Kinematic Modeling and Inverse Kinematics of Serial 6R Fragment of Molecule

2021 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Inverse Kinematics ◽  
Twist Angle ◽  
Structural Data ◽  
Data Bank ◽  
Kinematic Modeling ◽  
Link Length ◽  
Dna And Rna ◽  
Revolute Joints ◽  
In Series ◽  
Multiple Conformations

Abstract Depending on their mobilities around bond axes, molecules (e.g., proteins, DNA, and RNA) can be modeled as robotic manipulators. We focus on the serial 6R fragments, or the fragments containing six revolute joints connected in series, extracted from these molecules. We solved the inverse kinematics problems of the fragments. We obtained multiple conformations that maintained the relative position and orientation between both ends. Raghavan and Roth’s solution effectively conveys all real solutions. However, the solution is not directly applicable when some link lengths are zeros. To cope with the problem, in addition to the known method based on the modified elimination, we introduced the small-length link strategy. Here, by setting sufficiently small values for the zero-length links, we solved the inverse kinematics problems based on Raghavan and Roth’s solution combined with the symbolic formulation. Moreover, we formulated a method to systematically build manipulator models from structural data of molecules. We systematically identified the Danavit-Hartenberg parameters (link length, offset, and twist angle) and joint angles at the conformation in the structural data from the seven pairs of positions of atoms. Finally, using the structural data of a protein stored in the protein data bank, we demonstrated an application example of kinematic modeling and inverse kinematics calculation.

scholarly journals Robot Forward and Inverse Kinematics Research using Matlab

2019 ◽  
Vol 8 (2S3) ◽  
pp. 29-35
Keyword(s):  
Inverse Kinematics ◽  
Twist Angle ◽  
Inverse Kinematic ◽  
Forward Kinematics ◽  
Joint Angles ◽  
Link Length ◽  
Matlab Program ◽  
Kinematic Models ◽  
Position And Orientation ◽  
End Effectors

The joint arrangement of every robot can be described by the Denavit Hardenberg parameters. These parameters are enough to obtain a working of the robot described and Presented is a Matlab program which modelled Sorbet era 5u pluse given a set of corresponding DH parameters. The prim aim of this paper is to develop forward and inverse kinematic models of Sorbet era 5u plus using Matlab GUI in order to optimize the manipulative task execution. Forward kinematics analysis is done for the flexible twist angle, link lengths, and link offsets of each joints by varying joint angles to specify the position and orientation of the end effectors. Forward analysis can be used to provide the position of some point on the end effectors together with the orientation of the end effectors measured relative to a coordinate system fixed to ground for a specified set of joint variables. This simulation allows the user to get forward kinematics and inverse kinematics of Scorbot era 5u Plus of the modelled robot in various link length parameters and joint angles and corresponding end effectors position and orientation is going to validate with Rob cell software and compared with Lab view measured values.

Compensation for Geometric Parameter Errors of a Picking Manipulator

2012 ◽  
Vol 529 ◽  
pp. 240-245
Author(s):  
Yan Wang ◽  
Yi Yun Lu ◽  
Hong Bing Zhao
Keyword(s):  
Geometric Parameter ◽  
Error Compensation ◽  
Inverse Kinematics ◽  
Twist Angle ◽  
Error Model ◽  
Experimental Simulation ◽  
Link Length ◽  
Position Accuracy ◽  
Position Errors ◽  
Homogeneous Matrix

In order to enhance position accuracy of robots, the precise error model is established by applying homogeneous matrix without any differential or partial derivatives required in other methods. An articulated picking manipulator with four-degree-of-freedom is taken as example to analyze the position accuracy affected by errors of geometric parameters (link length, link offset and twist angle). Furthermore, an error compensation algorithm based on error model and inverse kinematics is proposed and applied to the picking manipulator. Experimental simulation was carried out for verifying the feasibility of the presented algorithm, and results show that the maximum position errors in x, y, z axis have declined from 3.2369mm, 9.5583mm, 1.002mm to 0.1334mm, -0.0488mm, -0.001mm after compensation, which could greatly improve the position accuracy of the picking manipulator.

