research-article

Concentration-Resilient Mixture Preparation with Digital Microfluidic Lab-on-Chip

Authors:

Sukanta Bhattacharjee,

Juinn-Dar Huang,

Bhargab B. BhattacharyaAuthors Info & Claims

ACM Transactions on Embedded Computing Systems (TECS), Volume 17, Issue 2

Article No.: 49, Pages 1 - 12

https://doi.org/10.1145/3157094

Published: 30 January 2018 Publication History

Abstract

Sample preparation plays a crucial role in almost all biochemical applications, since a predominant portion of biochemical analysis time is associated with sample collection, transportation, and preparation. Many sample-preparation algorithms are proposed in the literature that are suitable for execution on programmable digital microfluidic (DMF) platforms. In most of the existing DMF-based sample-preparation algorithms, a fixed target ratio is provided as input, and the corresponding mixing tree is generated as output. However, in many biochemical applications, target mixtures with exact component proportions may not be needed. From a biochemical perspective, it may be sufficient to prepare a mixture in which the input reagents may lie within a range of concentration factors. The choice of a particular valid ratio, however, strongly impacts solution-preparation cost and time. To address this problem, we propose a concentration-resilient ratio-selection method from the input ratio space so that the reactant cost is minimized. We propose an integer linear programming--based method that terminates very fast while producing the optimum solution, considering both uniform and weighted cost of reagents. Experimental results reveal that the proposed method can be used conveniently in tandem with several existing sample-preparation algorithms for improving their performance.

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Cited By

Yao YQiu DLiu HYang ZLiu XYang YDong C(2023)A Reliable and Secure Mobile Cyber-Physical Digital Microfluidic Biochip for Intelligent HealthcareIEEE Access10.1109/ACCESS.2023.333938611(137990-137998)Online publication date: 2023
https://doi.org/10.1109/ACCESS.2023.3339386
Ibrahim MZhong ZBhattacharya BChakrabarty K(2022)Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA BiochipsIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2021.310890941:8(2490-2503)Online publication date: Aug-2022
https://doi.org/10.1109/TCAD.2021.3108909
Mohammed SBhattacharjee SSong YChakrabarty KKarri RMohammed SBhattacharjee SSong YChakrabarty KKarri R(2021)Obfuscation for IP ProtectionSecurity of Biochip Cyberphysical Systems10.1007/978-3-030-93274-9_6(87-109)Online publication date: 21-Dec-2021
https://doi.org/10.1007/978-3-030-93274-9_6
Show More Cited By

Index Terms

Concentration-Resilient Mixture Preparation with Digital Microfluidic Lab-on-Chip
1. Hardware
  1. Electronic design automation
  2. Emerging technologies
    1. Electromechanical systems
      1. Microelectromechanical systems

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Published In

cover image ACM Transactions on Embedded Computing Systems

ACM Transactions on Embedded Computing Systems Volume 17, Issue 2

Special Issue on MEMCODE 2015 and Regular Papers (Diamonds)

March 2018

640 pages

ISSN:1539-9087

EISSN:1558-3465

DOI:10.1145/3160927

Editor:
Sandeep K. Shukla
Indian Institute of Technology, India

Issue’s Table of Contents

Copyright © 2018 ACM.

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Association for Computing Machinery

New York, NY, United States

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ACM Journals for the Design of Smart and Connected Systems

Publication History

Published: 30 January 2018

Accepted: 01 October 2017

Revised: 01 July 2017

Received: 01 March 2017

Published in TECS Volume 17, Issue 2

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Cited By

Yao YQiu DLiu HYang ZLiu XYang YDong C(2023)A Reliable and Secure Mobile Cyber-Physical Digital Microfluidic Biochip for Intelligent HealthcareIEEE Access10.1109/ACCESS.2023.333938611(137990-137998)Online publication date: 2023
https://doi.org/10.1109/ACCESS.2023.3339386
Ibrahim MZhong ZBhattacharya BChakrabarty K(2022)Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA BiochipsIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2021.310890941:8(2490-2503)Online publication date: Aug-2022
https://doi.org/10.1109/TCAD.2021.3108909
Mohammed SBhattacharjee SSong YChakrabarty KKarri RMohammed SBhattacharjee SSong YChakrabarty KKarri R(2021)Obfuscation for IP ProtectionSecurity of Biochip Cyberphysical Systems10.1007/978-3-030-93274-9_6(87-109)Online publication date: 21-Dec-2021
https://doi.org/10.1007/978-3-030-93274-9_6
Mohammed SBhattacharjee SSong YChakrabarty KKarri RMohammed SBhattacharjee SSong YChakrabarty KKarri R(2021)Watermarking for IP ProtectionSecurity of Biochip Cyberphysical Systems10.1007/978-3-030-93274-9_5(61-85)Online publication date: 21-Dec-2021
https://doi.org/10.1007/978-3-030-93274-9_5
Bhattacharjee SWille RHuang JBhattacharya B(2020)Storage-Aware Algorithms for Dilution and Mixture Preparation With Flow-Based Lab-on-ChipIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2019.290791139:4(816-829)Online publication date: Apr-2020
https://doi.org/10.1109/TCAD.2019.2907911
Dong CLiu LLiu HGuo WHuang XLian SLiu XHo T(2020)A Survey of DMFBs Security: State-of-the-Art Attack and Defense2020 21st International Symposium on Quality Electronic Design (ISQED)10.1109/ISQED48828.2020.9137016(14-20)Online publication date: Mar-2020
https://doi.org/10.1109/ISQED48828.2020.9137016
Bhattacharjee STang JPoddar SIbrahim MKarri RChakrabarty K(2019)Bio-chemical Assay Locking to Thwart Bio-IP TheftACM Transactions on Design Automation of Electronic Systems10.1145/336557925:1(1-20)Online publication date: 22-Nov-2019
https://dl.acm.org/doi/10.1145/3365579
Shayan MBhattacharjee STang JChakrabarty KKarri R(2019)Bio-Protocol Watermarking on Digital Microfluidic BiochipsIEEE Transactions on Information Forensics and Security10.1109/TIFS.2019.290718514:11(2901-2915)Online publication date: Nov-2019
https://doi.org/10.1109/TIFS.2019.2907185
Bhattacharjee SBanerjee AHo TChakrabarty KBhattacharya B(2019)Efficient Generation of Dilution Gradients With Digital Microfluidic BiochipsIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2018.283441338:5(874-887)Online publication date: May-2019
https://doi.org/10.1109/TCAD.2018.2834413

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