Molecular dynamics simulation for phase behavior of amphiphilic solution

The phase behavior of amphiphilic solution is investigated by molecular dynamics simulation of amphiphilic rigid dimers with explicit solvent molecules. Our simulations show that three kinds of phases (isotropic micellar, hexagonal and lamellar phases) are formed at a lower temperature by quenching from a random configuration of amphiphilic molecules in solution at a higher temperature. It is ascertained that an isotropic micellar phase changes into a hexagonal phase, and then into a lamellar phase as the amphiphilic concentration increases. It is also found that the global orientational order parameter can be used to distinguish these three kinds of phases. From the detailed analyses of the phase behavior, it is concluded that the hydrophilic repulsion plays an important role in the formation of the hexagonal phase while the hydrophobic attraction plays a crucial role in the formation of the lamellar phase.     

An enhanced force and contact position sensor for micro-manipulations

In micro-manipulations, force sensing devices play an important role in the control and the assembly of micro-objects. To protect these micro-objects from damage, we must have the ability to detect the value of the minute amount of interactive force (about a few μN) upon contact between the tip and the object. To detect this micro-force, we need an optimized design of force sensor to increase the strain values at the positions we place sensing components. Stress concentration can effectively amplify the strain values measured by the force sensors. This paper investigates the effect that the notches have on increasing the strain values at the positions we attach the sensing elements. In addition, the optimal design with a flexible structure improves the sensitivity of the sensor. An algorithm that can calculate both contact force and contact position on the sensor tip is also mentioned. Besides, an optimal location of strain gauges will ensure the accuracy and stability of the measurement. Finally, analysis and experiment are done to verify the proposed idea. Recommended by Editorial Board member Dong Hwan Kim under the direction of Editor Jae-Bok Song. This research was supported by the Ministry of Knowledge Economy and Korean Industrial Technology Foundation through the Human Resource Training Project for Strategic Technology. Tri Cong Phung received the B.S. degree in Mechanical Engineering from the HCM University of Technology, Vietnam in 2004 and the M.S. degree in Mechanical Engineering from Sungkyunkwan University in 2007. He is currently working toward a Ph.D. degree in Intelligent Robotics and Mechatronic System Laboratory (IRMS Lab), Mechanical Engineering from Sungkyunkwan University. His research interests include dexterous manipulation and touch sensors. Seung Hwa Ha received the B.S. degree in Korean University of Technology and Education, Korea in 2004. He received the M.S. degree in Mechanical Engineering from Sungkyunkwan University in 2008. He is currently working in Samsung Electronic Co. Ltd. His research interests are about strain gauge and high precision control. Yong Seok Ihn received the B.S. degree in School of Mechanical Engineering from the Sungkyunkwan University, Korea in 2006. He received the M.S. degree in Mechanical Engineering from the Sungkyunkwan University, in 2008. He is currently working toward a Ph. D. degree in the Computer Aided Modeling & Simulation Laboratory (CAMAS Lab), School of Mechanical Engineering at the Sungkyunkwan University in Korea. His research interests are precision mechatronics, dynamic system modeling, and control. Byung June Choi received the B.S. degree in School of Mechanical Engineering from the Sungkyunkwan University, Korea in 2002. He received the M.S. degree in Mechanical Engineer-ing from the Sungkyunkwan University, in 2005. He is currently working toward a Ph.D. degree in the Intelligent Robotics and Mechatronic System Laboratory (IRMS Lab), School of Mechanical Engineering at the Sungkyunkwan University in Korea. His research interests are mechanisms design, multi-robot system control, cooperation, path planning and task allocation algorithm. Sang Moo Lee was born in Seoul, Korea and educated in Seoul. He received the Ph.D. degree from the Seoul National University in Korea, in 1999. He is currently a Principal Researcher of Division for Applied Robot Technology at Korean Institute of Industrial Technology. His research interests include high-precision robot control, motion field network, and location system in outdoor environment for robots. Ja Choon Koo is an Associate Professor of School of Mechanical Engineering in Sungkyunkwan University in Korea. His major researches are in the field of design, analysis, and control of dynamics systems, especially micro precision mechatronic systems and energy transducers. He was an Advisory Engineer for IBM, San Jose, California, USA and a Staff Engineer for SISA, San Jose, CA, USA. He received the Ph.D. and M.S. degrees from the University of Texas at Austin and the B.S. from Hanyang University, Seoul, Korea. Hyouk Ryeol Choi received the B.S. degree from Seoul National University, Seoul, Korea, in 1984, the M.S. degree from Korea Advanced Institute of Science and Technology (KAIST), Daejon, Korea, in 1986, and the Ph.D. degree from Pohang University of Science and Technology (POSTECH), Pohang, Korea, in 1994, all in Mechanical Engineering. From 1986 to 1989, he was an Associate Engineer at LG Electronics Central Research Laboratory, Seoul. From 1993 to 1995, he was at Kyoto University, Kyoto, Japan, as a Grantee of scholarship from the Japanese Educational Ministry. From 2000 to 2001, he visited Advanced Institute of Industrial Science Technology (AIST), Tsukuba, Japan, as a Japan Society for the Promotion of Sciences (JSPS) Fellow. Since 1995, he has been with Sungkyunkwan University, Suwon, Korea, where he is currently a Professor in the School of Mechanical Engineering. He is an Associate Editor of the Journal of Intelligent Service Robotics and International Journal of Control, Automation and Systems (IJCAS), and IEEE Transactions on Robotics. His current research interests include dexterous mechanism, field application of robots, and artificial muscle actuators.     

