNA sequencing, Polymerase Chain Reaction (PCR), and drug discovery and development.  ...  There is an urgent need for collaboration between experts of drug discovery, microfluidic platform architecture and also machine learning to design a data-driven microfluidic architecture which improves  ...  steps on a digital microfluidic biochip [5] .  ... 
doi:10.5829/ije.2019.32.08b.13 fatcat:7qezfhg7evenvjc4cby7wnk45a

Design of Microfluidic Biochips (Dagstuhl Seminar 15352)

Krishnendu Chakrabarty, Tsung-Yi Ho, Robert Wille, Marc Herbstritt
2016 Dagstuhl Reports  
The goal of the seminar was to bring together experts in order to present and to develop new ideas and concepts for design automation algorithms and tools for microfluidic biochips.  ...  Advances in microfluidic technologies have led to the emergence of biochip devices for automating laboratory procedures in biochemistry and molecular biology.  ...  Algorithms for Automated Sample Preparation using Digital Microfluidic Biochips Our research envisions the algorithmic microfluidics and it expands the computer-aideddesign (CAD) research to develop DMF  ... 
doi:10.4230/dagrep.5.8.34 dblp:journals/dagstuhl-reports/ChakrabartyHW15 fatcat:ysb7qihxujdwtoh4xp36rwviau

Design and optimization of a digital microfluidic biochip for protein crystallization

Tao Xu, Krishnendu Chakrabarty, Vamsee K. Pamula
2008 2008 IEEE/ACM International Conference on Computer-Aided Design  
We present the design of a multi-well plate microfluidic biochip for protein crystallization; this biochip can transfer protein samples, prepare candidate solutions, and carry out crystallization automatically  ...  To reduce the manufacturing cost of such devices, we present an efficient algorithm to generate a pin-assignment plan for the proposed design.  ...  We have also described efficient droplet-routing algorithms for defect-tolerant well-loading. Fig. 1 : 1 Fabricated digital microfluidic arrays.  ... 
doi:10.1109/iccad.2008.4681589 dblp:conf/iccad/XuCP08 fatcat:5gaqew3it5ejfp5c34mh3ycbmu

Droplet-trace-based array partitioning and a pin assignment algorithm for the automated design of digital microfluidic biochips

Tao Xu, Krishnendu Chakrabarty
2006 Proceedings of the 4th international conference on Hardware/software codesign and system synthesis - CODES+ISSS '06  
We propose a partitioning algorithm based on the concept of "droplet trace", which is extracted from the scheduling and droplet routing results produced by a synthesis tool.  ...  Most prior work on CAD for biochips has assumed independent control of electrodes using a large number of (electrical) input pins.  ...  Thus, this novel technology is referred to as "digital microfluidics".  ... 
doi:10.1145/1176254.1176283 dblp:conf/codes/XuC06 fatcat:cukyfh3mfnc2vk3hdxex43qkri

Integrated droplet routing and defect tolerance in the synthesis of digital microfluidic biochips

Tao Xu, Krishnendu Chakrabarty
2008 ACM Journal on Emerging Technologies in Computing Systems  
Postsynthesis droplet routing does not guarantee that feasible droplet pathways can be found for area-constrained biochip layouts; nonroutable fabricated biochips must be discarded.  ...  As high-throughput bioassays are mapped to digital microfluidic platforms, the need for design automation techniques is being increasingly felt.  ...  In Section 3 we discuss related prior work on automated synthesis tools and postsynthesis droplet routing for digital microfluidic biochips.  ... 
doi:10.1145/1389089.1389091 fatcat:pseusgpvz5e6rfrcbrrzi2zbze

A high-performance droplet router for digital microfluidic biochips

Minsik Cho, David Z. Pan
2008 Proceedings of the 2008 international symposium on Physical design - ISPD '08  
In this paper, we propose a high-performance droplet router for digital microfluidic biochip (DMFB) design.  ...  When multiple droplets form a deadlock, our algorithm resolves it by backing off some droplets for concession.  ...  Yao-Wen Chang from National Taiwan University for providing experimental results of the network-flow based algorithm on our test designs.  ... 
doi:10.1145/1353629.1353672 dblp:conf/ispd/ChoP08 fatcat:qfeqw5gnwbhspjvqe23p4pay4a

System-level design automation tools for digital microfluidic biochips

Krishnendu Chakrabarty, Fei Su
2005 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis - CODES+ISSS '05  
Biochips based on digital microfluidics offer a powerful platform for massively parallel biochemical analysis such as clinical diagnosis and DNA sequencing.  ...  Current full-custom design techniques for digital microfluidic biochips do not scale well for increasing levels of system integration.  ...  Following the analogy of microelectronics, this novel approach is referred to as "digital microfluidics".  ... 
doi:10.1145/1084834.1084887 dblp:conf/codes/ChakrabartyS05 fatcat:swxbvv2wsbfejb2yyrpsfyjbsq

