Protein flexibility and dynamics using constraint theory

A new approach is presented for determining the rigid regions in proteins and the flexible joints between them. The short-range forces in proteins are modeled as constraints and we use a recently developed formalism from graph theory to analyze flexibility in the bond network. Forces included in the analysis are the covalent bond-stretching and bond-bending forces, salt bridges, and hydrogen bonds. We use a local function to associate an energy with individual hydrogen bonds, which then can be included or excluded depending on the bond strength. Colored maps of the rigid and flexible regions provide a direct visualization of where the motion of the protein can take place, consistent with these distance constraints. We also define a flexibility index that quantifies the local density of flexible or floppy modes, in terms of the dihedral angles that remain free to rotate in each flexible region. A negative flexibility index provides a measure of the density of redundant bonds in rigid regions. A new application of this approach is to simulate the maximal range of possible motions of the flexible regions by introducing Monte Carlo changes in the free dihedral angles, subject to the distance constraints. This is done using a method that maintains closure of the rings formed by covalent and hydrogen bonds in the flexible parts of the protein, and van der Waals overlaps between atoms are avoided. We use the locus of the possible motions of HIV protease as an example: movies of its motion can be seen at http://www.pa.msu.edu/~lei.     

A method for improving dynamic solutions in flexible multibody dynamics

This paper presents a method for improving dynamic solutions that are obtained from the dynamic simulation of flexible multibody systems. The mode-acceleration concept in linear structural dynamics is utilized in the proposed method for improving accuracy in the postprocessing stage. A theoretical explanation is made on why the proposed method improves the dynamic solutions in the context of the mode-acceleration method. A mode-acceleration equation for each flexible body is defined and the load term in the right hand side of the equation is represented as a combination of space-dependent and time-dependent terms so that efficient computation of dynamic solutions can be achieved. The load term is obtained from dynamic simulation of a flexible multibody system and a finite element method is used to compute dynamic solutions by quasi-static analyses. Numerical examples show the effectiveness of the proposed method.     

A systematic method of dynamics for flexible robot manipulators

In this article, a systematic method to derive dynamic equations of motion for flexible robot manipulators is developed by using the Lagrangian assumed modes method. The proposed method can be applied to dynamic simulation and control system design for flexible robot manipulators. In the proposed method, the link deflection is described by a truncated modal expansion. The operations of only 3x3 matrices and/or 3 × 1 vectors exist in the method. All the dynamics computations are performed in the link coordinate systems, where the kinematics informations are computed with the forward recursion from the base to the hand tip and the dynamics informations are computed with the return recursion. As generally compared with other existing methods, the method proposed in this article is, computationally, more simple, systematic, and efficient. A computational simulation for a single-link flexible robot manipulator is presented to verify the proposed method. © 1992 John Wiley & Sons, Inc.     

Motion optimization of human body for impulse-based applications

This paper presents the optimal motion generation of the kinematic redundant human body model for impulse-based applications. Inspired by effective and safe motion generation of the human body, we propose a motion generation algorithm considering the external and internal impulses. Firstly, the cost function is defined using the closed form model of external and internal impulses. Then, the self-motion is exploited by using the gradient projection method to generate the optimal motions. Furthermore, the proposed methodology is verified through simulations considering a 4-DOF planar human body model for landing on ground and ball kicking applications and a 3-DOF human arm model for sawing task. It is found that, considering the internal and external impulses for optimization, the optimized posture’s results are well identical to the human body behavior in daily impulse-based motions.     