Pseudo-interference stiffness estimation, a highly efficient numerical method for force evaluation in contact problems

This paper presents a novel method, Pseudo-Interference Stiffness Estimation (PISE), for evaluating the contact compliance and the contact load in the contacting elastic solids. The PISE method is based on the evaluation of the geometric overlap of two assumedly rigid bodies and estimation of the contact force based on this artificial overlap area (or volume). In this paper, an example of the dynamic simulation of two disk collision problem is solved both by PISE method and finite element contact model. The contact force and velocity changes during impact from both methods are shown to be in good agreement. However, PISE method is, computationally, orders of magnitude (about 3000 times in our numerical simulations) faster than finite element contact analysis. The proposed method will be of practical use in contact force approximation of contacting bodies, such as meshing of spur gear teeth, cam analysis and synthesis, robotic grabbing, and numerous other applications.     

A weighted residual relationship for the contact problem with Coulomb friction

In this work, a weighted residual relationship is proposed as an extension of the standard virtual work principle to deal with the large deformation contact problem with Coulomb friction. This weak form is a mixed relationship involving the displacements and the multipliers defined on the reference contact surface of the contactor and is shown to be equivalent to the strong form of the initial/boundary value contact problem. The discretization in space by means of the finite element method is carried out on the mixed relationship in a simple way in order to obtain the semi-discrete equation system. The contact tangent stiffness is derived and numerical examples are presented to assess the efficiency of the formulation.     

A mortar-based frictional contact formulation for large deformations using Lagrange multipliers

In this work a Lagrange multiplier method is proposed to solve 2D Coulomb frictional contact problems in the context of large deformations. As the proposed formulation is based on the mortar method, the constraints are imposed in a weak integral sense along the contact surface. In order to compute the contact integrals, we use a numerical integration based on the definition of the kinematical variables (gap, slip and their variations) at the quadrature points. The linearization of non-linear equations (virtual work and contact constraints) is developed in order to apply a Newton’s method. The examples show that the numerical integration still preserves the optimal rate of convergence of the finite element solution.     

Functionalized graphene as a nanostructured membrane for removal of copper and mercury from aqueous solution: A molecular dynamics simulation study

The purpose of the present study was to investigate the removal of copper and mercury using functionalized graphene as a nanostructured membrane. The molecular dynamics simulation method was used to investigate the removal ability of these ions from aqueous solution using functionalized graphene membrane. The studied systems included a functionalized graphene membrane which was placed in the aqueous ionic solution of CuCl₂ and HgCl₂. An external electrical field was applied along the z axis of the system. The results indicated that the application of electrical field on the system caused the desired ions to pass through the functionalized graphene membrane. The Fluorinated pore (F-pore) terminated graphene selectively conducted Cu²⁺ and Hg²⁺ ions. The calculation of the potential of mean force of ions revealed that Cu²⁺ and Hg²⁺ ions face a relatively small energy barrier and could not pass through the F-pore graphene unless an external electrical field was applied upon them. In contrast, the energy barrier for the Cl⁻ ion was large and it could not pass through the F-pore graphene. The findings of the study indicate that the permeation of ions across the graphene was a function of applied electrical fields. The findings of the present study are based on the detailed analysis and consideration of potential of mean force and radial distribution function curves.     

A simple approximation to rigid body dynamics for computer animation

Recently, the dynamics of linked articulated rigid bodies has become a valuable tool for making realistic three-dimensional computer animations. An exact treatment of rigid body dynamics, however, is based on rather non-intuitive results from classical mechanics (e.g. the Euler equations for rotating bodies) and it relies heavily on sophisticated numerical schemes to solve (large) sets of coupled non-linear algebraic and differential equations. As a result, articulated rigid bodies are not yet supported by most real-time animation systems. This paper discusses an approach to rigid body dynamics which is based on (both conceptually and algorithmically much simpler) point mechanics; this gives rise to an asymptotically exact numerical scheme (NSI) which is useful in the context of real-time animation, provided that the number of degrees of freedom of the simulated system is not too large. Based on NSI, a second scheme (NS2) is derived which is useful for approximating the motions of linked articulated rigid bodies; NS2 turns out to be sufficiently fast to give at least qualitative results in real-time simulation. In general, the algorithm NS2 is not necessarily (asymptotically) exact, but a quantitative analysis shows that in the absence of reaction forces it conserves angular momentum.     

