Fractal Analysis of the Binding and Dissociation Kinetics for Different Analytes on Biosensor Surfaces

373 Pages·2008·3.75 MB·English

by  Ajit Sadana

Fractal Analysis of the Binding and
Dissociation Kinetics for Different
Analytes on Biosensor Surfaces
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Fractal Analysis of the
Binding and Dissociation
Kinetics for Different
Analytes on Biosensor
Surfaces
Ajit Sadana
Department of Chemical Engineering, and National Center for Computational Hydroscience and
Engineering, University of Mississippi, University, MS, USA
AND
Neeti Sadana, MD
Department of Anesthesiology, University of Miami, Miami, Florida, USA
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Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Cost and Implications of Medical Care of Some Common Diseases . . . . . . . . . . . . . . . . 1
2 Modeling and Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2.1 Variable rate coefficient . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2.2 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.2.3 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2.4 Triple-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2.5 Pfeifer’s fractal binding rate theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3 BiosensorPerformance Parameters and theirEnhancement . . . . . . . . . . . . . . . . . . . 19
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4 Fractal Analysis of Harmful Bacteria, Toxins, and Pathogen
Detection on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5 Fractal Binding and Dissociation Kinetics of Disease-Related
Compounds on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
v
vi Contents
6 Fractal Analysis of Binding and Dissociation of Analytes that Help
Control Diseases on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
6.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
6.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
6.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
6.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
6.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
7 Fractal Analysis of Binding and Dissociation of Small Molecules
Involved in Drug Discovery on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
7.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
7.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
8 Fractal Binding and Dissociation Kinetics of Prion-Related
Interactions on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
8.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
8.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
8.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
8.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
8.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
9 Fractal Analysis of Binding and Dissociation of DNA–Analyte
Interactions on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
9.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
9.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
9.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
9.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
9.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
10 Fractal Analysis of Binding and Dissociation of Protein–Analyte
Interactions on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
10.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
10.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
10.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
10.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
10.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
10.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Contents vii
11 Fractal Analysis of Different Compounds Binding and Dissociation
Kinetics on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
11.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
11.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
11.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
11.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
11.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
11.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
12 Fractal Analysis of Binding and Dissociation Kinetics of Environmental
Contaminants and Explosives on BiosensorSurfaces . . . . . . . . . . . . . . . . . . . . . . . . 297
12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
12.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
12.2.1 Single-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
12.2.2 Dual-fractal analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
12.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
12.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
13 Market Size and Economics forBiosensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
13.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
13.2 Collaboration between Companies, Universities, and State and
Governmental Agencies: Trends in Collaboration . . . . . . . . . . . . . . . . . . . . . . . . . 320
13.3 Factors that Could Help Increase/Decrease Biosensor Markets . . . . . . . . . . . . . . . 322
13.4 Examples of Biosensor Companies, their Product, and their
Financial Backers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
13.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
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Preface
Applications for biosensors in diverse areas of application continue to increase. The initial
application for biosensors was for the effective management of diabetes mellitus (DM) by
the detection of glucose levels in blood. However, since then medical and other applica-
tions for biosensors are gradually increasing. The similarities between the detection of
harmful pathogens brought into focus by implied and realistic terrorist threats and bio-
markers for the early detection of disease is being exploited in the development of biosen-
sors for different applications. The present book in the series of books on analyte–receptor
interaction kinetics on biosensor surfaces has a co-author (Neeti Sadana, MD) to empha-
size the medical applications of biosensors, and to provide a better perspective of their
applications. The initial chapter now provides not only a balance for the whole book, but
also eases one into what to expect in the following chapters.
Fractal mathematics provides a convenient means to provide novel physical insights
into the kinetics of analyte–receptor reactions occurring on biosensor surfaces. It is hoped
that eventually this will help improve the biosensor performance parameters such as sen-
sitivity, selectivity, response time, stability, etc. with the eventual goal of, for example,
(a) the early detection of biomarkers for harmful and insidious diseases and (b) providing
emergency personnel that extra few minutes to help move large sections of human popu-
lation from terrorist threat affected areas.
Chapter 1 focuses on the vast medical implications of fractals in modern medical practice.
The cost of current health care on society and diseased individuals is examined. Common
illnesses such as cardiovascular disease, cancer, and diabetes mellitus are explored to find
practical uses for fractal theory.
Chapter 2 outlines the basic fractal theory to model the binding and the dissociation (if
applicable) kinetics used. Asimple single-fractal model to analyze the kinetics is initially
presented. This is then followed by dual- and triple-fractal models to analyze complex
binding and dissociation kinetics when a single-fractal analysis did not provide an ade-
quate fit. In Chapter 3 different examples are presented wherein the biosensor performance
parameters have been enhanced by experimental modification and validated by the fractal
theory kinetics presented. This includes enhancement of biosensor sensitivity, immobi-
lization, reproducibility, resolution performance, etc.
The detection of harmful bacteria, toxins, and pathogens on biosensor surfaces is out-
lined in Chapter 4. TV (CNN) news in the United Sates in February 2007 indicated the
concerns that consumers expressed over food items available in grocery stores, and the
number of illnesses and also deaths resulting from pathogenic bacteria-contaminated food
(particularly different types of meat). Suggestions were made to increase the testing for
these pathogenic bacteria (such as Salmonella, Listeria monocytogenes, and Escherichia
coli) by the governmental agencies responsible. One of the major themes for the book is
the application of biosensors for the early detection of insidious diseases, specifically their
biomarkers. This has been brought into proper perspective in the first chapter by an expert
ix