The Experts below are selected from a list of 282 Experts worldwide ranked by ideXlab platform
Sergei Grudinin - One of the best experts on this subject based on the ideXlab platform.
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nolb nonlinear rigid block normal mode analysis method
Journal of Chemical Theory and Computation, 2017Co-Authors: Alexandre Hoffmann, Sergei GrudininAbstract:We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the Rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues [Durand et al. Biopolymers 1994, 34, 759–771. Tama et al. Proteins: Struct., Funct., Bioinf. 2000, 41, 1–7]. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a Pure Rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions...
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NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method
2017Co-Authors: Alexandre Hoffmann, Sergei GrudininAbstract:We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the Rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues [Durand et al. Biopolymers 1994, 34, 759–771. Tama et al. Proteins: Struct., Funct., Bioinf. 2000, 41, 1–7]. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a Pure Rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions. For example, NOLB detects the spiral sliding motion of the TALE protein, which is capable of rapid diffusion along its target DNA. Overall, our method produces better structures compared to the standard approach, especially at large deformation amplitudes, as we demonstrate by visual inspection, energy, and topology analyses and also by the MolProbity service validation. Finally, our method is scalable and can be applied to very large molecular systems, such as ribosomes. Standalone executables of the NOLB normal-mode analysis method are available at https://team.inria.fr/nano-d/software/nolb-normal-modes/. A graphical user interface created for the SAMSON software platform will be made available at https://www.samson-connect.net
Alexandre Hoffmann - One of the best experts on this subject based on the ideXlab platform.
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nolb nonlinear rigid block normal mode analysis method
Journal of Chemical Theory and Computation, 2017Co-Authors: Alexandre Hoffmann, Sergei GrudininAbstract:We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the Rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues [Durand et al. Biopolymers 1994, 34, 759–771. Tama et al. Proteins: Struct., Funct., Bioinf. 2000, 41, 1–7]. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a Pure Rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions...
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NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method
2017Co-Authors: Alexandre Hoffmann, Sergei GrudininAbstract:We present a new conceptually simple and computationally efficient method for nonlinear normal-mode analysis called NOLB. It relies on the Rotations-translations of blocks (RTB) theoretical basis developed by Y.-H. Sanejouand and colleagues [Durand et al. Biopolymers 1994, 34, 759–771. Tama et al. Proteins: Struct., Funct., Bioinf. 2000, 41, 1–7]. We demonstrate how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a Pure Rotation about a certain center. We demonstrate the motions produced with the NOLB method on three different molecular systems and show that some of the lowest frequency normal modes correspond to the biologically relevant motions. For example, NOLB detects the spiral sliding motion of the TALE protein, which is capable of rapid diffusion along its target DNA. Overall, our method produces better structures compared to the standard approach, especially at large deformation amplitudes, as we demonstrate by visual inspection, energy, and topology analyses and also by the MolProbity service validation. Finally, our method is scalable and can be applied to very large molecular systems, such as ribosomes. Standalone executables of the NOLB normal-mode analysis method are available at https://team.inria.fr/nano-d/software/nolb-normal-modes/. A graphical user interface created for the SAMSON software platform will be made available at https://www.samson-connect.net
Jorge Melendez - One of the best experts on this subject based on the ideXlab platform.
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a low solar oxygen abundance from the first overtone oh lines
The Astrophysical Journal, 2004Co-Authors: Jorge MelendezAbstract:An extremely high resolution (>105) high signal-to-noise ratio (>103) solar spectrum has been used to measure 15 very weak first-overtone (Δv = 2) infrared OH lines, resulting in a low solar abundance of AO ≈ 8.6 when MARCS, three-dimensional, and spatially and temporally averaged three-dimensional model atmospheres are used. A higher abundance is obtained with Kurucz (AO ≈ 8.7) and Holweger & Muller (AO ≈ 8.8) model atmospheres. The low solar oxygen abundance obtained in this work is in good agreement with a recent three-dimensional analysis of [O I], O I, OH fundamental (Δv = 1) vibration-Rotation, and OH Pure Rotation lines. The present result gives further support for a low solar metallicity, and although using a low solar abundance with OPAL opacities ruins the agreement between the calculated and the helioseismic measurement of the depth of the solar convection zone, recent results from the Opacity Project show that the opacities near the base of the solar convection zone are larger than previously thought, lending further confidence to a low solar oxygen abundance.
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a low solar oxygen abundance from the first overtone oh lines
arXiv: Astrophysics, 2004Co-Authors: Jorge MelendezAbstract:An extremely high-resolution (> 10^5) high-S/N (> 10^3) solar spectrum has been used to measure 15 very weak first overtone (Delta v = 2) infrared OH lines, resulting in a low solar abundance of A(O) ~ 8.6 when MARCS, 3D, and spatially and temporally averaged 3D model atmospheres are used. A higher abundance is obtained with Kurucz (A(O) ~ 8.7) and Holweger & Muller (A(O) ~ 8.8) model atmospheres. The low solar oxygen abundance obtained in this work is in good agreement with a recent 3D analysis of [OI], OI, OH fundamental (Delta v = 1) vibration-Rotation and OH Pure Rotation lines (Asplund et al. 2004). The present result brings further support for a low solar metallicity, and although using a low solar abundance with OPAL opacities ruins the agreement between the calculated and the helioseismic measurement of the depth of the solar convection zone, recent results from the OP project show that the opacities near the base of the solar convection zone are larger than previously thought, bringing further confidence for a low solar oxygen abundance.
Lakmal Seneviratne - One of the best experts on this subject based on the ideXlab platform.
