Nanodevices for the Life Sciences

by Kumar, Challa S. S. R.

• ISBN13: 9783527313846
• ISBN10: 3527313842
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-09-22
• Publisher: Wiley-VCH

Summary

This is the first book to look at both nanodevices assembled from biomaterials as well as nanodevices of non-biological origin, providing systematic coverage of how both kinds can be used in the context of nanoscale life science research and development.

Author Biography

Challa Kumar is currently the Group Leader of Nanofabrication at the Center for Advanced Microstructures and Devices (CAMD), Baton Rouge, USA. His research interests are in developing novel synthetic methods for functional nanomaterials and innovative therapeutic, diagnostic and sensory tools based on nanotechnology. He has eight years of industrial R&D experience working for Imperial Chemical Industries and United Breweries prior to joining CAMD. He is the founding Editor-in-Chief of the Journal of Biomedical Nanotechnology, an international peer reviewed journal published by American Scientific Publishers, and the series editor for the ten-volume book series Nanotechnologies for the Life Sciences (NtLS) published by Wiley-VCH. He worked at the Max Planck Institute for Biochemistry in Munich, Germany, as a post doctoral fellow and at the Max Planck Institute for Carbon Research in Mnlheim, Germany, as an invited scientist. He obtained his Ph.D. degree in synthetic organic chemistry from Sri Sathya Sai Institute of Higher Learning, Prashanti Nilayam, India.