Non-linear dynamics of flexible multibody systems

In this work we set to examine several important issues pertinent to currently very active research area of the finite element modeling of flexible multibody system dynamics. To that end, we first briefly introduce three different model problems in non-linear dynamics of flexible 3D solid, a rigid body and 3D geometrically exact beam, which covers the vast majority of representative models for the particular components of a multibody system. The finite element semi-discretization for these models is presented along with the time-discretization performed by the mid-point scheme. In extending the proposed methodology to modeling of flexible multibody systems, we also present how to build a systematic representation of any kind of joint connecting two multibody components, a typical case of holonomic contraint, as a linear superposition of elementary constraints. We also indicate by a chosen model of rolling contact, an example of non-holonomic constraint, that the latter can also be included within the proposed framework. An important aspect regarding the reduction of computational cost while retaining the consistency of the model is also addressed in terms of systematic use of the rigid component hypothesis, mass lumping and the appropriate application of the explicit-implicit time-integration scheme to the problem on hand. Several numerical simulations dealing with non-linear dynamics of flexible multibody systems undergoing large overall motion are presented to further illustrate the potential of presented methodology. Closing remarks are given to summarize the recent achievements and point out several directions for future research.     

变拓扑柔性多体系统接触碰撞动力学研究

在实际工程领域中存在着大量接触碰撞等非连续动力学问题,现有的解决柔性多体系统连续动力学过程的建模理论与方法,已经无法解决或无法很好解决这些问题.本文基于变拓扑思想,提出了附加接触约束的柔性多体系统碰撞动力学建模理论；通过设计柔性圆柱杆接触碰撞实验,验证了所提出附加约束接触碰撞模型的有效性；针对柔性多体系统全局动力学仿真面临时间和空间的多尺度问题,提出多变量的离散方法,从而提高了柔性多体系统非连续动力学的仿真效率.     

Dynamics and Noncollocated Model‐Free Position Control for a Space Robot with Multi‐Link Flexible Manipulators

In this paper, both the dynamics and noncollocated model‐free position control (NMPC) for a space robot with multi‐link flexible manipulators are developed. Using assumed modes approach to describe the flexible deformation, the dynamic model of the flexible space robotic system is derived with Lagrangian method to represent the system dynamic behaviors. Based on Lyapunov's direct method, the robust model‐free position control with noncollocated feedback is designed for position regulation of the space robot and vibration suppression of the flexible manipulators. The closed‐loop stability of the space robotic system can be guaranteed and the guideline of choosing noncollocated feedback is analyzed. The proposed control is easily implementable for flexible space robot with both uncertain complicated dynamic model and unknown system parameters, and all the control signals can be measured by sensors directly or obtained by a backward difference algorithm. Numerical simulations on a two‐link flexible space robot are provided to demonstrate the effectiveness of the proposed control.     

Flexible multibody dynamics using coordinate reduction improved by dynamic correction

This paper is concerned with the efficient dynamic analysis of flexible multibody systems using a robust coordinate reduction technique. Unlike conventional static correction, the formulation is derived by dynamic correction that considers the inertia effect. In this formulation, the constraint and fixed-interface normal modes, which are representative modes in the typical coordinate reduction, are corrected by considering the truncated modal effect with the residual flexibility. Therefore, the proposed method can offer a more precise reduced system without increasing the dimension, which consequently leads to a more accurate and efficient flexible multibody simulation. We implement here the proposed method under augmented formulations of the floating reference frame approach, and test its performance with numerical examples.     

A differential approach for modeling revolute clearance joints in planar rigid multibody systems

A non-penetration approach of frictional contact analysis is presented for modeling revolute clearance joints of planar rigid multibody systems. In the revolute clearance joint, the motion modes of the journal are divided into three categories, namely, the free motion, collision, and permanent contact modes. The switch between different contact modes is identified by the state of the journal and bearing, including the gap and the normal relative velocity. When impact in the revolute clearance joint is detected, the collision process is simulated by the impulse-based differential approach, where Stronge’s improved model for restitution is employed to determine the relative velocity after impact. Instead of algebraic equations, the impact process is described by a set of ordinary differential equations (ODEs), which avoids solving complementarity problems. Moreover, in the permanent contact mode, the constraint-based approach and modified Coulomb’s friction law are adopted. The permanent contact mode maintains for most of the time and the governing ODEs are non-stiff. There is general agreement that the constraint-based approach is more efficient than the force-based method. A slider–crank mechanism with a revolute clearance joint is considered as a demonstrative application example where the comparison with the continuous contact force model is investigated.     

