Table Of Content

Error-Tolerant Biochemical Sample Preparation with Microfluidic Lab-on-Chip Microfluidic biochips have gained prominence due to their versatile applications to bio- chemistry and health-care domains such as point-of-care clinical diagnosis of tropical and cardiovascular diseases, cancer, diabetes, toxicity analysis, and for the mitigation of the global HIV crisis, among others. Microfluidic Lab-on-Chips (LoCs) offer a convenient platform for emulating various fluidic operations in an automated fashion. However, be- cause of the inherent uncertainty of fluidic operations, the outcome of biochemical experi- ments performed on-chip can be erroneous even if the chip is tested a priori and deemed to be defect-free. Error-Tolerant Biochemical Sample Preparation with Microfluidic Lab- on-Chip focuses on the issues encountered in reliable sample preparation with digital microfluidic biochips (DMFBs), particularly in an error-prone environment. It presents state-of-the-art error management techniques and underlying algorithmic challenges along with their comparative discussions. • Describes a comprehensive framework for designing a robust and error-tolerant biomedical system which will help in migrating from cumbersome medical laboratory tasks to small-sized LoC-based systems • Presents a comparative study on current error-tolerant strategies for robust sample preparation using DMFBs and reports on efficient algorithms for error-tolerant sample dilution using these devices • Illustrates how algorithmic engineering, cyber-physical tools, and software techniques are helpful in implementing fault-tolerance • Covers the challenges associated with design automation for biochemical sample preparation • Teaches how to implement biochemical protocols using software-controlled microfluidic biochips Interdisciplinary in its coverage, this reference is written for practitioners and researchers in biochemical, biomedical, electrical, computer, and mechanical engineering, especially those involved in LoC or bio-MEMS design. Emerging Materials and Technologies Series Editor: Boris I. Kharissov Atomic Force Microscopy for Energy Research Cai Shen Self-Healing Cementitious Materials Technologies, Evaluation Methods, and Applications Ghasan Fahim Huseien, Iman Faridmehr, Mohammad Hajmohammadian Baghban Thin Film Coatings Properties, Deposition, and Applications Fredrick Madaraka Mwema, Tien-Chien Jen, and Lin Zhu Biosensors Fundamentals, Emerging Technologies, and Applications Sibel A. Ozkan, Bengi Uslu, and Mustafa Kemal Sezgintürk Error-Tolerant Biochemical Sample Preparation with Microfluidic Lab-on-Chip Sudip Poddar and Bhargab B. Bhattacharya Geopolymers as Sustainable Surface Concrete Repair Materials Ghasan Fahim Huseien, Abdul Rahman Mohd Sam, and Mahmood Md. Tahir Nanomaterials in Manufacturing Processes Dhiraj Sud, Anil Kumar Singla, Munish Kumar Gupta Advanced Materials for Wastewater Treatment and Desalination A.F. Ismail, P.S. Goh, H. Hasbullah, and F. Aziz Green Synthesized Iron-Based Nanomaterials Application and Potential Risk Piyal Mondal and Mihir Kumar Purkait Polymer Nanocomposites in Supercapacitors Soney C George, Sam John and Sreelakshmi Rajeevan Polymers Electrolytes and their Composites for Energy Storage/Conversion Devices Achchhe Lal Sharma, Anil Arya and Anurag Gaur Hybrid Polymeric Nanocomposites from Agricultural Waste Sefiu Adekunle Bello Photoelectrochemical Generation of Fuels Edited by Anirban Das, Gyandeshwar Kumar Rao and Kasinath Ojha Emergent Micro- and Nanomaterials for Optical, Infrared, and Terahertz Applications Edited by Song Sun, Wei Tan, and Su-Huai Wei For more information about this series, please visit: www.routledge.com/Emerging-Materials-and-Technologies/book-series/CRCEMT Error-Tolerant Biochemical Sample Preparation with Microfluidic Lab-on-Chip Sudip Poddar and Bhargab B. Bhattacharya First edition published 2023 by CRC Press 6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742 and by CRC Press 4 Park Square, Milton Park, Abingdon, Oxon, OX14 4RN © 2023 Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, LLC Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, access www. copyright.com or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. For works that are not available on CCC please contact [email protected] Trademark notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. ISBN: 978-1-032-11380-7 (hbk) ISBN: 978-1-032-11385-2 (pbk) ISBN: 978-1-003-21965-1 (ebk) DOI: 10.1201/9781003219651 Typeset in Nimbus Roman by KnowledgeWorks Global Ltd. Publisher’s note: This book has been prepared from camera-ready copy provided by the authors. Dedication Toourparents,teachers,andstudents Tay&lF orra ncis Tay&lFo rra nGcriosu p http://taylorandfrancis.com Contents Foreword...................................................................................................................xi Acknowledgments...................................................................................................xiii Biographies..............................................................................................................xv SECTION I Introduction and Background Chapter1 Introduction.....................................................................................3 1.1 BasicsofMicrofluidicLab-on-Chips.....................................4 1.1.1 DigitalMicrofluidicLab-on-chips.............................5 1.1.2 Biochips based on Micro-Electrode Dot-Array (MEDA)architecture.................................................6 1.2 Basicsofsamplepreparationandvolumetricsplit-errors......9 1.3 Scopeofthebook.................................................................12 1.4 Organizationofthebook......................................................13 Chapter2 Background....................................................................................15 2.1 Preliminaries.........................................................................15 2.1.1 Mixingmodels.........................................................15 2.1.2 ConcentrationandDilutionfactors..........................16 2.1.3 AutomateddilutionofaSampleFluid.....................16 2.1.3.1 Linearandserialdilution.........................17 2.1.3.2 Exponentialandinterpolateddilution.....18 2.2 Prior-workonsamplepreparation........................................18 