A torque-canceling system using the inverse dynamics parallel solution scheme

A new torque-canceling system (TCS) that stabilizes mechanical sway of robots in motions with large inertia by considering the dynamics of the robot itself is discussed in this paper. The TCS cancels the reaction moment generated by the motion of an object by considering the precise dynamics of the object and the body of the robot itself. The dynamics and the reaction moments are calculated using an inverse dynamics parallel solution scheme that handles the dynamics of complex robotic structures by modeling them with finite elements. Once the reaction moment is known, it is canceled by applying an anti-torque to a torque-generating device. The TCS was verified by a simple experimental setup that enables rotational motion around a single axis in the previous paper. However, the effect of the TCS was not confirmed on those cases where mechanical sways are generated not only in the rotational axis of a rotor but also in the orthogonal axis. Therefore, those cases are tested to confirm the function of the TCS in multi-axial cases in this paper. Then, the TCS is mounted on a walking robot with a closed-loop structure and with a walking motion associated with boundary conditions that vary during the motion. The robot sways during its walking motion, and the validity of the TCS is verified by confirming the distances from standard landing point after a multi-step walking sequence.     

H-POSS表面润湿性的分子动力学模拟

采用分子动力学模拟方法研究了水滴在多面体低聚倍半硅氧烷(H-POSS)固体表面的润湿性能,H-POSS分子和水分子分别采用COMPASS力场和SPC力场模型。模拟得到H-POSS基体密度为1.84g/cm~3,且X射线衍射模拟发现基体具有明显衍射峰,表现出晶体特性,说明COMPASS力场适用于H-POSS基体的构建与研究。H-POSS表面水接触角的模拟值为104.9°,具有疏水性能。通过直接水解法由三氯硅烷(HSiCl_3)实验合成出H-POSS样品,傅立叶红外表征(FT-IR)发现,在2260、1142和871cm~(-1)波数位置出现吸收峰,证实了所合成的样品为H-POSS。其表面水接触角的实验值为109.3°,与模拟值的相对误差仅为4%,说明分子动力学方法可应用于计算H-POSS材料表面润湿性。模拟结果还表明体系温度影响H-POSS材料的表面润湿性,增大体系温度,表面疏水性能降低。     

二氢叶酸还原酶在盐溶液中的分子动力学模拟

为了研究嗜盐酶如何在高盐环境下维持稳定性与活性,本文以沃尔卡尼极嗜盐菌及大肠杆菌的二氢叶酸还原酶(DHFR)为模型,将二者分别置于5种不同盐浓度的水溶液中进行分子动力学模拟。经9ns动力学模拟,得到了二者在不同浓度盐溶液中的运动轨迹,通过对运动轨迹的分析,获取了二者在不同盐浓度下的动力学特性。结果发现嗜盐古生菌的二氢叶酸还原酶自身所形成盐桥及与溶剂所形成的氢键均比大肠杆菌的二氢叶酸还原酶多,而溶剂可及性表面则要小,二者差异均达极显著水平。同时还分析了这两种分子及其氨基酸残基的柔性等。     

叉指式微结构加速度传感器刚度的力法求解

采用结构力学的力法,建立了求解叉指式微结构加速度传感器刚度的力学模型。与材料力学方法相比,简化了推导过程,得到了便于微机计算的结论。     

A parallel algorithm for molecular dynamics simulation of branched molecules

To get an insight into the effects of molecular architecture in the behaviour of thin lubricant films we have devised an algorithm for simulation of branched molecules. We have used this algorithm successfully to simulate branched isomers of C₃₀. However the algorithm is flexible enough to be used for the simulation of more complex branched molecules. The resulting algorithm can be used in molecular dynamics simulation of branched molecules and could be helpful in designing new materials at the molecular level.     

Stabilization of robot motion and contact force interaction for third-order motor dynamics

An approach to the synthesis of control laws stabilizing motion and force in contact tasks, based on the exponential stability of the closed-loop control system, is described. When using the synthesized control laws, simultaneous stabilization of both motion and force is achieved with a preset quality of the transient responses. The task is solved in a most general form, taking into account the constraints on robot control, its position and the force of interaction of the robot and the environment, and the external perturbations and inaccuracies of the measuring sensors, when the environment dynamics is being described by nonlinear second-order differential equation, and the robot dynamics includes the third-order equations of the robot actuators dynamics.     