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Joint force decomposition and variation in unified inverse dynamics analysis of a metamorphic parallel mechanism
Meccanica, 2016Co-Authors: Dongming Gan, Jorge Dias, Jian S Dai, Lakmal SeneviratneAbstract:This paper presents a unified inverse kinematics and dynamics model of a metamorphic parallel mechanism with Pure Rotation and Pure translation phases. By altering one Rotation axis of the reconfigurable Hooke (rT) joints in the limbs, the mechanism can be switched into one of the two phases. To provide joint reaction forces for optimal design and control, Newton method is used in developing the dynamics model which is unified by combining geometric constraints and parameters in both phases. An analytical investigation provides special joint force decomposition and limb coordinate setup to decouple the dynamics equations between the platform and the limbs. This reduces the dynamics computation load from solving a 15 × 15 matrix to a 6 × 6 matrix. A numerical example is given to illustrate the proposed method and simulation results are explained and compared between the two phases. The work on this paper gives good reference for optimal design and control of this metamorphic parallel mechanism in different applications using two phases.
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unified kinematics and optimal design of a 3rrps metamorphic parallel mechanism with a reconfigurable revolute joint
Mechanism and Machine Theory, 2016Co-Authors: Dongming Gan, Jorge Dias, Lakmal SeneviratneAbstract:Abstract This paper introduces a new metamorphic parallel mechanism based on a reconfigurable revolute (rR) joint and the mechanism consists of three rRPS (rR joint-prismatic joint-spherical joint) limbs. Reconfiguration principle of the rR joint and the rRPS limb is explained, based on which the 3rRPS metamorphic parallel mechanism can be reconfigurable between two working motion types, Pure Rotation (3R) motion and one translation and two Rotation (1T2R) motion. Using the limb geometric constraint model, analytical forward kinematics is solved in a unified way for both motion types. Reciprocal screw based Jacobian is obtained for singularity analysis which is then used for singularity-free workspace analysis. Based on those, maximum singularity-free workspace and kinematics performance based criteria are applied in optimizing basic mechanism parameters considering input and passive joint limitations. A unified objective function with variable design priorities represented by function weights of the two topologies is proposed and examples are illustrated. The introduced new parallel mechanism covers the two very useful motion types, 3R and 1T2R, while the model in the paper provides basis of modeling and optimal design for further applications.
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variable motion force transmissibility of a metamorphic parallel mechanism with reconfigurable 3t and 3r motion
Journal of Mechanisms and Robotics, 2015Co-Authors: Dongming Gan, Jorge Dias, Lakmal Seneviratne, Jian S DaiAbstract:This paper presents a metamorphic parallel mechanism which can switch its motion between Pure translation (3T) and Pure Rotation (3R) motion. This feature stems from a reconfigurable Hooke (rT) joint of which one of the Rotation axes can be altered freely. More than that, based on the reconfiguration of the rT joint, workspace of both 3T and 3R motion can be tunable and the Rotation center of the 3R motion can be controlled along a line perpendicular to the base plane. Kinematics analysis is presented based on the geometric constraint of the parallel mechanism covering both 3T and 3R motion. Following these screw theory based motion/force transmission equations are obtained and their characteristics are investigated and linked to the singularity analysis using Jacobian matrix. Motion/force transmission indices can be used to optimize basic design parameters of the metamorphic parallel mechanism. This provides reference of this mechanism for potential applications requiring 3T and 3R motion.Copyright © 2015 by ASME
Matteoclaudio Palpacelli - One of the best experts on this subject based on the ideXlab platform.
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analysis and design of a reconfigurable 3 dof parallel manipulator for multimodal tasks
IEEE-ASME Transactions on Mechatronics, 2015Co-Authors: Matteoclaudio Palpacelli, Luca Carbonari, Giacomo Palmieri, Massimo CallegariAbstract:This paper presents the design of a reconfigurable 3-DoF parallel kinematics manipulator. The main feature of the device is the ability to change the mobility of its moving platform from Pure translation to Pure Rotation. The manipulator kinematics is conceived so that, when a particular configuration of the manipulator is reached, the transition between the two working modes is possible by changing the configuration of a metamorphic universal joint, which is used to connect the legs of the manipulator with the moving platform. The mechanical design of the joint, which is in fact a lockable spherical joint, is illustrated. With the joint integrated into the robot architecture, an instantaneous overconstrained kinematics is exploited to manage the phase of reconfiguration of the whole mechatronic device. A kineto-static analysis provides information about the influence of geometric parameters on its functional design. The manipulator shows simple kinematics and statics models, as well as good kinematic and static performances. Eventually, the versatility of the manipulator is shown by proposing some advanced manufacturing applications in which it could find use.
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analysis of kinematics and reconfigurability of a spherical parallel manipulator
IEEE Transactions on Robotics, 2014Co-Authors: Luca Carbonari, Massimo Callegari, Giacomo Palmieri, Matteoclaudio PalpacelliAbstract:This article presents the kinematic characterization of a 3-CPU parallel manipulator designed for motions of Pure Rotation. The machine has been conceived at the Polytechnic University of Marche and recent studies have shown that its kinematic architecture can be exploited for the realization of reconfigurable machines with different kinds of motions (Pure Rotational, Pure translational and planar motions among others). The 3-CPU concept has been subject to further investigations for a deeper understanding of this peculiar behaviour. After a brief introduction to these concepts, the paper faces the position and the differential kinematics of the 3-CPU spherical manipulator aiming at identifying workspace boundaries and its kinematic manipulability.