柔性臂漂浮基空间机器人建模与轨迹跟踪控制

利用拉格朗日法和假设模态方法建立了末端柔性的两臂漂浮基空间机器人的非线性动力学方程．通过坐标变换,推导出一种新的以可测关节角为变量的全局动态模型,并在此基础上运用基于模型的非线性解耦反馈控制方法得到关节相对转角与柔性臂的弹性变形部分解耦形式控制方程．最后,讨论了柔性臂漂浮基空间机器人的轨迹跟踪问题,并通过仿真实例计算,表明该模型转换及控制方法对于柔性臂漂浮基空间机器人末端轨迹跟踪控制的有效性．     

A two-step approach for model reduction in flexible multibody dynamics

In this work, a two-step approach for model reduction in flexible multibody dynamics is proposed. This technique is a combination of the Krylov-subspace method and a Gramian matrix based reduction approach that is particularly suited if a small reduced-order model of a system charged with many force-inputs has to be generated. The proposed methodology can be implemented efficiently using sparse matrix techniques and is therefore applicable to large-scale systems too. By a numerical example, it is demonstrated that the suggested two-step approach has very good approximation capabilities in the time as well as in the frequency domain and can help to reduce the computation time of a numerical simulation significantly.     

刚柔耦合系统动力学研究进展

首先简要回顾了柔性多体系统动力学前期研究的3个阶段．针对传统零次近似模型的缺陷提出了新的建模理论,并在新的一次近似耦合模型的基础上,就“动力刚化”问题和刚柔耦合动力学问题中的离散化方法与实验等方面进行研究;研制了供理论研究和动力学现象揭示的实验平台．文中对所取得的研究成果进行介绍．文末对今后的研究方向进行了展望．     

Application of perturbation techniques to flexible multibody system dynamics

In this paper, a matrix perturbation technique is developed for flexible bodies (substructures) that undergo large reference translational and rotational displacements. Although the governing dynamic equations of motion of such systems are highly nonlinear because of the large angular rotations and the resulting nonlinear inertia coupling between the reference motion and the elastic deformation, a generalized linear eigenvalue problem that defines the deformation mode shapes of the body with respect to the selected body reference is identified. This eigenvalue problem is solved only once and the variations in the body stiffness and inertia properties due to a change in selected design parameters are evaluated by using perturbation analysis techniques. The main advantage of using the proposed technique is to avoid a new finite element discretization when some design parameters are changed. This, in turn, substantially reduces the computational time, especially when large scale flexible bodies with complex geometry are considered. A numerical example is presented in order to demonstrate the use of the perturbation techniques developed in this paper in the design of flexible multibody systems.     

Robust adaptive boundary control of a flexible marine riser with vessel dynamics

In this paper, robust adaptive boundary control for a flexible marine riser with vessel dynamics is developed to suppress the riser’s vibration. To provide an accurate and concise representation of the riser’s dynamic behavior, the flexible marine riser with vessel dynamics is described by a distributed parameter system with a partial differential equation (PDE) and four ordinary differential equations (ODEs). Boundary control is proposed at the top boundary of the riser based on Lyapunov’s direct method to regulate the riser’s vibration. Adaptive control is designed when the system parametric uncertainty exists. With the proposed robust adaptive boundary control, uniform boundedness under the ocean current disturbance can be achieved. The proposed control is implementable with actual instrumentation since all the required signals in the control can be measured by sensors or calculated by a backward difference algorithm. The state of the system is proven to converge to a small neighborhood of zero by appropriately choosing design parameters. Simulations are provided to illustrate the applicability and effectiveness of the proposed control.     