Virtual Chain Approach for Mobility Analysis of Multiloop Deployable Mechanisms

2013 ◽  
Vol 135 (11) ◽  
Author(s):  
Hailin Huang ◽  
Zongquan Deng ◽  
Xiaozhi Qi ◽  
Bing Li
Keyword(s):  
Relative Motion ◽  
Twist Angle ◽  
Open Loop ◽  
Mobility Analysis ◽  
Link Length ◽  
Flexible Links ◽  
Single Loop ◽  
Kinematic Chains ◽  
In Series ◽  
Insight Into

In this paper, we present a virtual chain approach for the mobility analysis of multiloop deployable mechanisms. First, the relative motion of the links of single-loop units in multiloop mechanisms are analyzed using the equivalent motion of certain types of open-loop virtual kinematic chains; these kinematic chains comprise some types of joints connected in series by flexible links. This reveals that the links in these virtual chains are not rigid when the mechanism is moving. The parameters of these virtual kinematic chains (such as the link length, the twist angle of two adjacent revolute joint axes, and so on) are variable. By using this approach that involves equivalent kinematic chains, the multiloop mechanisms can be considered equivalent to single-loop mechanisms with flexible links; the closure equations of such multiloop mechanisms can also be derived. The analytical procedures are explained using examples of multiloop mechanisms in which Myard mechanisms as used as the basic single-loop units. A prototype is also fabricated to demonstrate the feasibility of the proposed multiloop mechanism. The proposed method yields a more intuitive and straightforward insight into the mobility of complicated multiloop mechanisms.

scholarly journals Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

2020 ◽  
Vol 21 (4) ◽  
pp. 1352 ◽  
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
József Tőzsér
Keyword(s):  
Structural Characteristics ◽  
Limited Proteolysis ◽  
Structural Data ◽  
Data Bank ◽  
Life Cycles ◽  
Evolutionary Relationships ◽  
Multiple Sequence ◽  
Dimer Interface ◽  
Viral Proteases ◽  
Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

Design, Kinematics and Prototype of a Flexible Robot Arm With Planar Springs

2015 ◽  
Author(s):  
Peng Qi ◽  
Hongbin Liu ◽  
Lakmal Seneviratne ◽  
Kaspar Althoefer
Keyword(s):  
Preliminary Test ◽  
Industrial Applications ◽  
Robot Arm ◽  
Kinematic Modeling ◽  
Flexible Robot ◽  
Element Analysis ◽  
Robot Arms ◽  
Environmental Interactions ◽  
In Series ◽  
Fea Simulation

Flexible robot arms have been developed for various medical and industrial applications because of their compliant structures enabling safe environmental interactions. This paper introduces a novel flexible robot arm comprising a number of elastically deformable planar spring elements arranged in series. The effects of flexure design variations on their layer compliance properties are investigated. Numerical studies of the different layer configurations are presented and finite Element Analysis (FEA) simulation is conducted. Based on the suspended platform’s motion of each planar spring, this paper then provides a new method for kinematic modeling of the proposed robot arm. The approach is based on the concept of simultaneous rotation and the use of Rodrigues’ rotation formula and is applicable to a wide class of continuum-style robot arms. At last, the flexible robot arms respectively integrated with two different types of compliance layers are prototyped. Preliminary test results are reported.

scholarly journals Allosteric modulation of the SARS-CoV-2 spike conformation

2021 ◽  
Author(s):  
Marco A Diaz-Salinas ◽  
Qi Li ◽  
Monir Ejemel ◽  
Yang Wang ◽  
James B Munro
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Structural Data ◽  
Correlation Spectroscopy ◽  
Host Cells ◽  
Parallel Solution ◽  
Real Time Analysis ◽  
Multiple Conformations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects host cells through binding to angiotensin-converting enzyme 2 (ACE2), which is mediated by the receptor-binding domain (RBD) of the viral spike (S) glycoprotein. Structural data and real-time analysis of conformational dynamics have shown that S can adopt multiple conformations, which mediate the exposure of the ACE2-binding site in the RBD. Here, using single-molecule Förster resonance energy transfer (smFRET) imaging we report the effects of ACE2 and antibody binding on the conformational dynamics of S from the Wuhan-1 strain and the B.1 variant (D614G). We found that antibodies that target diverse epitopes, including those distal to the RBD, stabilize the RBD in a position competent for ACE2 binding. Parallel solution-based binding experiments using fluorescence correlation spectroscopy (FCS) indicated antibody-mediated enhancement of ACE2 binding. These findings inform on novel strategies for therapeutic antibody cocktails.

Dynamics of redundant robots – inverse solutions

Robotica ◽  
1986 ◽  
Vol 4 (4) ◽  
pp. 263-267 ◽  
Author(s):  
Ronald L. Huston ◽  
Timothy P. King
Keyword(s):  
Inverse Kinematics ◽  
Degrees Of Freedom ◽  
Solution Algorithm ◽  
Redundant Robot ◽  
Redundant Robots ◽  
Revolute Joints ◽  
Inverse Kinematics Problem ◽  
Inverse Solutions ◽  
Natural Dynamics ◽  
Least Energy

