Rigidity Analysis of Protein Molecules

2015 ◽  
Vol 15 (3) ◽  
Author(s):  
Zahra Shahbazi ◽  
Ahmet Demirtas
Keyword(s):  
Protein Structure ◽  
Degrees Of Freedom ◽  
Kinematic Model ◽  
3D Structure ◽  
Closed Loops ◽  
Matlab Program ◽  
Acid Versus ◽  
Rigidity Analysis ◽  
Protein Molecules ◽  
Pebble Game

Intrinsic flexibility of protein molecules enables them to change their 3D structure and perform their specific task. Therefore, identifying rigid regions and consequently flexible regions of proteins has a significant role in studying protein molecules' function. In this study, we developed a kinematic model of protein molecules considering all covalent and hydrogen bonds in protein structure. Then, we used this model and developed two independent rigidity analysis methods to calculate degrees of freedom (DOF) and identify flexible and rigid regions of the proteins. The first method searches for closed loops inside the protein structure and uses Grübler–Kutzbach (GK) criterion. The second method is based on a modified 3D pebble game. Both methods are implemented in a matlab program and the step by step algorithms for both are discussed. We applied both methods on simple 3D structures to verify the methods. Also, we applied them on several protein molecules. The results show that both methods are calculating the same DOF and rigid and flexible regions. The main difference between two methods is the run time. It's shown that the first method (GK approach) is slower than the second method. The second method takes 0.29 s per amino acid versus 0.83 s for the first method to perform this rigidity analysis.

An Optimized Kinematic Mobility Analysis of Protein Molecules

2014 ◽  
Author(s):  
Ahmet Demirtas ◽  
Zahra Shahbazi
Keyword(s):  
Degrees Of Freedom ◽  
3D Structure ◽  
Computational Cost ◽  
Random Group ◽  
Kinematic Chains ◽  
Simulation Speed ◽  
Modified Method ◽  
Rigidity Analysis ◽  
Protein Molecules ◽  
Pebble Game

Understanding the 3D structure and consequently the motion of protein molecules contributes to simulate their function. Modeling protein molecules as kinematic chains has been used to predict protein molecules flexible and rigid regions as well as their degrees of freedom to predict their mobility. However, high computational cost for relatively large molecules is one of the major challenges in this field. In this paper we have combined our previously developed rigidity analysis (ProtoFold) with pebble game thus improving computational cost of our simulation. Here, we have determined the required time for all steps of ProtoFold and subsequently the most time consuming step. Results have shown that finding rigid loops inside the protein structure using graph theory and Grübler-Kutzbach criterion is the slowest part of the procedure, taking an average of 75% of the time required for the rigidity analysis. Therefore we have replaced this step with pebble game. The modified method has been applied to a random group of protein molecules and its efficiency in significantly improving the simulation speed has been verified.

Fast Kinematic Model of a Seven-Bar Linkage With a Single Compliant Link

2014 ◽  
Author(s):  
Alberto Borboni ◽  
Francesco Aggogeri ◽  
Rodolfo Faglia
Keyword(s):  
Degrees Of Freedom ◽  
Kinematic Model ◽  
Small Deformation ◽  
Rigid Bodies ◽  
Fast Method ◽  
Closed Loops ◽  
Torsion Effect ◽  
Kinematical Model ◽  
Kinetostatic Model ◽  
The Ideal

This work deals on a kinematical model of a parallel mechanism for biomedical applications. The mechanism is a linkage composed by three closed loops. It is composed by seven bars (one of them is the frame) constrained each other by ideal constraints (prismatic, rotary or lock joints). The ideal joints introduce 21 degrees of constraint, while the bars produce eighteen degrees of freedom when considered rigid. Six bars are really rigid, while one of them is compliant with respect to the others and allows the mobility of the mechanism. The kinematic of this seven-bar linkage is analyzed with the aim of Hermite’s polynomials. The proposed approach is based on the knowledge of kinematical constraints at the ends of the compliant beam, in terms of position and curvature. This knowledge is based on the fact that the rest of the structure is composed by rigid bodies and ideal concentrated constraints. The compliance affects the beam only with bending effects, furthermore, in this work, we consider only a planar linkage, thus the torsion effect is not considered, and the beam is constrained in ways that compression instability is negligible. Although the beam is subjected to important deformations, it is divided in parts, such that each part is subjected to a small deformation. In this way, we propose the Hermite’s polynomials to describe the shape of the beam. We tested this fast method to describe the kinematical behavior of the system with a kinetostatic model of a mechanical device, finding that it is reliable for the proposed application.