2.3 Effectofvolumetricsplit-errorsontargetconcentration......21 2.4 Error-correctionduringmulti-targetsamplepreparation......22 2.5 Conclusion............................................................................23 SECTION II Literature Review Chapter3 ErrorRecoveryMethodsforBiochips...........................................27 3.1 Designobjectivesforerror-recovery....................................27 3.2 ErrorRecoverywithregularDMFBs....................................29 3.2.1 Integratedcontrol-pathdesignanderrorrecovery...29 vii viii Contents 3.2.2 Synthesis of Protocols on DMFBs with opera- tionalvariability.......................................................30 3.2.3 Errorrecoveryincyber-physicalDMFBs................31 3.2.4 Dictionary-basedReal-timeErrorRecovery............32 3.2.5 Dynamicerrorrecoveryduringsamplepreparation33 3.2.6 Redundancy-basederrorrecoveryinDMFBs..........34 3.3 Error-recoverywithMEDABiochips...................................35 3.3.1 DropletSize-AwareandError-CorrectingSam- plePreparation.........................................................35 3.3.2 AdaptiveErrorRecoveryinMEDAbiochips..........37 3.3.3 Roll-ForwardErrorRecoveryinMEDABiochips..38 3.4 Conclusion............................................................................42 SECTION III Design Automation Methods Chapter4 Error-CorrectingSamplePreparationwithCyber-physical DMFBs ........................................................................................45 4.1 Automatedsamplepreparation.............................................46 4.1.1 RelatedPriorWork..................................................46 4.1.2 Roll-forwardSchemeforErrorRecovery................46 4.2 Motivationandproblemformulation....................................48 4.2.1 Errormodeling:effectoferrorsontarget-CFs........49 4.2.2 Impact of multiple errors on target-CF: error collapsing.................................................................51 4.2.3 criticalandnon-criticalerrors..................................52 4.2.4 Cancellationofconcentrationerroratthetarget......56 4.2.5 ProblemFormulation...............................................58 4.3 Error-correctingdilutionalgorithm......................................59 4.3.1 Reactionpath:criticaloperation..............................59 4.3.2 Roll-forwarderrorrecovery.....................................60 4.4 DesigninganLoCforimplementingECSP.........................64 4.4.1 Descriptionofthelayout..........................................64 4.4.2 Simulationoferror-correctingdilution....................64 4.5 ExperimentalResults............................................................65 4.6 Conclusions...........................................................................70 Chapter5 EffectofVolumetricSplit-ErrorsonTarget-Concentration..........73 5.1 Error-recoveryapproaches:priorart.....................................73 5.2 Cyber-physicaltechniqueforerror-recovery........................74 5.2.1 Compilationforerror-recovery................................74 5.2.2 Workingprincipleofcyber-physical-basedDMFBs75 5.3 Effectofsplit-errorsontarget-CFs.......................................77 5.3.1 Singlevolumetricsplit-error....................................77 Contents ix 5.3.2 Multiplevolumetricsplit-errors...............................78 5.4 Worst-caseerrorintarget-CF...............................................80 5.5 MaximumCF-error:Ajustification......................................84 5.6 Conclusion............................................................................89 Chapter6 Error-ObliviousSamplePreparationwithDMFBs.......................91 6.1 SamplepreparationusingDMFBs........................................92 6.1.1 Samplepreparation..................................................93 6.1.2 ErrorsinDMFB.......................................................93 6.1.2.1 Dispensingerror......................................93 6.1.2.2 Volumetricspliterror...............................93 6.1.2.3 Critical/non-criticalsetoferrors.............94 6.1.3 SummaryofPriorArt..............................................95 6.2 EOSP:MainIdea..................................................................96 6.2.1 Error-vector(E).......................................................97 6.3 Effectoferrors......................................................................99 6.3.1 CriticalandNon-criticalsetoferrors....................100 6.3.2 EffectofMultipleErrorsontarget-CFs.................101 6.4 Baselineapproachtoerror-obliviousness...........................103 6.5 Resultingmethodology.......................................................105 6.6 Experimentalresults...........................................................112 6.7 Conclusions.........................................................................118 Chapter7 Robust Multi-Target Sample Preparation On-Demand with DMFBs........................................................................................121 7.1 Motivation...........................................................................123 7.2 Basicsofsamplepreparation..............................................124 7.3 Literaturereview.................................................................125 7.4 On-demandmulti-targetdilution-problem(MTD).............126 7.4.1 Problemdefinition..................................................128 7.4.2 Mainresults............................................................129 7.5 Rapidproductionoftarget-CFson-the-fly..........................130 7.5.1 IntegerLinearProgramming(ILP)formulation....131 7.5.2 Approximationscheme..........................................132 7.6 Generatingpartialsetofconcentrationfactors...................136 7.7 Reductionofon-chipreservoirs..........................................138 7.8 Streamingofdifferentsourceconcentrations.....................139 7.9 Experimentalresults...........................................................141 7.9.1 PerformanceevaluationofILPandtheapproxi- mationscheme.......................................................141 7.9.2 PerformanceevaluationofBCSscheme................142 7.9.3 PerformanceevaluationofMTSE..........................142 7.9.4 Performance of the integrated dilution scheme withMTSE.............................................................142