Design, Modeling and Characterization of Bio-Nanorobotic Systems Mustapha Hamdi  Antoine Ferreira

Total Page:16

File Type:pdf, Size:1020Kb

Design, Modeling and Characterization of Bio-Nanorobotic Systems Mustapha Hamdi  Antoine Ferreira 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 ...
Recommended publications
  • Nmr Data on Ligand Effect Transmission in Triad
    JOURNAL OF NANOSCIENCE LETTERS Control of rotary motion at the nanoscale: Motility, actuation, self-assembly Petr Král*,†, Lela Vuković, Niladri Patra, Boyang Wang, Kyaw Sint, Alexey Titov Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA † Dedicated to my father, Salamoun Klein, a Holocaust survivor *Author for correspondence: Petr Král, email: [email protected] Received 20 Dec 2010; Accepted 9 Feb 2011; Available Online 20 Apr 2011 Abstract Controlling motion of nanoscale systems is of fundamental importance for the development of many emerging nanotechnology areas. We review a variety of mechanisms that allow controlling rotary motion in nanoscale systems with numerous potential applications. We discuss control of rotary motion in molecular motors, molecular propellers of liquids, nanorods rolling on liquids, nanochannels with rotary switching motion, and self- assembly of functional carbonaceous materials, guided by water nanodroplets and carbon nanotubes. Keywords: Rotary motion; Molecular motor; Molecular propeller; Nanopore; Nanochannels; Self-assembly 1. Introduction The proton concentration gradient across the membrane causes protons to pass through the F0 Rotary and cyclic motions provide unit, thereby rotating it. F0 drives the central motility to biological systems at different length stalk of the F1 unit, blocked from rotation by the scales. For example, flagella [1] and cilia [2] can side paddle. The rotation of the central stalk rotate and beat, respectively, to propel bacteria. inside F1 causes the synthesis of ATP. Their motion is powered by molecular motors. Alternatively, ATP can be consumed to power The molecular motor F1F0-ATP synthase, rotary molecular motors based on the F1 unit. schematically shown in Figure 1, synthesizes Cells can also transport molecules and micelles ATP during rotation powered by proton flow [3].
    [Show full text]
  • Artificial Molecular Machines
    REVIEWS Artificial Molecular Machines Vincenzo Balzani,* Alberto Credi, Françisco M. Raymo, and J. Fraser Stoddart* The miniaturization of components which its operation can be monitored ular machines, the most significant used in the construction of working and controlled, 4) the ability to make it developments in the field of artificial devices is being pursued currently by repeat its operation in a cyclic fashion, molecular machines are highlighted. the large-downward (top-down) fabri- 5) the timescale needed to complete a The systems reviewed include 1) chem- cation. This approach, however, which full cycle of movements, and 6) the ical rotors, 2) photochemically and obliges solid-state physicists and elec- purpose of its operation. Undoubtedly, electrochemically induced molecular tronic engineers to manipulate pro- the best energy inputs to make molec- (conformational) rearrangements, and gressively smaller and smaller pieces of ular machines work are photons or 3) chemically, photochemically, and matter, has its intrinsic limitations. An electrons. Indeed, with appropriately electrochemically controllable (co- alternative approach is a small-upward chosen photochemically and electro- conformational) motions in inter- (bottom-up) one, starting from the chemically driven reactions, it is possi- locked molecules (catenanes and ro- smallest compositions of matter that ble to design and synthesize molecular taxanes), as well as in coordination and have distinct shapes and unique prop- machines that do work. Moreover, the supramolecular complexes, including ertiesÐnamely molecules. In the con- dramatic increase in our fundamental pseudorotaxanes. Artificial molecular text of this particular challenge, chem- understanding of self-assembly and machines based on biomolecules and ists have been extending the concept of self-organizational processes in chem- interfacing artificial molecular ma- a macroscopic machine to the molec- ical synthesis has aided and abetted the chines with surfaces and solid supports ular level.
    [Show full text]
  • University of Groningen Controlling the Motion of Molecular Machines
    University of Groningen Controlling the motion of molecular machines at the nanoscale Ruangsupapichat, Nopporn IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2012 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Ruangsupapichat, N. (2012). Controlling the motion of molecular machines at the nanoscale. s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 09-10-2021 Controlling the Motion of Molecular Machines at the Nanoscale Nopporn Ruangsupapichat The work described in this thesis was carried out at the Stratingh Institute for Chemistry, University of Groningen, The Netherlands.
    [Show full text]
  • Bio-Nanorobotics: State of the Art and Future Challenges
