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TECHNICAL PAPERS

Kinematics and Workspace Analysis of Protein Based Nano-Actuators

[+] Author and Article Information
G. Sharma

Department of Mechanical and Industrial Eng.,  Northeastern University, 360 Huntington Ave., Boston, MA 02115

M. Badescu

 Jet Propulsion Laboratory (JPL), MS 67-119, 4800 Oak Grove Drive, Pasadena, CA 91109-8099

A. Dubey

Department of Mechanical and Industrial Eng.,  Northeastern University, 360 Huntington Ave., Boston, MA 02115 and Department of Mechanical and Aerospace Eng.,  Rutgers University, 98 Brett Road, Piscataway, NJ 08854

C. Mavroidis1

Department of Mechanical and Industrial Eng.,  Northeastern University, 360 Huntington Ave., Boston, MA 02115

S. M. Tomassone

Department of Chemical and Biochemical Eng.,  Rutgers University, 98 Brett Road, Piscataway, NJ 08854

M. L. Yarmush

Department of Biomedical Eng.,  Rutgers University, 617 Bowser Road, Piscataway, NJ 08854

1

Corresponding Author. Telephone: (617) 373-4121; Fax (617) 373-2921. Email mavro@coe.neu.edu

J. Mech. Des 127(4), 718-727 (Feb 25, 2005) (10 pages) doi:10.1115/1.1900751 History: Received September 15, 2004; Revised February 25, 2005

In this paper, a novel nanoscale protein based nano actuator concept is described. Molecular kinematic computational tools are developed and included in our Matlab Biokinematics Toolbox to study the protein nanomotor’s performance using geometric criteria. The computational tools include the development of the molecular motor direct and inverse kinematics using the protein’s Denavit and Hartenberg parameters and the corresponding homogeneous transformation matrices. Furthermore, the workspace calculation and analysis of the protein motor is performed.

Copyright © 2005 by American Society of Mechanical Engineers
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References

Figures

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Figure 1

(a) A vision of a nano-organism: carbon nano-tubes form the main body; peptide limbs can be used for locomotion and object manipulation. A biomolecular motor located at the head can propel the device in various environments; (b) A “nano-robot” flowing inside a blood vessel, finds an infected cell. The nanorobot attaches on the cell and projects a drug to repair or destroy the infected cell.

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Figure 2

(a) Graphical representation of the initial state of Loop36 region of VPL Actuator. The structure resembles three inverted hairpins with inner regions α-helical but outer regions are in a random loop configuration; (b) Low pH induced active conformation of the same trimer. The random loop region converts into an α-helical region and the bent hairpin structure straightens out producing a linear motion.

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Figure 3

Rotational degrees of freedom along a residue chain. Adjacent residues are separated by dashed lines; side chains are denoted by R, purple line represents the back-bone.

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Figure 4

Frames Fi−1 and Fi are attached to parent atom Qi−1 and Qi and bond rotation angle is αi−1

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Figure 5

(a) loop36 protein in the native state, (b) open state obtained from PDB (NMR experiment generated) which is similar to that generated by targeted molecular dynamics (TMD) study from our previous work (5), computation time for TMD was about 2h, (c) open state generated by molecular kinematics, computation time is less than 40s

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Figure 15

Orientation sphere for the most dexterous box (50×50×50 box resolution and 60×60 patch resolution)

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Figure 13

Orientation sphere for the most dexterous box (30×30×30 box resolution and 30×30 patch resolution)

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Figure 14

Dexterous workspace for 36 amino chain (50×50×50 box resolution and 60×60 patch resolution)

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Figure 6

One step of the CCD method

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Figure 7

Initial conformation of the protein (left) and one of the solutions found by CCD simulations (right)

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Figure 8

The dexterous solid angle

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Figure 10

Orientation sphere

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Figure 11

Flow chart diagram of the protein workspace analysis process

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Figure 12

Dexterous workspace for 36 amino acid chain (30×30×30 box resolution and 30×30 patch resolution)

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