Table of Contents

Preface	XIII
List of Contributors	XVII
1 The Physics and Modeling of Biofunctionalized Nanoelectromechanical Systems	1	(28)
Mark R. Paul and Jerry E. Solomon
1.1 Introduction	1	(3)
1.2 The Stochastic Dynamics of Micro- and Nanoscale Oscillators in Fluid	4	(15)
1.2.1 Fluid Dynamics at Small Scales	4	(4)
1.2.2 An Exact Approach to Determine the Stochastic Dynamics of Arrays of Cantilevers of Arbitrary Geometry in Fluid	8	(3)
1.2.3 An Approximate Model for Long and Slender Cantilevers in Fluid	11	(5)
1.2.4 The Stochastic Dynamics of a Fluid-coupled Array of (BIO)NEMS Cantilevers	16	(3)
1.3 The Physics Describing the Kinetics of Target Analyte Capture on the Oscillator	19	(5)
1.4 Detecting Noise in Noise: Signal-processing Challenges	24	(1)
1.5 Concluding Remarks	25	(1)
Acknowledgments	26	(1)
References	26	(3)
2 Mathematical and Computational Modeling: Towards the Development and Application of Nanodevices for Drug Delivery	29	(38)
John P. Sinek, Hermann B. Frieboes, Balakrishnan Sivaraman, Sandeep Sanga, and Vittorio Cristini
2.1 Introduction	29	(1)
2.2 RES Avoidance	30	(5)
2.2.1 A Statistical Model of Nanovector Surface Coverage	31	(4)
2.2.2 Modeling the Forces Mediating Protein Approach and Binding	35	(1)
2.3 Tumoral Vasculature and Hemodynamics	35	(12)
2.3.1 An Invasion Percolation Model of Vasculogenesis and Hemodynamics	37	(3)
2.3.2 Flow Simulations Using Anderson and Chaplain's Model	40	(5)
2.3.3 Particle Dynamics within the Tumoral Vasculature	45	(2)
2.4 Receptor–Ligand-mediated Binding	47	(7)
2.4.1 Bell's Deterministic Model	49	(3)
2.4.2 A Stochastic Model	52	(2)
2.5 Intratumoral and Cellular Drug Kinetics and Pharmacodynamics	54	(7)
2.5.1 A Two-Dimensional Model of Chemotherapy	55	(2)
2.5.2 Refinements of the Model	57	(4)
2.6 Conclusion	61	(1)
References	62	(5)
3 Nanolithography: Towards Fabrication of Nanodevices for Life Sciences	67	(42)
Johnpeter Ndiangui Ngunjiri, Jie-Ren Li, and Jayne Carol Garno
3.1 Introduction: Engineering Surfaces at the Nanoscale	67	(2)
3.2 Immobilization of Biomolecules for Surface Assays	69	(7)
3.2.1 Strategies for Linking Proteins to Surfaces	69	(1)
3.2.1.1 Electrostatic Immobilization	70	(1)
3.2.1.2 Covalent Immobilization	70	(1)
3.2.1.3 Molecular Recognition and Specific Interactions	71	(1)
3.2.1.4 Nonspecific Physical Adsorption to Surfaces	71	(3)
3.2.2 SAM Chemistry	74	(2)
3.3 Methods for Nanolithography with Proteins	76	(18)
3.3.1 Bias-induced Nanolithography of SAMs	78	(4)
3.3.2 Force-induced Nanolithography of SAMs	82	(5)
3.3.3 DPN of SAMs and Proteins	87	(4)
3.3.4 Latex Particle Lithography with Proteins	91	(3)
3.4 Detection of Protein Binding a the Nanoscale	94	(2)
3.5 Future Directions	96	(5)
3.5.1 Advantages of Nanoscale Detection	96	(1)
3.5.2 Development of Cantilever Arrays	97	(4)
3.5.3 Concluding Remarks	101	(1)
References	101	(8)
4 Microcantilever-based Nanodevices in the Life Sciences	109	(41)
Horatio D. Espinosa, Keun-Ho Kim, and Nicolaie Moldovan
4.1 Introduction	109	(2)
4.2 Microcantilevers	111	(15)
4.2.1 Microfabrication of Miniaturized Probes	112	(4)
4.2.2 Cantilever Probes for Nanopatterning	116	(5)
4.2.3 Elastomeric AFM Probes	121	(1)
4.2.4 Monolithically Fabricated Conductive Diamond Probes	122	(4)
4.3 Cantilevers with Integrated Micro- and Nanofluidics	126	(15)
4.3.1 Apertured Pyramidal Tips	126	(2)
4.3.2 Open-channel Cantilevered Microspotters	128	(5)
4.3.3 Closed-channel Cantilevered Nanopipettes	133	(3)
4.3.4 Micromachined Hypodermic Needle Arrays	136	(1)
4.3.5 NFPs	137	(4)
4.4 Applications	141	(2)
4.4.1 Patterning of DNA	141	(1)
4.4.2 Patterning of Proteins	142	(1)
4.4.3 Patterning of Viruses	143	(1)
4.5 Conclusions and Outlook	143	(1)
References	144	(6)
5 Nanobioelectronics	150	(39)
Ross Rinaldi and Giuseppe Maruccio
5.1 Introduction	150	(1)
5.2 Bio-self-assembly and Motivation	150	(3)
5.3 Fundamentals of the Bio-building Blocks	153	(2)
5.3.1 DNA	153	(1)
5.3.2 Proteins	154	(1)
5.4 Interconnection, Self-assembly and Device Implementation	155	(5)