Kinematic Motion Constraints of the Protein Molecule Chains

2011 ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilies¸ ◽  
Kazem Kazerounian
Keyword(s):  
Hydrogen Bonds ◽  
Degrees Of Freedom ◽  
Main Chain ◽  
Protein Structures ◽  
Protein Molecule ◽  
Correct Identification ◽  
Closed Loops ◽  
Motion Constraints ◽  
Protein Molecules ◽  
Internal Mobility

The function of protein molecules is defined by their 3-D geometry, as well as their internal mobility, which is heavily influenced by the internal hydrogen bonds. The correct identification of these hydrogen bonds and the prediction of their effect on the mobility of protein molecules can provide an invaluable mechanism to understand protein behavior. Applications of this study ranges from nano-engineering to new drug design. We are extending our recent approach from identifying main-chain main-chain hydrogen bonds to all types of hydrogen bonds that occur in protein structures, such as α-helices and β-sheets. We use the Gru¨bler-Kutzbach kinematic mobility criterion to determine the degrees of freedom of all closed loops (rigid loops as well as closed loops of one or more degrees of freedom) formed by Hydrogen bonds. Furthermore, we systematically develop constraint equations for non-rigid closed loops. Several examples of protein molecules from PDB are used to show that these additions both improve the accuracy of mobility analysis and enable us to study a broader range of the motion of protein molecules. This approach offers theoretical insight as well as extensive numerical efficiencies in protein simulations.

scholarly journals A New Approach of Soft Joint Based on a Cable-Driven Parallel Mechanism for Robotic Applications

Mathematics ◽  
2021 ◽  
Vol 9 (13) ◽  
pp. 1468
Author(s):  
Luis Nagua ◽  
Carlos Relaño ◽  
Concepción A. Monje ◽  
Carlos Balaguer
Keyword(s):  
Parallel Mechanism ◽  
Degrees Of Freedom ◽  
Kinematic Model ◽  
Experimental Tests ◽  
Humanoid Robots ◽  
Inverse Kinematic ◽  
Element Analysis ◽  
New Approach ◽  
Flexible Polymer ◽  
The Mathematical Model

A soft joint has been designed and modeled to perform as a robotic joint with 2 Degrees of Freedom (DOF) (inclination and orientation). The joint actuation is based on a Cable-Driven Parallel Mechanism (CDPM). To study its performance in more detail, a test platform has been developed using components that can be manufactured in a 3D printer using a flexible polymer. The mathematical model of the kinematics of the soft joint is developed, which includes a blocking mechanism and the morphology workspace. The model is validated using Finite Element Analysis (FEA) (CAD software). Experimental tests are performed to validate the inverse kinematic model and to show the potential use of the prototype in robotic platforms such as manipulators and humanoid robots.

Cooperation and Null-Space Control of Networked Omni-Directional Mobile Manipulators

2020 ◽  
Author(s):  
Michael John Chua ◽  
Yen-Chen Liu
Keyword(s):  
Degrees Of Freedom ◽  
Null Space ◽  
Kinematic Model ◽  
Mobile Manipulator ◽  
Main Task ◽  
Mobile Manipulators ◽  
Robot Arm ◽  
Task Space ◽  
End Effector ◽  
Mobile Base

Abstract This paper presents cooperation and null-space control for networked mobile manipulators with high degrees of freedom (DOFs). First, kinematic model and Euler-Lagrange dynamic model of the mobile manipulator, which has an articulated robot arm mounted on a mobile base with omni-directional wheels, have been presented. Then, the dynamic decoupling has been considered so that the task-space and the null-space can be controlled separately to accomplish different missions. The motion of the end-effector is controlled in the task-space, and the force control is implemented to make sure the cooperation of the mobile manipulators, as well as the transportation tasks. Also, the null-space control for the manipulator has been combined into the decoupling control. For the mobile base, it is controlled in the null-space to track the velocity of the end-effector, avoid other agents, avoid the obstacles, and move in a defined range based on the length of the manipulator without affecting the main task. Numerical simulations have been addressed to demonstrate the proposed methods.

A Model of the Human Spine: Forward and Inverse Kinematics

1992 ◽  
Author(s):  
Sunil Kumar Agrawal ◽  
Siyan Li ◽  
Glen Desmier
Keyword(s):  
Range Of Motion ◽  
Inverse Kinematics ◽  
Degrees Of Freedom ◽  
Kinematic Model ◽  
Joint Angles ◽  
Human Spine ◽  
Forward And Inverse Kinematics ◽  
Position And Orientation ◽  
Three Degrees Of Freedom ◽  
Adjacent Vertebra

Abstract The human spine is a sophisticated mechanism consisting of 24 vertebrae which are arranged in a series-chain between the pelvis and the skull. By careful articulation of these vertebrae, a human being achieves fine motion of the skull. The spine can be modeled as a series-chain with 24 rigid links, the vertebrae, where each vertebra has three degrees-of-freedom relative to an adjacent vertebra. From the studies in the literature, the vertebral geometry and the range of motion between adjacent vertebrae are well-known. The objectives of this paper are to present a kinematic model of the spine using the available data in the literature and an algorithm to compute the inter vertebral joint angles given the position and orientation of the skull. This algorithm is based on the observation that the backbone can be described analytically by a space curve which is used to find the joint solutions..

