Kinematic Modeling and Internal Motion Analysis of Proteins From a Robot Kinematics Viewpoint

2011 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Jacobian Matrix ◽  
Robot Manipulator ◽  
Kinematic Model ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Kinematic Modeling ◽  
Serial Link ◽  
Internal Motions ◽  
Basic Equations ◽  
External Forces

This paper discusses the kinematic modeling of proteins and the analysis of their internal motion from the viewpoint of robot kinematics. First, a kinematic model of a protein is introduced. This model consists of multiple serial link mechanisms and interaction lines (lines between alpha carbons). The protein model is regarded as a type of a robot manipulator that uses joint angles to control the lengths of the interaction lines, and the Jacobian matrix of the manipulator is derived. On the basis of this Jacobian matrix, the basic equations for calculating the deformation caused by external forces and evaluating the structural compliance of specified parts are derived. Finally, by combining the derived basic equations, we analyze the internal motions of lactoferrin and hemoglobin and compare the results with the reported measured characteristics of their internal motions. Despite the approximations by the model, the results obtained by the proposed method agree with the measured internal motion.

Structural Compliance Analysis and Internal Motion Properties of Proteins From a Robot Kinematics Perspective: Formulation of Basic Equations

2016 ◽  
Vol 8 (2) ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Kinematic Model ◽  
Structural Data ◽  
Forced Response ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Dihedral Angles ◽  
Protein Model ◽  
Applied Forces ◽  
Basic Equations ◽  
Structural Compliance

From a perspective of robot kinematics, we develop a method for predicting internal motion properties and understanding the functions of proteins from their three-dimensional (3D) structural data (protein data bank (PDB) data). The key ideas are based on the structural compliance analysis of proteins. In this paper, we mainly discuss the basic equations for the analysis. First, a kinematic model of a protein is introduced. Proteins are simply modeled as serial manipulators constrained by linear springs, where the dihedral angles on the main chains correspond to the joint angles of manipulators. Then, the kinematic equations of the protein model are derived. In particular, the forced response or the deformation caused by the forces in static equilibrium forms the basis for the structural compliance analysis. In the formulations, the protein models are regarded as manipulators that control the positions in the model or the distances between them, by the dihedral angles on the main chains. Next, the structural compliance of the protein model is defined, and a method for extracting the information about the internal motion properties from the structural compliance is shown. In general, the structural compliance refers to the relationship between the applied forces and the deformation of the parts surrounded by the application points. We define it in a more general form by separating the parts whose deformations are evaluated from those where forces are applied. When decomposing motion according to the magnitude of the structural compliance, we can infer that the lower compliance motion will easily occur. Finally, we show two application examples using PDB data of lactoferrin and hemoglobin. Despite using an approximate protein model, the predicted internal motion properties agree with the measured ones.

Investigation of Algorithms for Analyzing Protein Internal Motion From Viewpoint of Robot Kinematics

2010 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Main Chain ◽  
Control Strategies ◽  
Three Dimensional ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Redundant Manipulators ◽  
Serial Link ◽  
Protein Model ◽  
External Forces ◽  
And Control

We investigate various algorithms for analyzing the characteristics of the internal motion of proteins based on the analogies between their kinematic structures and robotic mechanisms. First, we introduce an artificial simple protein model, planar main chain (PMC), composed of a planar serial link mechanism to investigate the algorithms. Then, we develop algorithms for analyzing the conformational fluctuations by applying the manipulability analysis of robot manipulators and control strategies for redundant manipulators. Next, we develop algorithms for analyzing the conformational deformation caused by the external forces and to evaluate the compliances of the specified parts of proteins. Finally, we show that the proposed algorithms developed by using PMC models are applicable for the three dimensional main chain structures of real proteins, and may be used to analyze their characteristics of the internal motion. We also reveal some preliminary simulation results of the analysis of a real protein.

scholarly journals Kinematics of Serial Manipulators

2020 ◽  
Author(s):  
Ivan Virgala ◽  
Michal Kelemen ◽  
Erik Prada
Keyword(s):  
Rigid Body ◽  
Numerical Solutions ◽  
Kinematic Model ◽  
Inverse Kinematic ◽  
Body Motion ◽  
Robot Kinematics ◽  
Kinematic Modeling ◽  
Open Chain ◽  
Serial Manipulators ◽  
Serial Robot

This book chapter deals with kinematic modeling of serial robot manipulators (open-chain multibody systems) with focus on forward as well as inverse kinematic model. At first, the chapter describes basic important definitions in the area of manipulators kinematics. Subsequently, the rigid body motion is presented and basic mathematical apparatus is introduced. Based on rigid body conventions, the forward kinematic model is established including one of the most used approaches in robot kinematics, namely the Denavit-Hartenberg convention. The last section of the chapter analyzes inverse kinematic modeling including analytical, geometrical, and numerical solutions. The chapter offers several examples of serial manipulators with its mathematical solution.

