A Redundant Parallel Spherical Mechanism for Robotic Wrist Applications

Coelho, Tarcisio Antonio Hess

doi:10.1115/1.2735645

Cited by 33 publications

(10 citation statements)

References 12 publications

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“…The pressure was kept at 1 bar. During the MD simulations, the covalent bonds were constrained by the LINCS algorithm [ 45 , 46 ] and SPC water molecules [ 47 ] were constrained with the SETTLE algorithm [ 48 ]. The van der Waals interactions were used with a cutoff distance of 12 Å.…”

Section: Methodsmentioning

confidence: 99%

Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR

et al. 2018

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Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that belongs to the ATP binding cassette protein superfamily. Deletion of phenylalanine at position 508 (ΔF508) is the most common CF-associated mutation and is present in nearly 90% of CF patients. Currently, atomistic level studies are insufficient for understanding the mechanism by which the deletion of a single amino acid causes greatly reduced folding as well as trafficking and gating defects. To clarify this mechanism, we first constructed an atomic model of the inward-facing ΔF508-CFTR and performed allatom molecular dynamics (MD) simulations of the protein in a membrane environment. All of the computational methodologies used are based on those developed in our previous study for wild-type CFTR. Two important findings were obtained. First, consistent with several previous computational results, the deletion of F508 causes a disruption of a hydrophobic cluster located at the interface between the nucleotide binding domain 1 (NBD1) and intracellular loop 4 (ICL4). This exerts unfavorable influences on the correlated motion between ICLs and transmembrane domains (TMDs), likely resulting in gating defects. Second, the F508 deletion affected the NBD1–NBD2 interface via allosteric communication originating from the correlated motion between NBDs and ICLs. As a result, several unusual inter-residue interactions are caused at the NBD1–NBD2 interface. In other words, their correct dimerization is impaired. This study provided insight into the atomic-level details of structural and dynamics changes caused by the ΔF508 mutation and thus provides good insight for drug design.

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Section: Methodsmentioning

confidence: 99%

Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR

et al. 2018

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“…The simulations were performed in the isothermal-isochoric (NVT) ensemble with a Nosé−Hoover thermostat [29,30]. During the MD simulations, the covalent bonds were constrained by the LINCS algorithm [31,32], and the SPC water molecules were constrained with the SETTLE algorithm [33]. The van der Waals interactions were used with a cutoff distance of 4 nm.…”

Section: Computational Details Of Remd Simulationmentioning

confidence: 99%

Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins

et al. 2019

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Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant.The traditional view of the structure-function paradigm is that a protein's function is closely related to a uniquely rigid three-dimensional (3D) structure, which is determined by the protein's primary amino acid sequence. However, it has been accepted that a number of proteins do not adopt a unique 3D structure in solution; instead, they adopt randomcoil-like conformations [1][2][3]. Such proteins undergo a disorder-to-order transition as a requirement for biological function, and they are referred to as intrinsically disordered proteins (IDPs) [1][2][3].Group 3 late embryogenesis abundant (G3LEA) proteins are disordered in solution, but they structuralize into an α-helical structure during drying. To elucidate the origin of this unusual property, we performed replica exchange MD simulations for a peptide composed of two tandem repeat of an 11-mer motif characteristic to G3LEA proteins. It was revealed that its single chain alone exhibits no structuralization, but its two-helix bundle forms a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant in anhydrobiotic organisms.

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“…In addition, redundantly actuated SPMs [15], [16] have been proposed in recent decades; these SPMs allow for an increase in workspace [17], the enhancement of stiffness [18], [19], removal of singularity, and augmentation of dexterity [1], [20]. Many redundantly actuated SPMs have been studied for use in different applications, such as a robotic shoulder [21], wrist [22], and haptic device [23]. Recently, an improved parallel platform with a redundant limb that can adjust the pose in three directions was developed based on the traditional 3RPS parallel mechanism [24].…”

Section: Introductionmentioning

confidence: 99%

Design, Analysis, and Test of a Novel 2-DOF Spherical Motion Mechanism

Bian

Wang

2020

IEEE Access

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A novel two degree-of-freedom (DOF) ball-joint-like hydraulic spherical motion mechanism (SMM) for use in robotic applications is proposed to achieve smooth spherical motion in all directions. Unlike traditional systems that use serial or parallel mechanisms for generating multi-DOF rotations, the proposed SMM is capable of producing continuous 2-DOF rotational motions in a single joint without intermediate transmission mechanisms. The proposed SMM has a compact structure, low inertia, and high stiffness. First, the architecture and operating principle of the proposed SMM is introduced. Then, the kinematic model is established using Euler transformation, following which factors (such as workspace and dexterity) that have an impact on motion performance are evaluated. As the foundation of dynamics analysis and controller design, the Lagrange's equations of the second kind are used to establish the dynamic model. To achieve high tracking accuracy, the radial basis function neural network-based sliding mode controller is applied to the mechanism. The simulation results indicate that the designed controller not only improves trajectory tracking capability but also enhances robustness against external disturbance and system uncertainty. Finally, experiments are performed on a prototype SMM to validate the performance of the proposed SMM and evaluate the control method. INDEX TERMS Spherical motion mechanism, kinematic modeling, motion performance, dynamic modeling, radial basis function neural network-based sliding mode control.

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A Redundant Parallel Spherical Mechanism for Robotic Wrist Applications

Cited by 33 publications

References 12 publications

Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR

Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR

Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins

Design, Analysis, and Test of a Novel 2-DOF Spherical Motion Mechanism

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