Kinematics and workspace analysis of protein based nano-motors

Proceedings of the ASME Design Engineering Technical Conference

Volumn 2 B, Issue , 2004, Pages 1447-1456

  Sharma, G ^a   Badescu, M ^b   Dubey, A ^c   Mavroidis, C ^a   Sessa, T ^c   Tomassone, S M ^d   Yarmush, M L ^e  

^a Northeastern University   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d The State University of New Jersey   (United States)

^e RUTGERS UNIVERSITY   (United States)

Author keywords

Bionano Actuators; Molecular Kinematics; Molecular Motors; Workspace Analysis

Indexed keywords

ACTUATORS; AMINO ACIDS; BIOMEDICAL EQUIPMENT; CARBON NANOTUBES; DNA; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MOTORS; PH EFFECTS; PROTEINS; ROBOTICS;

BIONANO ACTUATORS; MOLECULAR KINEMATICS; MOLECULAR MOTORS; WORKSPACE ANALYSIS;

KINEMATICS;

EID: 13944251016     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1115/detc2004-57569     Document Type: Conference Paper

References (39)

1. Block S.M., 1998, "Kinesin, What Gives?" Cell, 93, 5-8.
2. Schnitzer M.J. and Block S.M., 1997, "Kinesin Hydrolyses One ATP per 8-nm Step", Nature, 388, 386-390.
3. Wang M.D., Schnitzer M.J., Yin H., Landick R., Gelles J., Block S. M., 1998, "Force and Velocity Measured for Single Molecules of RNA Polymerase", Science, 282, 902-907.
4. Kitamura K., Tokunaga M., Iwane A.H., Yanagida T., 1999, "A Single Myosin Head Moves along an Actin Filament with Regular Steps of ∼5.3nm", Nature, 397, 129.
5. Shingyoji C., Higuchi H., Yoshimura M., Katayama E. and Yanagida T., 1998, "Dynein arms are oscillating force generators", Nature, 393, 711-714.
6. Montemagno C.D., and Bachand G.D., 1999, "Constructing Nanomechanical Devices Powered by Biomolecular Motors", Nanotechnology, 10, 225-331.
7. Berg H.C., 1974, "Dynamic Properties of Bacterial Flagellar Motors", Nature, 249, 77-79.
8. Schalley C.A., Beizai K. and Vogtle F.K., 2001, "On the Way to Rotaxane-Based Molecular Motors: Studies in Molecular Mobility and Topological Chirality", Accounts of Chemical Research, 34, 465-476.
9. Erickson, H.P., 1997, "Stretching Single Protein Molecules: Titin is a Weird spring", Science, 276,1090-1092.
10. Mahadevan L. and Matsudaira P., 2000, "Motility Powered by Supramolecular Springs and Ratchets", Science, 288, 95-99.
11. Knoblauch M, Noll G.A., Muller T, Prufer D, Schneider-Huther I. et al. 2003. ATP-independent contractile proteins from plants. Nature Materials, 2: 600-603.
12. Seeman N. C., 1998, "DNA Nanotechnology: Novel DNA Constructions", Annual Review of Biophysics and Biomolecular Structure, 27, 225-48.
13. Tobias L, Swigon D., Coleman B.D., 2000, "Elastic Stability of DNA Configurations I - General Theory", Physical Review E, 61(1), 747-58.
14. Yuqiu J., Juang C-B, Keller D., Bustamante C., Beach D., Houseal T., and Builes E., 1992, "Mechanical, Electrical, and Chemical Manipulation of Single DNA Molecules", Nanotechnology, 3, 16-20.
15. Hu J., Zhang Y., Gao H., Li M., Hartmann U., 2002, "Artificial DNA Patterns by Mechanical Nanomanipulation", Nanoletters, 2, No. 1, 55-57.
16. Mao C., Sun W., Shen Z., and Seeman N., 1999, "A Nanomechanical Device Based on the B-Z Transition of DNA", Nature, 397, 144-146.
17. Yan H., Zhang X., Shen Z, and Seeman N., 2002, "A Robust DNA Mechanical Device Controlled by Hybridization Topology", Nature, 415, 62-65.
18. Yurke B., Turberfield A.J., Mills A.P., Simmel F.C., and Neumann J.L., 2000, "A DNA-Fuelled Molecular Machine Made of DNA" Nature, 406, 605-608.
19. Teodora M., Phillips G. N. Jr., and Kavraki L. E., "Molecular Docking: A Problem with Thousands of Degrees of Freedom", Proc. of the 2001 IEEE International Conference on Robotics and Automation (ICRA 2001), pp. 960-966, 2001.