Fast parallel Preconditioned Conjugate Gradient algorithms for robot manipulator dynamics simulation

In this paper fast parallel Preconditioned Conjugate Gradient (PCG) algorithms for robot manipulator forward dynamics, or dynamic simulation, problem are presented. By exploiting the inherent structure of the forward dynamics problem, suitable preconditioners are devised to accelerate the iterations. Also, based on the choice of preconditioners, a modified dynamic formulation is used to speedup both serial and parallel computation of each iteration. The implementation of the parallel algorithms on two interconnected processor arrays is discussed and their computation and communication complexities are analyzed. The simulation results for a Puma Arm are presented to illustrate the effectiveness of the proposed preconditioners. With a faster convergence due to preconditioning and a faster computation of iterations due to parallelization, the developed parallel PCG algorithms represent the fastest alternative for parallel computation of the problem withO(n) processors.     

分子动力学模拟蛋白质溶液吸附过程构象的变化

计算机模拟作为一种工具在药物分子设计、蛋白质工程、药物筛选等方面逐渐广泛应用起来。为了从分子水平上理解蛋白质吸附的机理，本文采用了刚体模型对聚十赖氨酸在固体表面吸附进行了分子动力学模拟。采用立方周期性边界条件，模拟在NVT条件下进行，各刚体的起始速度按Maxwell取样。初步研究了模拟过程中蛋白质构象的变化，跟踪了吸附过程中二面角φ和ψ的变化。研究结果表明，吸附过程中蛋白质二级结构发生了变化，C末端二级结构的变化最为明显。     

氯化钾溶液中离子水化的分子动力学模拟

使用Material Studio软件包中的COMPASS力场,采用分子动力学模拟的方法研究了温度为298.15 K时,浓度分别为1.065 mol/L、2.140 mol/L、3.129 mol/L的氯化钾溶液中离子水化的微观结构和动力学性质.发现浓度对离子近程水化的结构有一定的影响,随着溶液浓度的增加O-O径向分布...     

基于加速度传感器反馈的丝杠传动系统接触力控制

针对丝杠传动系统从自由空间运动过渡到约束空间力控制过程中,接触不同环境刚度时接触力的动态特性是不同的,并且存在冲击、高频振动甚至不稳定,以及稳态力跟踪阶段的扰动引起的不稳定问题,提出用加速度传感器反馈来增加系统力控制的阻尼,抑制在力控制的接触过渡过程和力维持跟踪过程中因为碰撞和外部扰动等原因产生的高频振动,克服单纯速度反馈控制带宽比较窄的局限性,增加系统的稳定性.建立了基于多传感器的实验平台,进行了接触力控制的实验比较研究,实验结果表明该方法是可行的.     

Factors responsible for the aggregation behavior of hydrophobic polyelectrolyte PEA in aqueous solution studied by molecular dynamics simulations

Self-association (i.e. interchain aggregation) behavior of atactic poly(ethacrylic acid) PEA in dilute aqueous solution as function of degree-of-neutralization by Na⁺ counter-ions (i.e. charge fraction f) was investigated by molecular dynamics simulations. Aggregation is found to occur in the range 0 ≤ f ≤0.7 in agreement with experimental results compared at specified polymer concentration C_p = 0.36 mol/l in dilute solution. The macromolecular solution was characterized and analysed for radius-of-gyration, torsion angle distribution, inter and intra-molecular hydrogen bonds, radial distribution functions of intermolecular and inter-atomic pairs, inter-chain contacts and solvation enthalpy. The PEA chains form aggregate through attractive inter-chain interaction via hydrogen bonding, in the range f < 0.7, in agreement with experimental observation. The numbers of inter-chain contacts decreases with f. A critical structural transition occurs at f = 0.7, observed via simulations for the first time, in R_g as well as inter-chain H-bonds. The inter-chain distance increases with f due to repulsive interactions between COO− groups on the chains. PEA-PEA electrostatic interactions dominant solvation enthalpy. The PEA solvation enthalpy becomes increasingly favorable with increase in f. The transition enthalpy change, in going from uncharged (acid) state to fully charged state (f = 1) is unfavorable towards aggregate formation.     

A parallel explicit solver for simulating impact and penetration of a three-dimensional body into a solid substrate

Some highlights of a recently developed finite element program capable of simulating the impact of a fast moving flexible or rigid object on a deforming substrate are briefly discussed. A finite element model specially tailored for this application and a parallel explicit solver using domain decomposition and message passing technologies were developed. A typical numerical example is presented.