...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...

...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...

... 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...

...Gregory S. Chirikjian; Kazem Kazerounian; Constantinos Mavroidis 28 02 2005 02 03 2005 design nanotechnology kinematics hydrogen bonds proteins molecular biophysics machinery Nanomachines are devices that are in the size range of billionths of meters ( 10...

...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...

...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...

...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...

...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...

..., 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...