On Protein/Nucleic Acid Based Hyper Redundant Bio-nano-robot

Hyper redundant bio-nano-robot integrates the advantages of hyper redundant robot and bio-nano-robot with extensive potential applications, and has drawn attention of more and more researchers. In this thesis, the modeling, kinematics, design and control of hyper redundant bio-nano-robot are studied from the view of robotic mechanism.Firstly, the mechanism methods are introduced to the modeling of protein polypeptide. From the view of mechanism, the peptide unit can be taken as the basic component (linkage) and the single covalent bond "Cα-C" and "N-Cα" can be seen as the revolute joints. And therefore, the mechanism model of protein polypeptide chain is established as a hyper redundant robot, which is of significance to solve protein structure relevant problems by using mechanism methods.Secondly, based on the mechanism model of protein polypeptide chain, the Denavit-Hartenberg method is employed to obtain the kinematical equation for the polypeptide. With the equation, the forward kinematics simulation is done easily. And the dihedral angles in homology modeling method can be determined perfectly by solving the inverse kinematics, which means the prediction accuracy for homology modeling method is improved dramatically and also implies that the method developed in this thesis is promising for protein structure prediction.Thirdly, a new protein-based space nano-tweezer and its design and control are proposed. The molecular dynamics simulation results show that it is feasible to control the motion of the space nano-tweezer by way of changing the PH value of solution without residue variation.Finally, the mechanism methods are applied to the modeling of nucleic acid. And the mechanism models of single-stranded nucleic acid (RNA) and double-stranded DNA are built respectively, which have paved the way of solving nucleic acids structure problems by using mechanism methods. The molecular dynamics simulation in this thesis is done with VMD and NAMD. The motion analysis and simulation is completed by MATLAB.