Design, Modeling and Characterization of Bio-Nanorobotic Systems Mustapha Hamdi Antoine Ferreira Design, Modeling and Characterization of Bio-Nanorobotic Systems Dr. Mustapha Hamdi Dr. Antoine Ferreira Institut PRISME Institut PRISME ENSI Bourges ENSI Bourges 88 Boulevard Lahitolle 88 Boulevard Lahitolle 18020 Bourges 18020 Bourges France France [email protected] [email protected] ISBN 978-90-481-3179-2 e-ISBN 978-90-481-3180-8 DOI 10.1007/978-90-481-3180-8 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2010937677 © Springer Science+Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Cover design: eStudio Calamar S.L. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) To my family, on whose constant encouragement and love I have relied throughout my time at the Academy. I am grateful also to the examples of my brother, It is to them that I dedicate this work. Acknowledgements I would like to thank Prof. Y. Touré for giving me opportunities to make the most out of my thesis years in the PRISME institute. I would like to thank Prof. A. Ferreira my thesis advisor for his scientific guiding and suggestions through the thesis work. It is a pleasure to thank the reviewers of my thesis: Prof. B. Courtois and Prof. S. Fatikow for their detailed reports on this thesis. The quality of the manuscript is definitively improved thanks to their comments. My sincere gratitude also goes to the rest of my thesis committee: Prof. B. Nelson and Prof. A. Voda. A special thank and appreciation to Professor Constantinos Mavroidis, Professor Director of the Biomedical Mechatronics Laboratory Department of Mechanical and Industrial Engineering, for his scientific guiding and suggestions during the fruitful collaboration about Bio-nanodevices prototyping and characterization. It is difficult to overstate my appreciation to Prof. Bradley Nelson, supervisor of the Multi-Scale Robotics Laboratory in the ETH of Zurich with whom I began to learn about experimentation and fabrication of carbon nanotubes based nanode- vices. Not only a great mentor, he has also been a cornerstone in my professional development. I have also to thank the Multi-Scale Robotics Laboratory team: Dr. Lixin dong, Dr. Arun Subramanian and Ph.D. student Kaiyu Shou. People in my institute helped me during my scientific explorations. I feel privi- leged to thank all of them and particularly the following researchers for both their insightful comments and the enjoyable discussions: A. Ben Ali and V. Idasiak. Of course, this research would not have been possible without the financial support of the FSE and the Region of Cher. For these I would like to acknowledge the financial support from the ENSI of Bourges. vii Contents 1 Current State-of-the-Art on Nanorobotic Components and Design .1 1 Introduction ............................. 1 2 Nanorobotics Device Structures ................... 2 3 Virtual Reality Techniques for Bio-nanotechnology Design .... 25 4 Modeling and Characterization Methods .............. 34 5 Conclusion . ............................. 35 References . ............................. 36 2 Methodology of Design and Characterization of Bionano- and Nanorobotic Devices ........................... 41 1 Introduction ............................. 41 2 Design and Characterization Methodology of Biological Nanodevices ............................. 42 3 Co-prototyping of Nanorobotic Structures ............. 63 4 Conclusion . ............................. 71 References . ............................. 72 3 Design and Computational Analysis of Bio-Nanorobotic Structures .75 1 Introduction ............................. 75 2 Characterization of Protein-based Nanosprings . ......... 77 3 Multiscale Design and Modeling of Protein-based Nanomechanisms 91 4 DNA Nanorobotics .........................103 5 Design and Computational Analysis of a Linear Nanotube ServomotorUsingDNAActuation.................104 6 Multiscale Platform as Application for Drug Delivery Characterization...........................122 7 Conclusion . .............................122 References . .............................124 4 Characterization and Prototyping of Nanostructures .........129 1 Introduction .............................129 2 Characterization of NEMS Based on Linear Bearings .......130 ix x Contents 3 Design of Rotatory Nanomotors Based on Head to Head Nanotubes Shuttles: Phase 6 . ...................138 4 Attogram Mass Transport and Vaporization Through Carbon Nanotube . .............................145 5 Conclusion . .............................151 References . .............................152 5 Conclusion and Future Prospects ....................155 1 Conclusion . .............................155 2 Future Prospects ...........................157 List of Figures Fig. 1.1 Drug delivery nanorobotic system for the propulsion and navigation in the cardiovascular system through the induction of force from magnetic gradients generated by a clinical Magnetic Resonance Imaging (MRI) . ................... 