scholarly journals Kinematic Modelling of FES Induced Sit-to-stand Movement in Paraplegia

2017 ◽  
Vol 7 (6) ◽  
pp. 3060
Author(s):  
Mohammed Ahmed ◽  
M. S. Huq ◽  
B. S. K. K. Ibrahim
Keyword(s):  
Dynamic Model ◽  
Initial Phase ◽  
Degrees Of Freedom ◽  
Kinematic Model ◽  
Future Research ◽  
Upper Limbs ◽  
Body System ◽  
Segmental Dynamics ◽  
Sit To Stand ◽  
Kinematic Modelling

FES induced movements from indication is promising due to encouraging results being obtained by scholars. The kinematic model usually constitute the initial phase towards achieving the segmental dynamics of any rigid body system. It can be used to ascertain that the model is capable of achieving the desired goal. The dynamic model builds on the kinematic model and is usually mathematically cumbersome depending on the number of degrees-of-freedom. This paper presents a kinematic model applicable for human sit-to-stand movement scenario that will be used to obtain the dynamic model the FES induced movement in a later study. The study shows that the 6 DOF conceptualized sit-to-stand movement can be achieved conveniently using 4 DOF. The 4 DOF has an additional joint compared to similar earlier works which makes more it accurate and flexible. It is more accurate in the sense that it accommodates additional joint i.e. the neck joint whose dynamics could be captured. And more flexible in the sense that if future research uncover more contributions by the segments it can be easily incorporated including that of other segments e.g. the trunk, neck and upper limbs.

Protein Molecules as Natural Nano Bio Devices: Mobility Analysis

2010 ◽  
Author(s):  
Zahra Shahbazi ◽  
Horea T. Ilies¸ ◽  
Kazem Kazerounian
Keyword(s):  
Degrees Of Freedom ◽  
Conformational Transitions ◽  
Living Cells ◽  
Mobility Analysis ◽  
Folding Process ◽  
Kinematic Chains ◽  
Protein Molecules ◽  
Kinematic Models ◽  
Lower Mobility ◽  
Molecular Components

Proteins are nature’s nano-robots in the form of functional molecular components of living cells. The function of these natural nano-robots often requires conformational transitions between two or more native conformations that are made possible by the intrinsic mobility of the proteins. Understanding these transitions is essential to the understanding of how proteins function, as well as to the ability to design and manipulate protein-based nano-mechanical systems [1]. Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process.

Numerical and experimental performance estimation for a ExoFing - 2 DOFs finger exoskeleton

Robotica ◽  
2021 ◽  
pp. 1-13
Author(s):  
G Carbone ◽  
M Ceccarelli ◽  
C. E. Capalbo ◽  
G Caroleo ◽  
C Morales-Cruz
Keyword(s):  
Degrees Of Freedom ◽  
Experimental Validation ◽  
Index Finger ◽  
Kinematic Model ◽  
Experimental Tests ◽  
Performance Estimation ◽  
Experimental Performance ◽  
Finger Motion ◽  
User Friendly ◽  
Operation Characteristics

Abstract This paper presents a numerical and experimental validation of ExoFing, a two-degrees-of-freedom finger mechanism exoskeleton. The main functionalities of this device are investigated by focusing on its kinematic model and by computing its main operation characteristics via numerical simulations. Experimental tests are designed and carried out for validating both the engineering feasibility and effectiveness of the ExoFing system aiming at achieving a human index finger motion assistance with cost-oriented and user-friendly features.

Bioinspired Algorithms in Solving Three-Dimensional Protein Structure Prediction Problems

2017 ◽  
pp. 316-337
Author(s):  
Raghunath Satpathy
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
3D Structure ◽  
Prediction Method ◽  
Optimization Methods ◽  
Point Of View ◽  
Living Organisms ◽  
Prediction Problems

Proteins play a vital molecular role in all living organisms. Experimentally, it is difficult to predict the protein structure, however alternatively theoretical prediction method holds good for it. The 3D structure prediction of proteins is very much important in biology and this leads to the discovery of different useful drugs, enzymes, and currently this is considered as an important research domain. The prediction of proteins is related to identification of its tertiary structure. From the computational point of view, different models (protein representations) have been developed along with certain efficient optimization methods to predict the protein structure. The bio-inspired computation is used mostly for optimization process during solving protein structure. These algorithms now a days has received great interests and attention in the literature. This chapter aim basically for discussing the key features of recently developed five different types of bio-inspired computational algorithms, applied in protein structure prediction problems.

Sign in / Sign up

Export Citation Format

Share Document