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Keywords: proteins
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Journal Articles
Article Type: Research Papers
J. Mech. Des. April 2009, 131(4): 041001.
Published Online: March 20, 2009
...Sung K. Koh; Guangjun Liu; Wen-Hong Zhu A continuous protein synthesis formulation based on the design principles applied to topology optimization problems is proposed in this paper. In contrast to conventional continuous protein design methods, the power law (PL) protein design formulation...
Journal Articles
Article Type: Research Papers
J. Mech. Des. November 2007, 129(11): 1130–1136.
Published Online: November 28, 2006
...Raghavendran Subramanian; Kazem Kazerounian Pauling et al. (1951, “The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain,” Proc. Natl. Acad. Sci. U.S.A., 37(4), pp. 205–211 ) in their seminal paper in 1951 reported numerical values for the bond lengths...
Journal Articles
Article Type: Research Papers
J. Mech. Des. March 2007, 129(3): 312–319.
Published Online: March 13, 2006
... simple and straightforward process. In this paper, we present and analyze three new efficient methodologies to find all the dihedral angles of a peptide chain for a given conformation. Comparison of these results with the dihedral angle values reported in the protein data bank (PDB) indicates significant...
Journal Articles
Article Type: Introduction
J. Mech. Des. July 2005, 127(4): 695–698.
Published Online: March 2, 2005
...Gregory S. Chirikjian; Kazem Kazerounian; Constantinos Mavroidis design nanotechnology kinematics hydrogen bonds proteins molecular biophysics machinery Given the tremendous potential impact of nanodevices, rational design approaches to these systems based on first principles...
Journal Articles
Article Type: Technical Papers
J. Mech. Des. July 2005, 127(4): 718–727.
Published Online: February 25, 2005
...G. Sharma; M. Badescu; A. Dubey; C. Mavroidis; S. M. Tomassone; M. L. Yarmush 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...
Journal Articles
Article Type: Technical Papers
J. Mech. Des. July 2005, 127(4): 728–735.
Published Online: February 25, 2005
...Sung K. Koh; G. K. Ananthasuresh; Christopher Croke The notion of optimization is inherent in the design of a sequence of amino acid monomer types in a long heteropolymer chain of a protein that should fold to a desired conformation. Building upon our previous work wherein continuous...
Journal Articles
Article Type: Technical Papers
J. Mech. Des. July 2005, 127(4): 712–717.
Published Online: August 5, 2004
...Kazem Kazerounian; Khalid Latif; Carlos Alvarado This paper presents an efficient and novel computational protein prediction methodology called kineto-static compliance method. Successive kineto-static fold compliance is a methodology for predicting a protein molecule’s motion under the effect...
Journal Articles
Article Type: Technical Papers
J. Mech. Des. July 2005, 127(4): 699–711.
Published Online: August 5, 2004
...Kazem Kazerounian; Khalid Latif; Kimberly Rodriguez; Carlos Alvarado Proteins are evolution’s mechanisms of choice. The study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains...
Journal Articles
Article Type: Technical Papers
J. Mech. Des. January 2004, 126(1): 40–45.
Published Online: March 11, 2004
..., treatments, and drugs for a variety of diseases. Given the vast body of knowledge in theoretical, applied, and analytical kinematics and robotics, the conspicuous absence of the kinematics community from current molecular science research relating to the prediction of protein folding, protein docking...