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E-raamat: Algorithms for Sample Preparation with Microfluidic Lab-on-Chip

  • Formaat: 178 pages
  • Ilmumisaeg: 01-Sep-2022
  • Kirjastus: River Publishers
  • ISBN-13: 9781000795783
  • Formaat - PDF+DRM
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  • Formaat: 178 pages
  • Ilmumisaeg: 01-Sep-2022
  • Kirjastus: River Publishers
  • ISBN-13: 9781000795783

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Recent microfluidic technologies have brought a complete paradigm shift in automating biochemical processing on a tiny lab-on-chip (a.k.a. biochip) that replaces expensive and bulky instruments traditionally used in implementing bench-top laboratory protocols. Biochips have already made a profound impact on various application domains such as clinical diagnostics, DNA analysis, genetic engineering, and drug discovery, among others. They are capable of precisely manipulating micro-/pico-liter quantities of fluids, and provide integrated support for mixing, storage, transportation, and sensing, on-chip. In almost all bioprotocols, sample preparation plays an important role, which includes dilution and mixing of several fluids satisfying certain volumetric ratios. However, designing algorithms that minimize reactant-cost and sample-preparation time suited for microfluidic chips poses a great challenge from the perspective of protocol mapping, scheduling, and physical design.

Algorithms for Sample Preparation with Microfluidic Lab-on-Chip bridges the widening gap between biologists and engineers by introducing, from the fundamentals, several state-of-the-art computer-aided-design (CAD) algorithms for sample preparation with digital and flow-based microfluidic biochips.

Technical topics discussed in the book include:

- Basics of digital and flow-based microfluidic lab-on-chip
- Comprehensive review of state-of-the-art sample preparation algorithms
- Sample-preparation algorithms for digital microfluidic lab-on-chip
- Sample-preparation algorithms for flow-based microfluidic lab-on-chip
Preface ix
List of Figures
xi
List of Tables
xv
List of Abbreviations
xvii
1 Introduction
1(14)
1.1 Basics of Microfiuidic Biochips
2(4)
1.2 Design Automation of Microfiuidic Biochips
6(1)
1.3 Sample Preparation with Microfiuidic Biochips
7(6)
1.4 Organization of the Book
13(2)
2 Sample Preparation with Microfiuidic Biochips: A Review
15(14)
2.1 Dilution Algorithms for DMFB
17(4)
2.1.1 Single-target Dilution Algorithms
17(2)
2.1.2 Multiple-target Dilution Algorithms
19(1)
2.1.3 Generation of Dilution Gradients
20(1)
2.2 Mixing Algorithms for DMFB
21(1)
2.3 Droplet Streaming Algorithms
22(1)
2.4 Dilution and Mixing Algorithms for CFMB
22(2)
2.5 Summary
24(5)
3 Multiple Dilution Sample Preparation on Digital Microfiuidic Biochips
29(14)
3.1 Related Work
30(1)
3.2 Tree-pruning-based Dilution Algorithm
31(7)
3.2.1 Proposed Methodology
31(7)
3.3 Experimental Results
38(4)
3.4 Conclusions
42(1)
4 Efficient Generation of Dilution Gradients with Digital Microfluidic Biochips
43(30)
4.1 Literature Review
44(1)
4.2 Linear Gradient
45(6)
4.3 Exponential Gradient
51(4)
4.4 Complex-shaped Gradients
55(9)
4.4.1 Digital Curve Representation of a Gradient Profile
58(1)
4.4.2 Identification of DSS on a Gradient Profile
58(6)
4.5 Experimental Results
64(7)
4.5.1 Linear Gradient
64(1)
4.5.2 Exponential Gradients
65(3)
4.5.3 Parabolic, Sinusoidal, and Gaussian Gradients
68(3)
4.6 Conclusions
71(2)
5 Concentration-Resilient Mixture Preparation
73(18)
5.1 Related Work
74(2)
5.2 Motivation and Problem Definition
76(3)
5.3 Proposed Method
79(3)
5.3.1 An ILP Formulation for Optimal Solution
80(2)
5.4 Experimental Results
82(7)
5.5 Conclusions
89(2)
6 Dilution and Mixing Algorithms for Flow-based Microfluidic Biochips
91(34)
6.1 Sample Preparation and Mixing Models
92(3)
6.2 Related Work
95(1)
6.3 Motivation and Contribution
96(3)
6.4 Overview of the Proposed Method
99(1)
6.5 Dilution
100(9)
6.5.1 Approximation of the Target Concentration Factor
101(1)
6.5.2 Modeling of Dilution
102(5)
6.5.3 Dilution Algorithm
107(2)
6.6 Mixture Preparation
109(8)
6.6.1 Approximation of the Target Mixture-Ratio
109(1)
6.6.2 Generalized Mixing Algorithm
109(2)
6.6.3 SMT-based Modeling of Reagent-saving Mixing
111(4)
6.6.4 Reagent-Saving Mixing Algorithm
115(2)
6.7 Experimental Results
117(7)
6.7.1 Performance Evaluation for Dilution
118(1)
6.7.2 Performance Evaluation for Reagent-Saving Mixing
119(4)
6.7.3 Performance of FloSPA on Real-life Dilution and Mixing Ratios
123(1)
6.8 Conclusions
124(1)
7 Storage-Aware Algorithms for Dilution and Mixture Preparation with Flow-Based Lab-on-Chip
125(16)
7.1 Related Works
126(1)
7.2 Storage-Aware Sample Preparation
127(9)
7.2.1 Overview
128(1)
7.2.2 Storage-Aware Dilution
128(5)
7.2.3 Overview of the Storage-Aware Mixing
133(3)
7.3 Experimental Results
136(2)
7.3.1 Performance for Dilution
136(1)
7.3.2 Performance for Mixing
137(1)
7.4 Conclusions
138(3)
8 Conclusion and Future Directions
141(2)
Bibliography 143(14)
Index 157(2)
About the Authors 159
Sukanta Bhattacharjee, Bhargab B. Bhattacharya, Krishnendu Chakrabarty