Defect-Tolerant Design and Optimization of a Digital Microfluidic Biochip for Protein Crystallization

Tao Xu, Krishnendu Chakrabarty, Vamsee K. Pamula
2010 IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems  
Recently, droplet-based "digital" microfluidics have been used for executing protein assays on a chip.  ...  We present the design of a multi-well-plate microfluidic biochip for protein crystallization; this biochip can transfer protein samples, prepare candidate solutions, and carry out crystallization automatically  ...  Index Terms-Digital microfluidics, droplet routing, lab-onchip, pin-constrained biochip design, route scheduling, well-plate chip. I.  ... 
doi:10.1109/tcad.2010.2042888 fatcat:cxopih2dojhgzbomsw6sykmvrq

A Novel Double Fault Diagnosis and Detection Technique in Digital Microfluidic Biochips [chapter]

Sagarika Chowdhury, Rajat Kumar Pal, Goutam Saha
2015 Lecture Notes in Computer Science  
This paper presents a rigorous offline double fault diagnosis as well as a detection technique for Digital Microfluidic Biochips (DMFBs).  ...  In this paper, the proposed algorithm detects double faults anywhere in the chip satisfying the dynamic fluidic constraints and improves the fault diagnosis time to an extent.  ...  A network flow based routing algorithm has been proposed in [12] for the droplet routing problem on biochips [13] .  ... 
doi:10.1007/978-3-319-24369-6_15 fatcat:jcj3mmcn2vhxhhkka2wgrmer2i

A droplet routing technique for fault-tolerant digital microfluidic devices

Xiao Zhang, Frits van Proosdij, Hans G. Kerkhoff
2008 2008 IEEE 14th International Mixed-Signals, Sensors, and Systems Test Workshop  
This paper describes a droplet routing technique for a fault-tolerant digital microfluidic platform.  ...  Efficient droplet routing is one of the key approaches for realizing fault-tolerant microfluidic biochips. It requires that run-time diagnosis and fault recovery can be made possible in such systems.  ...  CONCLUSIONS This paper presented a novel method for routing droplets on a digital microfluidic device to ensure a fault-tolerant behavior.  ... 
doi:10.1109/ims3tw.2008.4581596 fatcat:dw6z5la7zfeurccw2zmmtihuoa

Automated design of pin-constrained digital microfluidic biochips under droplet-interference constraints

Tao Xu, William L. Hwang, Fei Su, Krishnendu Chakrabarty
2007 ACM Journal on Emerging Technologies in Computing Systems  
We propose a design automation method for pin-constrained biochips that manipulate nanoliter volumes of discrete droplets on a microfluidic array.  ...  The design procedure relies on a droplet-trace-based array partitioning scheme and an efficient pin assignment technique, referred to as the "Connect-5 algorithm."  ...  Thus, this novel technology is referred to as "digital microfluidics."  ... 
doi:10.1145/1295231.1295235 fatcat:t6luimczujfqjjysoaoj724kka

High-level synthesis of digital microfluidic biochips

Fei Su, Krishnendu Chakrabarty
2008 ACM Journal on Emerging Technologies in Computing Systems  
Current techniques for full-custom design of droplet-based "digital" biochips do not scale well for concurrent assays and for next-generation system-on-chip (SOC) designs that are expected to include microfluidic  ...  We propose a system design methodology that attempts to apply classical high-level synthesis techniques to the design of digital microfluidic biochips.  ...  ACKNOWLEDGMENTS We thank Tao Xu of Duke University for helping with the simulations.  ... 
doi:10.1145/1324177.1324178 fatcat:mwygtsi5sjewtdz4uhyvtygpne

Design Automation for Digital Microfluidic Biochips

Tsung-Yi Ho
2014 IPSJ Transactions on System LSI Design Methodology  
The "digital" microfluidic biochips (DMFBs) 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.  ...  Therefore, microfluidic research is witnessing a paradigm shift from the continuous-flowbased architecture to droplet-based architecture or, in particular, the digital microfluidic biochip (DMFB) [6]  ... 
doi:10.2197/ipsjtsldm.7.16 fatcat:6cskxmi2szbrtiyyiabqpry4uy

Defect-Aware High-Level Synthesis and Module Placement for Microfluidic Biochips

Tao Xu, Krishnendu Chakrabarty, Fei Su
2008 IEEE Transactions on Biomedical Circuits and Systems  
As chemists adapt more bioassays for concurrent execution on such "digital" droplet-based microfluidic platforms, system integration, design complexity, and the need for defect tolerance are expected to  ...  Recent advances in microfluidics technology have led to the emergence of miniaturized biochip devices, also referred to as lab-on-a-chip, for biochemical analysis.  ...  Schematic of a digital microfluidic biochip [14] . As in traditional IC design, the automated design of a digital microfluidic biochip can be divided into two major phases.  ... 
doi:10.1109/tbcas.2008.918283 pmid:23852633 fatcat:z6imlaefzvhwhh5ez4lt4hbs5a
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