Analyzing Internal Motion of Proteins From Viewpoint of Robot Kinematics: Formulation of Group Forced Response Method

2012 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Structures ◽  
Computational Cost ◽  
Three Dimensional ◽  
Structural Data ◽  
Simple Calculation ◽  
Forced Response ◽  
Internal Motion ◽  
Robot Kinematics ◽  
Internal Motions ◽  
Applied Forces

An analogous relationship exists between the kinematic structures of proteins and robotic mechanisms. Hence, using this analogy, we attempt to understand the internal motions of proteins from the perspective of robot kinematics. In this study, we propose a method called group forced response (GFR) method for predicting the internal motion of proteins on the basis of their three-dimensional structural data (PDB data). In this method, we apply forces in static equilibrium to groups of atoms (e.g., secondary structures, domains, and subunits) and not to specific atoms. Furthermore, we predict the internal motion of proteins by analyzing the relative motion caused among groups by the applied forces. First, we show a method for approximately modeling protein structures as a robotic mechanism and the basic kinematic equations of the model. Next, the GFR method is formulated (e.g., Jacobian matrix for group motions, magnitude of forces applied to groups, and decomposition of motions into modes according to structural compliances). Finally, we present example applications of the proposed method in real protein structures. Despite the approximations in the model, low computational cost, and use of simple calculation parameters, the results almost agree with measured internal motions.

scholarly journals Realtime Motion Assessment For Rehabilitation Exercises: Integration Of Kinematic Modeling With Fuzzy Inference

2014 ◽  
Vol 4 (4) ◽  
pp. 267-285 ◽  
Author(s):  
Wenbing Zhao ◽  
Roanna Lun ◽  
Deborah D. Espy ◽  
M. Ann Reinthal
Keyword(s):  
Fuzzy Inference ◽  
Kinematic Model ◽  
Integrated Approach ◽  
Kinematic Modeling ◽  
Motion Data ◽  
Fuzzy Interference System ◽  
Novel Approach ◽  
Motion Assessment ◽  
Rehabilitation Exercises ◽  
Rehabilitation Exercise

Abstract This article describes a novel approach to realtime motion assessment for rehabilitation exercises based on the integration of comprehensive kinematic modeling with fuzzy inference. To facilitate the assessment of all important aspects of a rehabilitation exercise, a kinematic model is developed to capture the essential requirements for static poses, dynamic movements, as well as the invariance that must be observed during an exercise. The kinematic model is expressed in terms of a set of kinematic rules. During the actual execution of a rehabilitation exercise, the similarity between the measured motion data and the model is computed in terms of their distances, which are then used as inputs to a fuzzy interference system to derive the overall quality of the execution. The integrated approach provides both a detailed categorical assessment of the overall execution of the exercise and the degree of adherence to individual kinematic rules.

Pose Accuracy Analysis of Robot Manipulators Based on Kinematics

2011 ◽  
Vol 201-203 ◽  
pp. 1867-1872 ◽  
Author(s):  
Jian Ye Zhang ◽  
Chen Zhao ◽  
Da Wei Zhang
Keyword(s):  
Matrix Theory ◽  
Robot Manipulators ◽  
Error Model ◽  
Robot Kinematics ◽  
Accuracy Analysis ◽  
Serial Link ◽  
End Effector ◽  
Surface Graph ◽  
Position And Orientation ◽  
Kinematics Parameters

The pose accuracy of robot manipulators has long become a major issue to be considered in its advanced application. An efficient methodology to generate the end-effector position and orientation error model of robotic manipulator has been proposed based on the differential transformation matrix theory. According to this methodology, a linear error model that described the end-effector position and orientation errors due to robot kinematics parameters errors has been presented. A computer program to generate the error model and perform the accuracy analysis on any serial link manipulator has been developed in MATLAB. This methodology and software are applied to the accuracy analysis of a Phantom Desktop manipulator. The positioning error of the manipulator in its workspace cross section (XOZ) has been plotted as 3D surface graph and discussed.