5.4.1 Interconnecting Molecules	157	(1)
5.4.2 Delivering Molecules	158	(2)
5.5 Devices Based on DNA and DNA Bases	160	(17)
5.5.1 Charge Transfer in DNA	161	(3)
5.5.2 DNA Conductivity	164	(1)
5.5.2.1 Near-ohmic Behavior (Activated Hopping Conductor)	164	(1)
5.5.2.2 Semiconducting (Bandgap) Behavior	168	(1)
5.5.2.3 Insulating Behavior	169	(1)
5.5.2.4 Discussion of DNA Conductivity	170	(1)
5.5.2.5 Other Applications of DNA in Molecular Electronics	173	(4)
5.6 Devices Based on Proteins	177	(6)
5.7 Conclusions	183	(1)
Acknowledgments	183	(1)
References	184	(5)
6 DNA Nanodevices: Prototypes and Applications	189	(28)
Friedrich C. Simmel
6.1 Introduction	189	(1)
6.2 DNA as a Material for Nanotechnology	189	(4)
6.2.1 Nanoscale Science	189	(1)
6.2.2 Biophysical and Biochemical Properties of Nucleic Acids	190	(3)
6.2.3 DNA Nanoconstruction	193	(1)
6.3 Simple DNA Devices	193	(5)
6.3.1 Conformational Changes Induced by Small Molecules and Ions	193	(3)
6.3.2 Hybridization-driven Devices	196	(2)
6.4 Towards Functional Devices	198	(11)
6.4.1 Walk and Roll	199	(3)
6.4.2 Interaction with Proteins	202	(4)
6.4.3 Information Processing	206	(1)
6.4.4 Switchable Networks and Hybrid Materials	207	(2)
6.5 Autonomous Behavior	209	(3)
6.5.1 Driving Devices with Chemical Reactions	209	(1)
6.5.2 Genetic Control	210	(2)
6.6 Conclusion	212	(1)
Acknowledgments	213	(1)
References	213	(4)
7 Towards the Realization of Nanobiosensors Based on G-protein-coupled Receptors	217	(24)
Cecilia Pennetta, Vladimir Akimov, Eleonora Alfinito, Lino Reggiani, Tatiana Gorojankina, Jasmina Minic, Edith Pajot-Augy, Marie-Annick Persuy, Roland Salesse, Ignacio Casuso, Abdelhamid Errachid, Gabriel Gomila, Oscar Ruiz, Josep Samitier, Yanxia Hou, Nicole Jaffrezic, Giorgio Ferrari, Laura Fumagalli, and Marco Sampietro
7.1 Introduction	217	(3)
7.2 Preparation and Immobilization of GPCRs on Functionalized Surfaces	220	(1)
7.3 Signal Techniques	221	(1)
7.4 Theoretical Approach	222	(2)
7.5 The Impedance Network Model	224	(7)
7.6 Equilibrium Fluctuations	231	(4)
7.7 Conclusions	235	(1)
Acknowledgments	236	(1)
References	236	(5)
8 Protein-based Nanotechnology: Kinesin–Microtubule-driven Systems for Bioanalytical Applications	241	(31)
William O. Hancock
8.1 Introduction	241	(1)
8.2 Kinesin and Microtubule Cell Biology and Biophysics	242	(3)
8.2.1 Kinesin Motility Assays	244	(1)
8.3 Theoretical Transport Issues for Device Integration	245	(4)
8.3.1 Diffusion versus Transport Times	247	(2)
8.4 Interaction of Motor Proteins and Filaments with Synthetic Surfaces	249	(3)
8.4.1 Motor Adsorption	249	(2)
8.4.2 Microtubule Immobilization	251	(1)
8.5 Controlling the Direction and Distance of Microscale Transport	252	(7)
8.5.1 Directing Kinesin-driven Microtubules	252	(3)
8.5.2 Movement in Enclosed Microchannels	255	(2)
8.5.3 Immobilized Microtubule Arrays	257	(2)
8.6 Cargo Attachment	259	(3)
8.6.1 Maximum Cargo Size	261	(1)
8.7 System Design Consideration	262	(3)
8.7.1 Protein Stability and Lifetime	262	(2)
8.7.2 Sample Introduction and Detection	264	(1)
8.7.3 Analyte Detection and Collection	265	(1)
8.8 Conclusion	265	(1)
Acknowledgments	266	(1)
References	266	(6)
9 Self-assembly and Bio-directed Approaches for Carbon Nanotubes: Towards Device Fabrication	272	(45)
Arianna Filoramo
9.1 Introduction	272	(2)
9.2 CNTs: Basic Features, Synthesis and Device Applications	274	(4)
9.2.1 Basic Features	274	(2)
9.2.2 Synthesis of Nanotubes	276	(1)
9.2.3 Device Applications	277	(1)
9.3 Fabrication of CNT Transistors and Self-assembly Approaches	278	(2)
9.4 In situ CVD Growth	280	(1)
9.5 Selective Deposition of CNTs by SAM-assisted Techniques	281	(10)
9.5.1 Methodology and Key Parameters	282	(6)
9.5.2 Performance of CNTFETs Fabricated by the SAM Method	288	(3)
9.6 DNA-directed Self-assembly	291	(13)
9.6.1 The Assembly of the Scaffold	292	(2)
9.6.2 Selective Attachment of the DNA Scaffold on the Surface Microscale Electrodes	294	(1)
9.6.3 Positioning of Nano-objects or Nanodevices on the Scaffold	295	(3)
