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  • Phase II NIAC Grant

    FINAL REPORT

    BIO-NANO-MACHINES FOR SPACE APPLICATIONS

    Submitted to:

    Dr. Robert A. Cassanova, Director NASA Institute for Advanced Concepts (NIAC)

    555A Fourteenth Street, N.W. Atlanta, Georgia 30318

    Tel: (404) 347-9633, FAX: (404) 347-9638 Email: bcass@niac.usra.edu

    Principal Investigator: Constantinos Mavroidis, Ph.D., Professor

    Department of Mechanical and Industrial Engineering Northeastern University, 375 Snell Engineering Center

    360 Huntington Avenue, Boston, MA 02115, USA TEL: 617-373-4121, FAX: 617-373-2921

    EMAIL: mavro@coe.neu.edu, WEBPAGE: http://www.coe.neu.edu/~mavro

    July 23, 2006

  • 2

    List of Contributors

    The people who contributed towards the completion of the NIAC Phase II project are

    listed below:

    a) Ajay Ummat – Is a PhD student in the Mechanical Engineering department at

    Northeastern University, Boston, MA. He is the main author of the NIAC reports

    and contributed towards the design and conceptualization of space applications

    and the computational framework for designing bio nano machines.

    b) Prof. Constantinos Mavroidis – Is a Professor in the Department of Mechanical

    and Industrial Engineering, Northeastern University, Boston. He is the Principal

    Investigator for this project and the main contributor towards the

    conceptualization and design of the bio nano machines and the space applications.

    c) Prof. Martin L.Yarmush – Is a Professor of Surgery and Bioengineering,

    Harvard Medical School, Boston. He is the co-Principal Investigator for this

    project and his main contribution is towards the experimental activities for the

    project, which includes protein characterization, mutations and its dynamics.

    d) Marianna Bei, D.M.D., D.M.Sc. – Is an Assistant Professor of Dermatology,

    Harvard Medical School, Boston. She is a no cost consultant for this project and

    her expertise in biology helped us conceptualize the design of bio nano robotics

    and its components.

    e) Gaurav Sharma – Is a PhD student in the Mechanical Engineering department at

    Northeastern University, Boston. His contribution was towards the design of a

    nano- hinge, a bio nano component which could be used for space applications.

  • 3

    f) Atul Dubey - Is a PhD student in the Mechanical Engineering department at

    Rutgers University, New Jersey. His contribution was towards the design of Viral

    Protein Linear actuator, a bio nano component.

    g) John Kundert-Gibbs – Is a Computer science professor at Clemson university

    and he helped us design an animated movie which shows the working of NTXp

    (Networked TerraXplorers) space application.

    h) Dr. Kaushal Rege – Works at the Center for Engineering in Medicine,

    Massachusetts General Hospital, Boston. He helped in the experimental activities

    involving characterization of Viral Protein linear actuator, its structure and

    dynamics.

    i) Dr. Monica Casali – Works at the Center for Engineering in Medicine,

    Massachusetts General Hospital, Boston and contributed towards structural

    characterization of Viral Protein Linear actuator.

  • 4

    Overview This Phase II NIAC grant started on September 1, 2004. The project goals included:

    a) The identification and study (computationally and experimentally) of protein and

    DNA configurations that can be used as bio-nano-machine components.

    b) The design of two macro-scale devices for space application that will be using

    bio-nano-component assemblies. These devices are:

    b.1) The Networked TerraXplorer (NTXp) that is a long and light-weight

    network of channels containing millions of bio-nano-robotic elements with

    ultra-enhanced sensing and signaling capabilities for the detailed mapping

    and exploration of very large planetary surfaces.

    b.2) The All Terrain Astronaut Bio-Nano Gears (ATB) that will serve as an

    extra layer of shield on the astronaut providing early detection and

    protection against dangerous and harmful environments or aiding in healing

    damages caused to the astronaut.

    During the two year period for the project, the following research activities took place

    and are described in detail in this report:

  • 5

    List of Research Activities

    1. Establishment of the design requirements for the NTXp and the ATB due to the planetary environmental conditions

    2. Identification and characterization of the bionano machine components for use in space

    3. Initiation of the system level design of NTXp

    4. Detailed description of the design and control principles of bionanorobotic systems. This chapter on bionanorobotic systems was written to serve as our guideline for the design and control of all bionano components for the NTXp and the ATB and will be included in the final report of this project.

    5. Identification and characterization of four bionano machine components for use in space.

    6. Sensor-signaling dynamics.

    7. Description of the computational framework for the optimization of the bio nano components.

    8. Setup of the computational studies on the effect of UV radiations of the bio nano components. Ab initio studies on small atomic systems and amino acids

    9. Effect of temperature on bio-nano-components.

    10. Effect of temperature on the atomic level.

    11. Nanofluidics actuator for NTXp transport mechanism.

    12. Design of ATB and radiation responsive molecular assembly for astronauts.

    13. Listing of future work and goals of this non invasive design for detecting space radiations.

    14. A brief overview of the world’s toughest bug which can sustain very high degree of radiations.

  • 6

    Table of Contents

    Chapter 1: Bionanorobotics - A Field Inspired by Nature......................................................... 9

    1.1 Introduction ................................................................................................................... 9

    1.2 Biomolecular Machines: Background and Significance........................................... 15

    1.2.1 Significance ......................................................................................................... 15

    1.2.2 Brief Review of Biomolecular Machines ............................................................ 19

    1.2.2.1 The ATPase Motor ............................................................................................... 19

    1.2.2.2 Kinesin and Myosin ............................................................................................. 20

    1.2.2.3 The Flagella Motors ............................................................................................ 21

    1.2.2.4 Other Motors and Mechanisms........................................................................... 21

    1.2.2.5 DNA-Based Molecular Nanomachines, Joints and Actuators ............................. 23

    1.2.3 Nanosensors ......................................................................................................... 23

    1.3 Design and Control Philosophies for Nanorobotic Systems..................................... 25

    1.3.1 The Roadmap....................................................................................................... 26

    1.3.2 Design Architecture for the Bio-Nanorobotic Systems ....................................... 31

    1.4 Self Replication – mimetics a novel property of living systems............................... 42

    1.4.1 Significance ......................................................................................................... 42

    1.4.2 Applications ......................................................................................................... 43

    1.4.3 The Design of Life Mimetic Systems .................................................................. 44

    1.4.3.1 Intrinsic Material ................................................................................................. 44

    1.4.3.2 Interaction Laws ................................................................................................. 45

    1.4.3.3 Self-Balancing...................................................................................................... 45

    1.4.3.4 Growth and its Growth Limit............................................................................... 46

    1.4.3.5 Self-Filtering and Self Healing ............................................................................ 46

    1.4.4 Self Replication – A Gedankenexperiment.......................................................... 47

  • 7

    1.4.5 Design Parameters for Self-Replicating Systems ................................................ 51

    1.4.5.1 Selection of Intrinsic Materials............................................................................ 51

    1.4.5.2 Defining the External Gradient Parameters........................................................ 51

    1.4.5.3 Generating Stable Alignment and Internal Gradients ......................................... 51

    1.5 Conclusions .............................................