SUMMARYThe dynamics of “simple, redundant robots” are developed. A “redundant” robot is a robot whose degrees of freedom are greater than those needed to perform a given kinetmatic task. A “simple” robot is a robot with all joints being revolute joints with axes perpendicular or parallel to the arm segments. A general formulation, and a solution algorithm, for the “inverse kinematics problem” for such systems, is presented. The solution is obtained using orthogonal complement arrays which in turn are obtained from a “zero-eigenvalues” algorithm. The paper concludes with an assertion that this solution, called the “natural dynamics solution,” is optimal in that it requires the least energy to drive the robot.

scholarly journals The influence of stereochemically active lone-pair electrons on crystal symmetry and twist angles in lead apatite-2Htype structures

2014 ◽  
Vol 78 (2) ◽  
pp. 325-345 ◽  
Author(s):  
T. Baikie ◽  
M. Schreyer ◽  
F. Wei ◽  
J. S. Herrin ◽  
C. Ferraris ◽  
...  
Keyword(s):  
Single Crystal ◽  
Twist Angle ◽  
Lone Pair ◽  
Structural Data ◽  
Structural Adaptation ◽  
X Ray Diffraction ◽  
Temperature Changes ◽  
Waste Stabilization ◽  
Lone Pair Electrons ◽  
Oxide Ion

AbstractLead-containing (Pb-B-X)-2Hapatites encompass a number of [AF]4[AT]6[(BO4)6]X2compounds used for waste stabilization, environmental catalysis and ion conduction, but the influence of the stereochemically active lone-pair electrons of Pb2+on crystal chemistry and functionality is poorly understood. This article presents a compilation of existing structural data for Pb apatites that demonstrate paired electrons of Pb2+at both theAFandATresults in substantial adjustments to the PbFO6metaprism twist angle, φ. New structure refinements are presented for several natural varieties as a function of temperature by single-crystal X-ray diffraction (XRD) of vanadinite-2H(ideally Pb10(VO4)6Cl2), pyromorphite-2H(Pb10(PO4)6Cl2), mimetite-2H/M(Pb10(As5+O4)6Cl2) and finnemanite-2H(Pb10(As3+O3)6Cl2). A supercell for mimetite is confirmed using synchrotron single-crystal XRD. It is suggested the superstructure is necessary to accommodate displacement of the stereochemically active 6s2lone-pair electrons on the Pb2+that occupy a volume similar to an O2−anion. We propose that depending on the temperature and concentration of minor substitutional ions, the mimetite superstructure is a structural adaptation common to all Pb-containing apatites and by extension apatite electrolytes, where oxide ion interstitials are found at similar positions to the lonepair electrons. It is also shown that plumbous apatite framework flexes substantially through adjustments of the PbFO6metaprism twist-angles (φ) as the temperature changes. Finally, crystalchemical [100] zoning observed at submicron scales will probably impact on the treatment of diffraction data and may account for certain inconsistencies in reported structures.

Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

2015 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Data Bank ◽  
Complex Shape ◽  
Structural Data ◽  
Data Bank ◽  
Robot Kinematics ◽  
Motion Prediction ◽  
Serial Manipulators ◽  
Localized Structures ◽  
Motion Modes ◽  
Structural Compliance

On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

Residue Level Inverse Kinematics of Peptide Chains in the Presence of Observation Inaccuracies and Bond Length Changes

2006 ◽  
Vol 129 (3) ◽  
pp. 312-319 ◽  
Author(s):  
Raghavendran Subramanian ◽  
Kazem Kazerounian
Keyword(s):  
Dihedral Angle ◽  
Inverse Kinematics ◽  
Data Bank ◽  
Residue Level ◽  
Peptide Chain ◽  
Euclidean Norm ◽  
Dihedral Angles ◽  
Structural Error ◽  
Length Changes ◽  
Value Decomposition

The process of calculating the dihedral angles of a peptide chain from atom coordinates in the chain is called residue level inverse kinematics. The uncertainties and experimental observation inaccuracies in the atoms’ coordinates handicap this otherwise 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 improvements. While these improvements benefit most modeling methods in protein analysis, it is in particular, very significant in homology modeling where the dihedral angles are the generalized coordinates (structural variables). The first method presented here fits a best plane through five atoms of each peptide unit. The angle between the successive planes is defined as the dihedral angle. The second method is based on the zero-position analysis method. Successive links in this method rotate by the dihedral angles so as to minimize the structural error between respective atoms in the model conformation with given atoms’ coordinates. Dihedral angle final values correspond to the minimum structural error configuration. In this method, singular value decomposition technique is used to best fit the atoms in the two conformations. The third method is a variant of the second method. In this instead of rotating all the links successively only three links are matched each time to extract the dihedral angle of the middle link. By doing so, the error accumulation on the successive links is reduced. This paper focuses on the Euclidean norm as the measure of merit (structural error) to compare different methods with the PDB. This Euclidean norm is further, minimized by optimizing the geometrical features of the peptide plane.

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