Component-oriented high-level synthesis for continuous-flow microfluidics considering hybrid-scheduling

Technological innovations in continuous-flow microfluidics require updated automated synthesis methods. As new microfluidic components and biochemical applications are constantly introduced, the current functionality-based application mapping methods and the fixed-time-slot scheduling methods are insufficient to solve the new design challenges. In this work, we propose a component-oriented general device concept that enables precise description of operations and devices, and adapts well to technological updates. Applying this concept, we propose a layering algorithm together with a mathematical modeling method to synthesize binding and hybrid-scheduling solutions that support both fixed schedule and real-time decisions. We also consider potential chip layout and optimize the number of flow channels among devices to save routing efforts. Experimental results demonstrate that our solution fully utilizes the chip resources and can handle operations with different requirements.

[1]  A. Levchenko,et al.  Lab-on-a-chip devices as an emerging platform for stem cell biology. , 2010, Lab on a chip.

[2]  S. Quake,et al.  Multistep Synthesis of a Radiolabeled Imaging Probe Using Integrated Microfluidics , 2005, Science.

[3]  S. Quake,et al.  Versatile, fully automated, microfluidic cell culture system. , 2007, Analytical chemistry.

[4]  Luke P. Lee,et al.  Single-cell enzyme concentrations, kinetics, and inhibition analysis using high-density hydrodynamic cell isolation arrays. , 2006, Analytical chemistry.

[5]  Stephen R. Quake,et al.  Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm , 2012, Cell.

[6]  Yici Cai,et al.  Integrated Flow-Control Codesign Methodology for Flow-Based Microfluidic Biochips , 2015, IEEE Design & Test.

[7]  Samuel Aparicio,et al.  High-throughput microfluidic single-cell RT-qPCR , 2011, Proceedings of the National Academy of Sciences.

[8]  Yanju Wang,et al.  Integrated microfluidic and imaging platform for a kinase activity radioassay to analyze minute patient cancer samples. , 2010, Cancer research.

[9]  Tsung-Yi Ho,et al.  A top-down synthesis methodology for flow-based microfluidic biochips considering valve-switching minimization , 2013, ISPD '13.

[10]  Mohamed Ibrahim,et al.  Integrated and real-time quantitative analysis using cyberphysical digital-microfluidic biochips , 2016, 2016 Design, Automation & Test in Europe Conference & Exhibition (DATE).

[11]  Joseph B Hiatt,et al.  Automated microfluidic chromatin immunoprecipitation from 2,000 cells. , 2009, Lab on a chip.

[12]  Ulf Schlichtmann,et al.  Sieve-valve-aware synthesis of flow-based microfluidic biochips considering specific biological execution limitations , 2016, 2016 Design, Automation & Test in Europe Conference & Exhibition (DATE).

[13]  Ulf Schlichtmann,et al.  Columba: Co-layout synthesis for continuous-flow microfluidic biochips , 2016, 2016 53nd ACM/EDAC/IEEE Design Automation Conference (DAC).

[14]  Roland Zengerle,et al.  Technologies for Single-Cell Isolation , 2015, International journal of molecular sciences.

[15]  Stephen Quake,et al.  A nanoliter rotary device for polymerase chain reaction , 2002, Electrophoresis.

[16]  Axel Scherer,et al.  A microfluidic processor for gene expression profiling of single human embryonic stem cells. , 2008, Lab on a chip.

[17]  Paul Pop,et al.  Architectural synthesis of flow-based microfluidic large-scale integration biochips , 2012, CASES '12.

[18]  Timothy B. Stockwell,et al.  Nanoliter Reactors Improve Multiple Displacement Amplification of Genomes from Single Cells , 2007, PLoS genetics.

[19]  Ulf Schlichtmann,et al.  Reliability-aware synthesis for flow-based microfluidic biochips by dynamic-device mapping , 2015, 2015 52nd ACM/EDAC/IEEE Design Automation Conference (DAC).

[20]  T. N. Vijaykumar,et al.  Aquacore: a programmable architecture for microfluidics , 2007, ISCA '07.

[21]  Paul Pop,et al.  System-level modeling and synthesis of flow-based microfluidic biochips , 2011, 2011 Proceedings of the 14th International Conference on Compilers, Architectures and Synthesis for Embedded Systems (CASES).

[22]  R. Zengerle,et al.  Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications. , 2010, Chemical Society reviews.