20. Finn P. W., Halperin D., Kavraki L. E., Latombe J.-C., Motwani R., Shelton C., and Venkat S., 1996, "Geometric Manipulation of Flexible Ligands", LNCS Series Applied Computational Geometry- Towards Geometric Engineering, 1148, 67-78.
21. Kim, M.K., Chirikjian, G.S. and Jemigan, R.L., 2002, "Elastic Models of Conformational Transitions in Macromolecules", Journal of Molecular Graphics and Modeling, 21:151-160.
22. Kim, M.K., Jernigan, R.L., and Chirikjian, G.S., 2002, "Efficient Generation of Feasible Pathways for Protein Conformational Transitions", Biophysical Journal, 83, 1620-1630.
23. Finn P. W. and Kavraki L. E., 1999, "Computational Approaches to Drug Design", Algorithmica, 347-371.
24. LaValle S. M., Finn P. W., Kavraki L. E., and Latombe J.-C., 2000 "A Randomized Kinematics-based Approach to Pharmacophore-Constrained Conformational Search and Database Screening", Journal of Computational Chemistry, 21(9), 731-747.
25. Gardiner E. J., Willett P. and Artymiuk P. J., 2000, "Graph- theoretic techniques for macromolecular docking", Journal of Chemical Information and Computer Sciences, 40, 273-279.
26. Jones G., Willett P., Glen R. C., Leach A. R., Taylor R., 1999, "Further development of a genetic algorithm for ligand docking and its application to screening combinatorial libraries", ACS Symposium Series (Rational Drug Design: Novel Methodology and Practical Applications), 719, 271-291.
27. Lipton M., and Still W., 1998, "The Multiple Minimum Problem in Molecular Modeling. Tree Searching Internal Coordinate Conformational Space" Journal of Computational Chemistry, 9, 343-355.
28. Smellie A., Kahn S. D., and Teig S. L., 1995, "Analysis of Conformational Coverage - 1. Validation and Estimation of Coverage", Journal of Chemical Information and Computer Science, 35, 285-294.
29. Zhang M., Kavaraki L., 2002, "A new method for fast and accurate derivation of molecular conformations", Journal of Chemical Information and Computer Science, 42, 64-70.
30. Wilson I.A., Skehel J.J., Wiley D.C., 1981, "Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution", Nature, 289, 377-373.
31. Skehel J.J., Bayley P.M., Brown E.B., Martin S.R., Waterfield M.D., White J.M., Wilson I.A., Wiley D.C., 1982, "Changes in the conformation of influenza virus hemagglutinin at the pH optimum of virus-mediated membrane fusion", PNAS USA, 79, 968-972.
32. Sauter N.K, Bednarski M.D., Wurzburg B.A., Hanson J.E., Whitesides G.M., Skehel J.J., and Wiley, D.C., 1989, "Hemagglutinins from Two Influenza Virus Variants Bind to Sialic Acid Derivatives with Millimolar Dissociation Constants: A 500 MHz Proton Nuclear Magnetic Resonance Study", Biochemistry, 28, 8388-8396.
33. Carr C. M. and Kim P., 1993, "A Spring-Loaded Mechanism for the Conformational Change of Influenza Hemagglutinin," Cell, 73, 823-832.
34. Denavit J., and Hartenberg S., 1955, "A Kinematic Notation for Lower Pair Mechanisms Based on Matrices", ASME Journal of Applied Mechanics, pp 215-221.
35. McCarthy J., 2000, "Geometric Design of Linkages", Springer Publications NY.
36. Wang L.C.T, Chen C.C, 1991, "A Combined Optimization Method for Solving the Inverse Kinematics Problem of Mechanical Manipulators", IEEE Transactions on Robotics and Automation, 7(4):489-499.
37. Canutescu A. A. and Dunbrack, R. L. Jr. "Cyclic Coordinate Descent: A Robotics Algorithm for Protein Loop Closure", Protein Science, Vol. 12, pp. 963-972, 2003.
38. Badescu, M., and Mavroidis, C., "Workspace Analysis of Reconfigurable Robotic Arms Using Parallel Platforms as Modules", Proceedings of the 2003 ASME International Mechanical Engineering Congress and Exposition (IMECE'2003), Washington, D.C., November 16-21, 2003, Paper IMECE2003-42963.
39. Badescu, M. and Mavroidis, C., "New Performance Indices and Workspace Analysis of Reconfigurable Hyper-Redundant Robotic Arms", Int. J. of Robotics Research, 2004, (in press).