Dynamic boundary control of a Euler-Bernoulli beam

A flexible beam, clamped to a rigid base at one end and free at the other end is considered. To stabilize the beam vibrations, a dynamic boundary force control and a dynamic boundary torque control applied at the free end of the beam are proposed. It is proved that with the proposed controls, the beam vibrations decay exponentially. The proof uses a Lyapunov functional, based on the energy functional of the system     

基于内流动力学的海洋输油柔性立管鲁棒边界控制

海洋输油柔性立管的振动是引起立管疲劳破坏的主要原因,对其研究边界控制是消除振动疲劳、减少断裂的有效方法.本文引入内流动力学,完善了立管原始无穷维分布参数模型,更好地表达了柔性立管的动力学响应.为抑制柔性立管在内外流激励下的振动奠下基础,本文用Lyapunov直接法对柔性立管系统的稳定性和状态一致有界性进行了证明,设计了边界控制器调节柔性立管的振动,其中控制器使用了符号函数来消除不确定性环境扰动对振动控制效果的影响,提高了系统的鲁棒性.仿真实验表明本文所设计的控制算法有效地减少了柔性立管的振动偏移量.     

On the air damping of flexible microbeam in free space at the free-molecule regime

Predicting air damping is crucial in the design of high Q microelectromechanical systems. In the past, air damping of rigid microbeam in free space at molecular regime is usually estimated using the free molecular model proposed by Christian (Vacuum 16:175–178, 1966), air damping of flexible microbeam is estimated using the model proposed by Blom (J Vac Sci Technol B 10:19–26, 1992). The relation between the two models is Q _Blom = 3Q _Christian. In this paper, a general proof is presented that shows the Christian’s model is valid for the air damping of flexible microbeam in free space at molecular regime. By comparing with the experimental results available in the literatures (Blom et al. in J Vac Sci Technol B 10:19–26, 1992; Yasumura et al. in J Micromech Syst 9:117–125, 2000), we conclude that the Christian’s model is the best choice in predicting the air damping of flexible microbeam in free space at the molecular regime.     

Distributed structural dynamics control of flexible manipulators —I. Structural dynamics and distributed viscoelastic actuator

Reducing structural dead weight has become of increasing importance in the design of new generation lightweight and high-speed robot manipulators. However, due to the nature of structural flexibility, the dynamic oscillation associated with robot structures can affect the operation accuracy and precision. This work, in two parts, presents a study on the vibration control of elastic or flexible robot structures. Effects of distributed passive (Part I) and active (in Part II) actuators on elastic robot structures are studied. The proposed distributed passive viscoelastic actuator (in Part I) is a layer (or layers) of viscoelastic polymer directly attached to the flexible robot element, the oscillation of which is to be controlled. The passive actuator is activated by the oscillation of the robot structure and it automatically dissipates vibration energy and constrains the undesirable motion to eliminate the disturbance and to maintain a precise robot trajectory. A finite element program capable of analyzing flexible links is developed. Results obtained from the finite element simulation are presented.     

Effective input order of dynamics learning tree

In this paper, we discuss about the learning performance of dynamics learning tree (DLT) while mainly focusing on the implementation on robot arms. We propose an input-order-designing method for DLT. DLT has been applied to the modeling of boat, vehicle, and humanoid robot. However, the relationship between the input order and the performance of DLT has not been investigated. In the proposed method, a developer is able to design an effective input order intuitively. The proposed method was validated in the model learning tasks on a simulated robot manipulator, a real robot manipulator, and a simulated vehicle. The first/second manipulator was equipped with flexible arm/finger joints that made uncertainty around the trajectories of manipulated objects. In all of the cases, the proposed method improved the performance of DLT.     

Control of a class of nonlinear uncertain systems via compensatedinverse dynamics approach

The tracking control problem of a class of nonlinear systems via inverse dynamics method is addressed. The motivation for the study stems from the need to control practical systems arising from aerospace and mechanical engineering. Because modeling uncertainties and external disturbances are always present in these systems, inverse dynamics technique is not applicable directly. A compensated inverse dynamics approach is proposed to account for the effect of uncertainties. The compensation is achieved by adaptive and robust schemes. Application of the proposed strategy to the vibration suppression of a two-bay flexible truss structure is presented