scholarly journals Kinematic Modeling of Six-Axis Industrial Robot and its Parameter Identification: A Tutorial

2021 ◽  
Vol 15 (5) ◽  
pp. 599-610
Author(s):  
Md. Moktadir Alam ◽  
◽  
Soichi Ibaraki ◽  
Koki Fukuda
Keyword(s):  
Present Model ◽  
Industrial Robot ◽  
Local Coordinate System ◽  
Kinematic Model ◽  
Kinematic Modeling ◽  
Positioning Accuracy ◽  
Rotary Axis ◽  
Model Based ◽  
Absolute Positioning ◽  
The Absolute

In advanced industrial applications, like machining, the absolute positioning accuracy of a six-axis robot is indispensable. To improve the absolute positioning accuracy of an industrial robot, numerical compensation based on positioning error prediction by the Denavit and Hartenberg (D-H) model has been investigated extensively. The main objective of this study is to review the kinematic modeling theory for a six-axis industrial robot. In the form of a tutorial, this paper defines a local coordinate system based on the position and orientation of the rotary axis average lines, as well as the derivation of the kinematic model based on the coordinate transformation theory. Although the present model is equivalent to the classical D-H model, this study shows that a different kinematic model can be derived using a different definition of the local coordinate systems. Subsequently, an algorithm is presented to identify the error sources included in the kinematic model based on a set of measured end-effector positions. The identification of the classical D-H parameters indicates a practical engineering application of the kinematic model for improving a robot’s positioning accuracy. Furthermore, this paper presents an extension of the present model, including the angular positioning deviation of each rotary axis. The angular positioning deviation of each rotary axis is formed as a function of the axis’ command angles and the direction of its rotation to model the effect of the rotary axis backlash. The identification of the angular positioning deviation of each rotary axis and its numerical compensation are presented, along with their experimental demonstration. This paper provides an essential theoretical basis for the error source diagnosis and error compensation of a six-axis robot.

scholarly journals A New Approach to the Solution of Robot Kinematics Based on Relative Transformation Matrices

2016 ◽  
Vol 5 (3) ◽  
pp. 213
Author(s):  
Mohammad Reza Elhami ◽  
Iman Dashti
Keyword(s):  
Robot Manipulator ◽  
Robot Kinematics ◽  
Coordinate Frame ◽  
End Effector ◽  
New Approach ◽  
Transformation Matrices ◽  
The World ◽  
Convenient Approach ◽  
Position And Orientation ◽  
Relative Transformation

In analyzing robot manipulator kinematics, we need to describe relative movement of adjacent linkages or joints in order to obtain the pose of end effector (both position and orientation) in reference coordinate frame. Denavit-Hartenberg established a method based on a 4×4 homogenous matrix so called “A” matrix. This method used by most of the authors for kinematics and dynamic analysis of the robot manipulators. Although it has many advantages, however, finding the elements of this matrix and link/joint’s parameters is sometimes complicated and confusing. By considering these difficulties, the authors proposed a new approach called ‘convenient approach’ that is developed based on “Relative Transformations Principle”. It provides a very simple and convenient way for the solution of robot kinematics compared to the conventional D-H representation. In order to clarify this point, the kinematics of the world known Stanford manipulator has been solved through D-H representation as well as convenient approach and the results are compared.

Kinematic modeling and control of mobile robot for large-scale workpiece machining

2020 ◽  
pp. 095440542093370
Author(s):  
Bo Tao ◽  
Xingwei Zhao ◽  
Sijie Yan ◽  
Han Ding
Keyword(s):  
Mobile Robot ◽  
Large Scale ◽  
Screw Theory ◽  
Kinematic Model ◽  
Speed Control ◽  
Constant Speed ◽  
Mobile Platform ◽  
Robot Arm ◽  
Kinematic Modeling ◽  
Robotic Machining

Safety and reliability are significant in the sense of robotic machining for large-scale workpieces. In this article, a control scheme is proposed to ensure the safe motion of the mobile robot. Screw theory is used to analyze the motion of the mobile robot. The mobile platform with Mecanum wheels can be considered as a mechanism with four driven screws in series. An auxiliary reference position of the mobile platform is calculated based on the kinematic model, and the motion of the mobile platform and robot arm can be decoupled to handle its redundant degrees of freedom. Constant speed control is investigated to reduce the interaction force between the robot and platform. Experiments are conducted on the mobile robotic machining task for a large-scale wind turbine blade. The mobile robot moves steadily and smoothly owing to the constant speed control with an auxiliary target.

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