3 Fig. 1.2 Sketch of the way to make a single-wall carbon nanotube, starting from a graphene sheet ........................ 4 Fig. 1.3 Sketches of three different SWNT structures that are examples of (a) a zig-zag-type nanotube, (b) an armchair-type nanotube, (c) a helical nanotube ........................... 4 Fig. 1.4 Longitudinal and right view of a concentric multiwall carbon nanotube . ............................. 6 Fig. 1.5 Image of two neighboring chiral SWNTs within a SWNT bundle as seen using high-resolution scanning tunneling microscopy (courtesy of Prof. Yazdani, University of Illinois at Urbana, USA) 7 Fig. 1.6 (Color online) The alpha-helix. The chain path with average helical parameters is indicated showing (a) the alpha carbons only, (b) the backbone fold with peptide dipoles and (c) the full structure with backbone hydrogen bonds in red. All three chains run from top to bottom (that is, the amino-terminal end is at the top). Note that the individual peptide dipoles align to produce a macrodipole with its positive end at the amino-terminal end of the helix. Note also that the amino-terminal end has unsatisfied hydrogen-bond donors (N–H groups) whereas the carboxy-terminal end has unsatisfied hydrogen-bond acceptors (C O groups). Usually a polar side chain is found at the end of = the helix, making hydrogen bonds to these donors and acceptors; such a residue is called a helix cap (adapted from [36])...... 8 Fig. 1.7 (a) Deca-alanine protein. (b) Helix bundle repressor of primer protein(ROP)............................ 9 xi xii List of Figures Fig. 1.8 Coiled-coil alpha-helical interactions: (a) Two interacting alpha helices of tropomyosin shown in a chain representation; (b) a space-filling representation of the separate alpha helices of tropomyosin with the hydrophobic side chains shown as dark protrusions; (c) the tropomyosin dimer showing how the hydrophobic side chains interdigitate in the coiled coil in a knobs in holes arrangement ........................ 10 Fig. 1.9 The structure of collagen. Collagen is a three-chain fibrous protein in which each chain winds round the others. The rise per residue is much larger than in an alpha helix. (a) Three interacting alpha helices of tropocollagen; (b) representation with the hydrophobic side chains . ................... 10 Fig. 1.10 The structure of the beta sheet: The left figure shows a mixed beta sheet, that is one containing both parallel and antiparallel segments. Note that the hydrogen bonds are more linear in the antiparallel sheet. On the right are edge-on views of antiparallel (top) and parallel sheets (bottom). The corrugated appearance gives rise to the name pleated sheet for these elements of secondary structure. Consecutive side chains, indicated here as numbered geometric symbols, point from alternate faces of both types of sheet (adapted from [36])................. 11 Fig. 1.11 (Color online) Two proteins that form a complex through hydrogen bonding between beta strands (the Rap-Raf complex, PDB 1gua). Two antiparallel edge strands of individual beta sheets hydrogen bond to each other at the protein-protein interface, forming a continuous mixed sheet that stabilizes the complex. The protein on the right contains a parallel beta sheet where each strand is connected to the next by an alpha helix, such as the one indicated with the yellow arrow. These helices pack against the faces of the sheet (adapted from [36])......... 12 Fig. 1.12 (Color online) Beta barrel. In this retinol-binding protein (PDB 1rlb), a large antiparallel beta sheet curves all the way around so that the last strand is hydrogen bonded to the first, forming a closed cylinder. The interior of this beta barrel is lined with hydrophobic side chains; nonpolar molecules such as retinol (shown in red) can bind inside [36]................. 12 Fig. 1.13 (Color online) Fibronectin fragment. A cartoon of the secondary structure is displayed (beta-sheet in yellow, turns in light blue) within a transparent connolly surface ................ 13 Fig. 1.14 Immunoglobulin protein I27 model. Fibrillin protein model ...