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.

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.

scholarly journals Quadrotor Unmanned Aerial Vehicles: Visual Interface for Simulation and Control Development

2021 ◽  
Author(s):  
Manuel A. Rendón
Keyword(s):  
Control Strategies ◽  
Basin Of Attraction ◽  
Three Dimensional ◽  
Research Area ◽  
Visual Evaluation ◽  
Development Platform ◽  
Planning Algorithm ◽  
Thrust Vector ◽  
And Control ◽  
Visual Interface

Quadrotor control is an exciting research area. Despite last years developments, some aspects demand a deeper analysis: How a quadrotor operates in challenging trajectories, how to define trajectory limits, or how changing physical characteristics of the device affects the performance. A visual interface development platform is a valuable tool to support this effort, and one of these tools is briefly described in this Chapter. The quadrotor model uses Newton-Euler equations with Euler angles, and considers the effect of air drag and propellers’ speed dynamics, as well as measurement noise and limits for propeller speeds. The tool is able to test any device just by setting a few parameters. A three-dimensional optimal trajectory defined by a set of waypoints and corresponding times, is calculated with the help of a Minimum Snap Trajectory planning algorithm. Small Angle Control, Desired Thrust Vector (DTV) Control and Geometric Tracking Control are the available strategies in the tool for quadrotor attitude and trajectory following control. The control gains are calculated using Particle Swarm Optimization. Root Mean Square (RMS) error and Basin of Attraction are employed for validation. The tool allows to choose the control strategy by visual evaluation on a graphical user interface (GUI), or analyzing the numerical results. The tool is modular and open to other control strategies, and is available in GitHub.

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.

scholarly journals THREE-DIMENSIONAL KINEMATIC ANALYSIS OF STEPPING OVER OBSTACLES IN YOUNG SUBJECTS

2004 ◽  
Vol 16 (03) ◽  
pp. 157-164 ◽  
Author(s):  
HAO-LING CHEN ◽  
TUNG-WU LU ◽  
H. C. LIN
Keyword(s):  
Lower Limb ◽  
Control Strategies ◽  
Three Dimensional ◽  
Joint Kinematics ◽  
Obstacle Crossing ◽  
Obstacle Clearance ◽  
Foot Clearance ◽  
Young Subjects ◽  
And Control ◽  
Obstacle Height

A better understanding of the kinematics and control strategies adopted during obstacle crossing is essential for the prevention of injuries associated with falls in the elderly. The effects of obstacle height on the foot clearance, foot-obstacle distance and joint kinematics have presented significant controversy. This may be related to the selection of obstacle height, whether the obstacles are normalized to the leg length, and to the calculation of the foot-obstacle clearance, as well as the extraction of representative joint angles for the analysis. In this study, fourteen young healthy adults wearing 28 infrared retroreflective markers walked and crossed obstacles of heights of 0%, 10%, 20% and 30% of their leg lengths in a gait laboratory equipped with a 3D motion analysis system. Three-dimensional joint kinematics of the lower limb were calculated. Foot clearances were calculated using the heel and toe markers. The results suggested that young subjects maintained a constant margin of leading foot clearance when crossing higher obstacles (higher than 79.4mm) and a constant trailing foot clearance for all obstacle heights. Both toe-obstacle and heel-obstacle horizontal distances were not affected by obstacle height. Apart from the peak values, kinematic variables for the leading limb should be considered both when the toe and heel cross the obstacle while only those when the toe crosses the obstacle for the trailing limb. Not only in the sagittal plane, motions of the lower limb in the other two planes were also important when investigating the kinematics of the leading limb during obstacle crossing. The present study clarified some of the controversies in the literature of obstacle-crossing through careful comparisons of kinematic variables obtained from different study aspects. The results will be helpful for future studies to gain insight into the kinematics and control strategies adopted during obstacle-crossing.

scholarly journals Actuation and Control Strategies for Miniature Robotic Surgical Systems

2004 ◽  
Vol 127 (4) ◽  
pp. 537-549 ◽  
Author(s):  
Jason M. Stevens ◽  
Gregory D. Buckner
Keyword(s):  
Minimally Invasive ◽  
Control Strategies ◽  
Three Dimensional ◽  
Robotic Systems ◽  
End Effector ◽  
Cardiac Procedures ◽  
Recovery Times ◽  
Dynamics And Control ◽  
On Line ◽  
And Control

During the past 20years, tremendous advancements have been made in the fields of minimally invasive surgery (MIS) and minimally invasive, robotically assisted (MIRA) cardiac surgery. Benefits from MIS include reduced pain and trauma, reduced risks of post-operative complications, shorter recovery times, and more aesthetically pleasing results. MIRA approaches have extended the capabilities of MIS by introducing three-dimensional vision, eliminating hand tremors, and enabling the precise articulation of smaller instruments. These advancements come with their own drawbacks, however. Robotic systems used in MIRA cardiac procedures are large, costly, and do not offer the miniaturized articulation necessary to facilitate tremendous advancements in MIS. This paper demonstrates that miniature actuation can overcome some of the limitations of current robotic systems by providing accurate, repeatable control of a small end effector. A 10× model of a two link surgical manipulator is developed, using antagonistic shape memory alloy wires as actuators, to simulate motions of a surgical end-effector. Artificial neural networks are used in conjunction with real-time visual feedback to “learn” the inverse system dynamics and control the manipulator endpoint trajectory. Experimental results are presented for indirect, on-line learning and control. Manipulator tip trajectories are shown to be accurate and repeatable to within 0.5mm. These results confirm that SMAs can be effective actuators for miniature surgical robotic systems, and that intelligent control can be used to accurately control the trajectory of these systems.

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.

Effective infection prevention and control strategies in a large accredited psychiatric facility in Singapore

2020 ◽  
Author(s):  
Daniel Poremski ◽  
Sandra Henrietta Subner ◽  
Grace Lam Fong Kin ◽  
Raveen Dev Ram Dev ◽  
Mok Yee Ming ◽  
...  
Keyword(s):  
Mental Health ◽  
Prevention And Control ◽  
Infection Prevention ◽  
Control Strategies ◽  
Infection Prevention And Control ◽  
Psychiatric Facility ◽  
Essential Services ◽  
Community Transmission ◽  
And Control

The Institute of Mental Health in Singapore continues to attempt to prevent the introduction of COVID-19, despite community transmission. Essential services are maintained and quarantine measures are currently unnecessary. To help similar organizations, strategies are listed along three themes: sustaining essential services, preventing infection, and managing human and consumable resources.

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