Search Results (6)

Numerical simulations of protein folding enable the design of protein-based nanomachines and nanorobots by predicting folded three-dimensional protein structures with high accuracy and revealing the protein conformation transitions during folding and unfolding. In the kinetostatic compliance method (KCM) for folding simulations, protein molecules are represented as ensembles of rigid nano-linkages connected by chemical bonds, and the folding process is driven by the kinetostatic influence of nonlinear interatomic force fields until the system converges to a free-energy minimum of the protein. Despite its strengths, the conventional KCM framework demands an excessive number of iterations to reach folded protein conformations, with each iteration requiring costly computations of interatomic force fields. To address these limitations, this work introduces a family of sign gradient descent (SGD) algorithms for predicting folded protein structures. Unlike the heuristic-based iterations of the conventional KCM framework, the proposed SGD algorithms rely on the sign of the free-energy gradient to guide the kinetostatic folding process. Owing to their faster and more robust convergence, the proposed SGD-based algorithms reduce the computational burden of interatomic force field evaluations required to reach folded conformations. Their effectiveness is demonstrated through numerical simulations of KCM-based folding of protein backbone chains. Full article

This paper presents a novel redundant-actuated 4-PSS&S compliant parallel micro-rotation mechanism (P represents the actuated prismatic joint and S denotes the spherical pair) with three rotational degrees of freedom. First, compliance models of the flexure spherical hinge, each branch and the whole mechanism are established using the compliance matrix method. Then, the mechanism is simplified as an equivalent spring system to establish two kinetostatic models, with their correctness validated through finite element simulations. Finally, a comparative analysis is conducted on the performance of the 3-PSS&S mechanism, non-redundant-actuated 4-PSS&S mechanism and redundant-actuated 4-PSS&S mechanism. The results show the following: ① For the 4-PSS&S mechanism, redundant actuation with optimized actuating force distribution effectively reduces the peak actuating force by up to 50% (average 40.95%), achieving an average 10.79% reduction compared to the 3-PSS&S mechanism. ② The 4-PSS&S mechanism’s output stiffness increases by 26.68% in the θ_x and θ_y directions and by 33.31% in the θ_z direction compared to the 3-PSS&S mechanism. ③ Optimal force distribution significantly reduces the parasitic axis drift of the redundant-actuated 4-PSS&S mechanism at the constrained flexure spherical hinge S3, indicating higher motion accuracy. ④ The workspace volume of the redundant-actuated 4-PSS&S mechanism expands by 94.32% compared to the 3-PSS&S mechanism and by 372.89% compared to the non-redundant-actuated 4-PSS&S mechanism. Full article

The kinetostatic compliance method (KCM) models protein molecules as nanomechanisms consisting of numerous rigid peptide plane linkages. These linkages articulate with respect to each other through changes in the molecule dihedral angles, resulting in a kinematic mechanism with hyper degrees of freedom. Within the KCM framework, nonlinear interatomic forces drive protein folding by guiding the molecule’s dihedral angle vector towards its lowest energy state in a kinetostatic manner. This paper proposes a numerical integrator that is well suited to KCM-based protein folding and overcomes the limitations of traditional explicit Euler methods with fixed step size. Our proposed integration scheme is based on pseudo-transient continuation with an adaptive step size updating rule that can efficiently compute protein folding pathways, namely, the transient three-dimensional configurations of protein molecules during folding. Numerical simulations utilizing the KCM approach on protein backbones confirm the effectiveness of the proposed integrator. Full article

A novel 2PRS-2PSS (P represents the prismatic pair, R represents the revolute hinge, S represents the spherical hinge) compliant parallel micromanipulator with two translational DOFs and two rotational DOFs is presented, and its compliance model and kinetostatic model are sequentially developed and analyzed. Initially, an analytical model used to describe the compliance of this micromanipulator was developed using the compliance matrix method (CMM). Through a comparison with finite element analysis, the accuracy of this analytical model is confirmed, and the influence of various dimensional and structural parameters on the compliance behavior is investigated. Subsequently, the micromanipulator is treated as an equivalent spring system, allowing for the derivation of its governing equation based on the established compliance model. From this equation, a kinetostatic model relating input forces to output displacements is derived. Validation of this model is performed by comparing analytical results with finite element simulations under specific motion trajectories, revealing a maximum relative error of 6.18%. This close agreement verifies the accuracy of the kinetostatic model. Finally, the impact of the parameters of the flexure hinge on the mapping matrix is examined to offer insights into minimizing undesired displacements, providing valuable guidance for optimizing the micromanipulator’s performance. Full article

In order to expand the range of motion performance of the 3-PSS-compliant parallel micro-motion platform, a variable inclination angle of the mechanism’s guide rails was introduced to construct a category of generalized 3-PSS compliant parallel micro-motion platforms with distinct configurations (exhibiting different motion performances) but identical motion patterns (three translational degrees of freedom). The compliance and kinetostatics of such micro-motion platform are modeled and analyzed. Firstly, the compliance model is established based on the coordinate transformation method. Then, simplifying the micro-motion platform into a spring system, the kinetostatic model in terms of input force–output displacement is established based on the compliance model using the compliance matrix method. For practical application considerations, the kinetostatic model in terms of input displacement–output displacement is further derived based on the input force–output displacement model. Then, the correctness of the established compliance model and kinetostatic model is successively verified through finite element simulation. Finally, using two specified motion trajectories (spatial spiral trajectory and planar circular trajectory) as examples, an analysis is conducted on the influence of guide rail inclination angle variations on the kinetostatic performance of the micro-motion platform. This analysis serves as guidance for the rational design of such micro-motion platforms. Full article

In a micro-manipulation system, the compliant gripper is used for gripping, handling and assembling of objects. Large displacement and anti-buckling characteristics are desired in the design of the gripper. In this paper, a compliant gripper with these two characteristics is proposed, modelled and verified. The large displacement is enabled by using distributed compliance in a double-slider kinematic mechanism. An inverted flexure arrangement enables the anti-buckling of the gripper when closing the two jaws. A pseudo-rigid-body model (PRBM) method with the help of virtual work principle is employed to obtain several desired analytical relations including the amplification coefficient and kinetostatics. The results of the finite element analysis (FEA) are shown to be consistent with the results of the derived analytical model. An experimental test was carried out through a milling machined aluminium alloy prototype, the results of which verify the good performance of the compliant gripper. Full article