Design Automation for Microfluidics

Front-End Research for Continous-Flow Microfluidics

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 overcome the new design challenges. Our group therefore has developed a series of front-end design automation methods for continuous-flow microfluidics, with a focus on introducing new components and application characteristics, to provide more practical and effective solutions to the front-end design problems.

In recent years, we also work on the synchronization with real-time systems. Studies have shown a need for an interactive firmware layer in microfluidic platforms that can collect data from on-chip sensors, make decisions based on the collected data, and appropriately allocate resources.

COLUMBA: Co-Layout Design Automation Tool for Microfluidic Large-Scale Integration

Current continuous-flow microfluidic large-scale integration (mLSI) is designed manually, which is time-consuming and error-prone. In recent years, design automation research for mLSI evolves rapidly, aiming to replace manual labor by computers. Our group has developed Columba, which takes plain-text netlist descriptions as inputs, and performs simultaneous placement and routing for multiple layers while ensuring the planarity of each layer. The outputs of Columba are AutoCAD-compatible designs that fulfill all designs rules and can be directly used for mask fabrication (an example of the designs fabricated from Columba outputs are shown on the right). Columba is the first large-scale design automation tool that can seamlessly synchronize with the manufacturing flow of mLSI.

Our future targets are to synchronize Columba with front-end design automation methods and with biochemical applications. We are seeking for collaborations with bioengineering and biochemical experts.

Synthesis and Testing for Homogeneous Microfluidic Large-Scale Integration

Recent advances in manufacturing technologies of continuous-flow microfluidic large-scale integration (mLSI) have enabled valve density to reach 1 million per cm2, and consequently mLSI within a homogeneous architecture (all channel walls and device walls are built by valves) has emerged to achieve higher flexibility and reconfigurability. By controlling the states of valves, channels, storages and mixers can be constructed and destructed dynamically during the assay process.

Our group has worked on developing synthesis and testing methods for homogeneous mLSI. For the synthesis part, our targets include the formation of the devices and the validation of the fluid routing. For the testing part, we focus on modeling representative manufacturing defects and developing efficient defect-screening techniques. We hope that our design automation solutions can facilitate the industrial adoption of homogeneous mLSI.

Selected Publications

Fangda Zuo, Mengchu Li, Tsun-Ming Tseng, Tsung-Yi Ho, Ulf Schlichtmann
Relative-Scheduling-Based High-Level Synthesis for Flow-Based Microfluidic Biochips
In: IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
November 2021
(Paper)

Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, Ulf Schlichtmann
An Efficient Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39(2), 359 -- 372
February 2020
(Paper)

Tsun-Ming Tseng, Mengchu Li, Yushen Zhang, Tsung-Yi Ho, Ulf Schlichtmann
Cloud Columba: Accessible Design Automation Platform for Production and Inspiration
In: IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
November 2019
(Invited Paper) (Paper)

Mengchu Li, Tsun-Ming Tseng, Yanlu Ma, Tsung-Yi Ho, Ulf Schlichtmann
VOM: Flow-Path Validation and Control-Sequence Optimization for Multilayered Continuous-Flow Microfluidic Biochips
In: IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
November 2019
(Paper)

Tsun-Ming Tseng, Mengchu Li, Daniel Nestor Freitas, Travis McAuley, Bing Li, Tsung-Yi Ho, Ismail Emre Araci, Ulf Schlichtmann
Columba 2.0: A Co-Layout Synthesis Tool for Continuous-Flow Microfluidic Biochips
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 37(8), 1588 - 1601
August 2018
(Paper) (Video1) (Video2) (Video3)

Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, Ulf Schlichtmann
Fault-tolerant valve-based microfluidic routing fabric for droplet barcoding in single-cell analysis
In: Design, Automation and Test in Europe (DATE)
March 2018

Yasamin Moradi, Krishnendu Chakrabarty, Ulf Schlichtmann
An Efficient Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Single-Cell Analysis
In: IEEE European Test Symposium
2018

Mengchu Li, Tsun-Ming Tseng, Bing Li, Tsung-Yi Ho, Ulf Schlichtmann
Component-Oriented High-Level Synthesis for Continuous-Flow Microfluidics Considering Hybrid-Scheduling
In: ACM/IEEE Design Automation Conference (DAC)
June 2017
(Paper)

Chunfeng Liu, Bing Li, Hailong Yao, Paul Pop, Tsung-Yi Ho, Ulf Schlichtmann
Transport or Store? Synthesizing Flow-based Microfluidic Biochips using Distributed Channel Storage
In: ACM/IEEE Design Automation Conference (DAC)
June 2017
(Paper)(Slides)(BibTeX)

Chunfeng Liu, Bing Li, Bhargab B. Bhattacharya, Krishnendu Chakrabarty, Tsung-Yi Ho, Ulf Schlichtmann
Testing Microfluidic Fully Programmable Valve Arrays (FPVAs)
In: Design, Automation and Test in Europe (DATE)
March 2017
(pdf)(ppt)

Tsun-Ming Tseng, Bing Li, Mengchu Li, Tsung-Yi Ho, Ulf Schlichtmann
Reliability-aware Synthesis with Dynamic Device Mapping and Fluid Routing for Flow-based Microfluidic Biochips
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 35(12), 1981 - 1994
December 2016
(Paper)

Tsun-Ming Tseng, Mengchu Li, Bing Li, Tsung-Yi Ho, Ulf Schlichtmann
Columba: Co-Layout Synthesis for Continuous-Flow Microfluidic Biochips
In: ACM/IEEE Design Automation Conference (DAC)
June 2016
(Paper)

Mengchu Li, Tsun-Ming Tseng, Bing Li, Tsung-Yi Ho, Ulf Schlichtmann
Sieve-valve-aware Synthesis of Flow-based Microfluidic Biochips Considering Specific Biological Execution Limitations
In: Design, Automation and Test in Europe (DATE)
March 2016
(Paper)

Tsun-Ming Tseng, Bing Li, Ulf Schlichtmann, Tsung-Yi Ho
Storage and Caching: Synthesis of Flow-based Microfluidic Biochips
IEEE Design and Test 32(6), 69 - 75
December 2015
(Paper)

Tsun-Ming Tseng, Bing Li, Tsung-Yi Ho, Ulf Schlichtmann
Reliability-aware Synthesis for Flow-based Microfluidic Biochips by Dynamic-device Mapping
In: ACM/IEEE Design Automation Conference (DAC)
June 2015
(Paper)