    19 Bio-Nanorobotics: State of the Art and Future Challenges 19.1 Introduction.............................................. 19-1 19.2 Nature’s Nanorobotic Devices .......................... 19-4 Protein-Based Molecular Machines • DNA-Based Molecular Machines • Inorganic (Chemical) Molecular Machines • Ummat A., Sharma G., Other Protein-Based Motors Under Development and Mavroidis C. 19.3 Nanorobotics Design and Control...................... 19-19 Northeastern University Design of Nanorobotic Systems • Control of Nanorobotic Dubey A. Systems Northeastern University, 19.4 Conclusions .............................................. 19-33 Rutgers University References ....................................................... 19-33 19.1 Introduction Nanotechnology can best be defined as a description of activities at the level of atoms and molecules that have applications in the real world. A nanometer is a billionth of a meter, that is, about 1/80,000 of the diameter of a human hair, or 10 times the diameter of a hydrogen atom. The size-related challenge is the ability to measure, manipulate, and assemble matter with features on the scale of 1 to 100 nm. In order to achieve cost-effectiveness in nanotechnology it will be necessary to automate molecular manufacturing. The engineering of molecular products needs to be carried out by robotic devices, which have been termed as nanorobots. A nanorobot is essentially a controllable machine at the nanometer or molecular scale that is composed of nanoscale components. The field of nanorobotics studies the design, manufacturing, programming, and control of the nanoscale robots. This review chapter focuses on the state of the art in the emerging field of nanorobotics, its applications and discusses in brief some of the essential properties and dynamical laws which make this field more challenging and unique than its macroscale counterpart.
    [Show full text]
  • Artificial Molecular Machines
    REVIEWS Artificial Molecular Machines Vincenzo Balzani,* Alberto Credi, Françisco M. Raymo, and J. Fraser Stoddart* The miniaturization of components which its operation can be monitored ular machines, the most significant used in the construction of working and controlled, 4) the ability to make it developments in the field of artificial devices is being pursued currently by repeat its operation in a cyclic fashion, molecular machines are highlighted. the large-downward (top-down) fabri- 5) the timescale needed to complete a The systems reviewed include 1) chem- cation. This approach, however, which full cycle of movements, and 6) the ical rotors, 2) photochemically and obliges solid-state physicists and elec- purpose of its operation. Undoubtedly, electrochemically induced molecular tronic engineers to manipulate pro- the best energy inputs to make molec- (conformational) rearrangements, and gressively smaller and smaller pieces of ular machines work are photons or 3) chemically, photochemically, and matter, has its intrinsic limitations. An electrons. Indeed, with appropriately electrochemically controllable (co- alternative approach is a small-upward chosen photochemically and electro- conformational) motions in inter- (bottom-up) one, starting from the chemically driven reactions, it is possi- locked molecules (catenanes and ro- smallest compositions of matter that ble to design and synthesize molecular taxanes), as well as in coordination and have distinct shapes and unique prop- machines that do work. Moreover, the supramolecular complexes, including ertiesÐnamely molecules. In the con- dramatic increase in our fundamental pseudorotaxanes. Artificial molecular text of this particular challenge, chem- understanding of self-assembly and machines based on biomolecules and ists have been extending the concept of self-organizational processes in chem- interfacing artificial molecular ma- a macroscopic machine to the molec- ical synthesis has aided and abetted the chines with surfaces and solid supports ular level.
    [Show full text]
  • Artificial Molecular Rotors
    Chem. Rev. 2005, 105, 1281−1376 1281 Artificial Molecular Rotors Gregg S. Kottas,† Laura I. Clarke,‡ Dominik Horinek,† and Josef Michl*,† Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695 Received September 8, 2004 Contents 5.4.2. Piano-Stool (Half-Sandwich) Transition 1330 Metal Complexes and Related 1. Introduction 1281 Compounds 2. Scope 1282 5.4.3. Complexes Bearing More Than One Cp 1331 3. Theoretical Issues 1285 Ring 3.1. Overview of Characteristic Energies 1285 5.4.4. Bisporphyrinato and Related Complexes 1331 3.1.1. Inertial Effects 1285 5.4.5. Metal Atoms as “Ball Bearings” 1334 3.1.2. Friction in Molecular Systems 1286 5.5. Rope-Skipping Rotors and Gyroscopes 1335 3.1.3. The Fluctuation−Dissipation Theorem 1286 5.6. Rotators in Inclusion (Supramolecular) 1338 3.1.4. Other Energies in the System 1287 Complexes 3.2. Rotor Behavior in Non-interacting Systems 1288 5.6.1. Rotation in Host−Guest Complexes 1338 3.2.1. Driven Motion 1288 5.6.2. Rotation in Self-Assembled Architectures 1340 3.2.2. Driving Fields 1291 5.6.3. Rotations in Molecular “Onion” 1342 3.2.3. Random Motion 1292 Complexes 3.2.4. Utilizing Rotor Systems in the Random 1297 5.7. Driven Unidirectional Molecular Rotors 1344 Motion Regime 5.7.1. Light-Driven Unidirectional Molecular 1345 3.3. Interacting Rotors 1298 Rotors 3.3.1. Steric Interactions 1298 5.7.2. Chemically Driven Rotors 1347 3.3.2. Electrostatic Interactions 1299 6.
    [Show full text]