9.6.4 Realization of Electrical Connections and Circuitry	298	(5)
9.6.5 Fabrication of DNA-directed CNT Devices	303	(1)
9.7 Conclusion	304	(1)
References	305	(12)
10 Nanodevices for Biosensing: Design, Fabrication and Applications	317	(31)
Laura M. Lechuga, Kirill Zinoviev, Laura C. Carrascosa, and Miguel Moreno
10.1 Introduction	317	(1)
10.2 From Biosensor to Nanobiosensor Devices	318	(3)
10.2.1 Overview	318	(2)
10.2.2 Biological Functionalization of Nanobiosensors	320	(1)
10.3 Nanophotonic Biosensors	321	(9)
10.3.1 Overview	321	(1)
10.3.2 Integrated Mach–Zehnder Interferometer (MZI) Nanodevice	322	(1)
10.3.2.1 Design and Fabrication	323	(1)
10.3.2.2 Characterization and Applications	325	(4)
10.3.3 Integration in Microsystems	329	(1)
10.4 Nanomechanical Biosensors	330	(14)
10.4.1 Overview	330	(1)
10.4.2 Working Principle	330	(2)
10.4.3 Detection Systems	332	(1)
10.4.4 Design of a Standard Microcantilever Sensor	333	(1)
10.4.4.1 Fabrication of a Standard Microcantilever Sensor	334	(1)
10.4.4.2 Optical Waveguide Microcantilever: Design and Fabrication	337	(1)
10.4.4.2.1 Principle of Operation and Theoretical Analysis	338	(1)
10.4.4.2.2 Fabrication and Characterization	339	(3)
10.4.5 Biosensing Applications of Nanomechanical Sensors	342	(2)
10.5 Conclusions and Future Goals	344	(1)
Acknowledgments	344	(1)
References	344	(4)
11 Fullerene-based Devices for Biological Applications	348	(38)
Ginka H. Sarova, Tatiana Da Ros, and Dirk M. Guldi
11.1 Introduction	348	(1)
11.2 Solubility	348	(2)
11.3 Toxicity	350	(1)
11.4 DNA Photocleavage	351	(25)
11.4.1 Photodynamic Therapy (PDT)	353	(5)
11.4.2 Fullerene-mediated Electron Transfer Across Membranes	358	(4)
11.4.3 Neuroprotective Activity via Radical Scavenging	362	(5)
11.4.4 Enzyme Inhibition and Antiviral Activity	367	(2)
11.4.5 Antibacterial Activity	369	(2)
11.4.6 Fullerenes as Nanodevices in Monoclonal Immunology	371	(2)
11.4.7 Fullerenes as Radiotracers	373	(2)
11.4.8 Fullerenes as Vectors	375	(1)
Acknowledgments	376	(1)
References	376	(10)
12 Nanotechnology for Biomedical Devices	386	(50)
Lars Montelius
12.1 Introduction	386	(2)
12.2 Nanotechnologies	388	(9)
12.2.1 Overview of Nanotechnologies and Nanotools	388	(1)
12.2.1.1 NIL	393	(1)
12.2.1.2 Other Lithography Techniques	393	(1)
12.2.1.3 Scanning Probes	395	(2)
12.3 Applications	397	(26)
12.3.1 Introduction	397	(1)
12.3.2 Biomedical Applications based on Nanostructured Passive Surfaces	397	(1)
12.3.2.1 Separation, Concentration and Enriching Structures	398	(1)
12.3.2.2 Molecular Motors Transported in Nanometer Channels	400	(1)
12.3.2.3 Topographical Structures, Cells and Guidance of Neurons	401	(4)
12.3.3 Biomedical Applications utilizing Active Nanostructured Surfaces	405	(4)
12.3.4 Protein Chips	409	(3)
12.3.5 Protein Interactions	412	(3)
12.3.6 Biomedical Applications using Nanowires	415	(1)
12.3.7 Biomedical Applications using Nanoparticles	416	(1)
12.3.8 Biomedical Applications using SPM Technology	416	(1)
12.3.8.1 Imaging of Biomolecules using SPM	418	(1)
12.3.8.2 Force Detection of Single Molecular Events	418	(1)
12.3.8.3 Cantilever-based Detection of Molecular Events	418	(5)
12.4 Discussion and Outlook	423	(1)
Acknowledgments	424	(1)
References	425	(11)
13 Nanodevices in Nature	436	(24)
Alexander G. Volkov and Courtney L. Brown
13.1 Introduction	436	(1)
13.2 Multielectron Processes in Bioelectrochemical Nanoreactors	437	(1)
13.3 Cytochrome Oxidase: A Nanodevice for Respiration	438	(5)
13.3.1 Nanodevice Architectonics	441	(1)
13.3.2 Activation Energy and Mechanism of Oxygen Reduction	442	(1)
13.3.3 Proton Pump	443	(1)
13.4 Photosynthetic Electrochemical Nanoreactors, Nanorectifiers, Nanoswitches and Biologically Closed Electrically Circuits	443	(5)
13.5 Phototropic Nanodevices in Green Plants: Sensing the Direction of Light	448	(3)
13.6 Membrane Transport and Ion Channels	451	(2)
13.7 Molecular Motors	453	(2)
13.8 Nanodevices for Electroreception and Electric Organ Discharges	455	(1)
13.9 Neurons	456	(1)
References	456	(4)
Index	460