Free energy calculation of single molecular interaction using Jarzynski’s identity method: the case of HIV-1 protease inhibitor system

Jarzynski’ identity(JI) method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and experiments.However,JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs.In this paper,we applied a huge number of steered molecular dynamics(SMD) simulations to dissociate the protease of human immunodeficiency type I virus(HIV-1 protease) and its inhibitors.We showed that because of intrinsic complexity of the ligand-receptor system,the energy barrier predicted by JI method at high pulling rates is much higher than experimental results.However,with a slower pulling rate and fewer switch times of simulations,the predictions of JI method can approach to the experiments.These results suggested that the JI method is more appropriate for reconstructing free energy landscape using the data taken from experiments,since the pulling rates used in experiments are often much slower than those in SMD simulations.Furthermore,we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distribution in SMD simulations.     

On elastocapillarity: A review

Elastocapillary phenomena involving elastic deformation of solid structures coupled with capillary effects of liquid droplets/films can be observed in a diversity of fields,e.g.,biology and microelectromechanical systems(MEMS).Understanding the physical mechanisms underlying these phenomena is of great interest for the design of new materials and devices by utilizing the effects of surface tension at micro and nano scales.In this paper,some recent developments in the investigations on elastocapillary phenomena are briefly reviewed.Especially,we consider the deformation,adhesion,self-assembly,buckling and wrinkling of materials and devices induced by surface tensions or capillary forces.The main attention is paid to the experimental results of these phenomena and the theoretical analysis methods based on continuum mechanics.Additionally,the applications of these studies in the fields of MEMS,micro/nanometrology,and biomimetic design of advanced materials and devices are discussed.     

润滑薄油膜承载力的测量

利用面接触润滑油膜测量系统研究了固定倾角滑块轴承承载力问题.在滑块倾角和载荷固定不变的条件下测得油膜厚度与速度的关系,经过参数转换,得到无量纲承载量曲线.这不同于传统方法中在不同收敛比下对油膜压力的直接测量.结果表明:在薄油膜条件下实际承载量曲线和理论曲线表现了相同的变化趋势;实测值小于理论值;理论认为无量纲承载量唯一由收敛比决定,而实验结果表明无量纲承载量曲线受滑块倾角、载荷和润滑油性质的影响.     

基于改进位移模式的一维有限元超收敛算法

将多尺度方法的思想与超收敛计算的解析公式结合起来,提出了改进有限元位移模式的算法。利用超收敛计算的解析公式,将高阶有限元解的位移模式用常规有限元解的位移模式表示。用常规有限元解的位移模式与高阶有限元解的位移模式之和构造新的位移模式,采用积分形式推导了单元刚度矩阵。该算法在前处理和后处理两个阶段都使用超收敛计算公式,在常规试函数的基础上,增加了高阶试函数,使得单元内平衡方程的残差减少,从而达到提高精度的目标。对于线性单元,本文结点和单元的位移、导数都达到了h4阶的超收敛精度。     

Goldstein线搜索下Levenberg-Marquardt方法的全局收敛性

给出在Goldstein线搜索条件下求解非线性方程的Levenberg-Marquardt方法, 在较为温和的条件下证明了该方法的全局收敛性, 并且利用该方法对广义互补问题进行了求解分析.     

连续型动态规划的新算法研究

提出了求解一维连续型动态规划问题的自创算法----离散近似迭代法,并结合双收敛方法求解多维连续型动态规划问题. 该算法的基本思路为：在给定其它状态向
量序列的基础上,每次对一个状态变量序列进行离散近似迭代,并找出该状态变量的最优序列,直到所有状态向量序列都检查完.当模型为非凸非凹动态规划时,
证明了该算法的收敛性.当模型为凸动态规划时,证明了该算法的线性收敛性. 最后,以一个具体算例验证了该模型和算法的有效性.     

基于指数收敛的四旋翼无人机鲁棒自适应飞行控制

针对四旋翼无人机鲁棒自适应飞行问题,提出了一种基于指数收敛的控制方法。考虑到四旋翼系统的欠驱动、强耦合等非线性特性,采用线性化反馈控制策略实现对其轨迹追踪飞行能力的基本控制;针对线性化反馈控制易受系统内外部未知干扰等影响,采用基于指数收敛干扰观测器组合控制设计,实现四旋翼飞行的鲁棒与自适应控制;线性反馈及状态观测器控制系统基于指数收敛稳定。进行了仿真分析,结果表明,干扰观测器对四旋翼系统中存在的未知干扰具有很好的估计能力,所设计的基于指数收敛控制系统,结构简单,且具有较强的干扰抑制能力和较高的系统稳定性,满足四旋翼无人机的鲁棒及自适应飞行能力要求。     

一类重心权Hermite有理插值的二阶导数收敛性

研究了一类特殊情形\left(m=\mathrm{1}\right)的重心权Hermite有理插值,证明了该插值函数的二阶导数r_{\mathrm{1}}^{″}\text{?}\left(x\right)在插值节点和非插值节点处分别以O\left(h^{\mathrm{2}d-\mathrm{1}}\right)和O\left(h^{\mathrm{2}d-\mathrm{3}}\right)的速度收敛于函数f^{″}\text{?}\left(x\right)。数值例子进一步验证了方法的有效性。     

Metrically Regular Mapping and Its Utilization to Convergence Analysis of a Restricted Inexact Newton-Type Method

In the present paper,we study the restricted inexact Newton-type method for solving the generalized equation 0∈f(x)+F(x),where X and Y are Banach spaces,f:X→Y is a Frechet differentiable function and F:X■Y is a set-valued mapping with closed graph.We establish the convergence criteria of the restricted inexact Newton-type method,which guarantees the existence of any sequence generated by this method and show this generated sequence is convergent linearly and quadratically according to the particular assumptions on the Frechet derivative of f.Indeed,we obtain semilocal and local convergence results of restricted inexact Newton-type method for solving the above generalized equation when the Frechet derivative of f is continuous and Lipschitz continuous as well as f+F is metrically regular.An application of this method to variational inequality is given.In addition,a numerical experiment is given which illustrates the theoretical result.     

大口径光学元件磁流变加工驻留时间求解算法

为了解决大口径光学元件磁流变高精度加工问题,基于矩阵运算模型,提出了SBB(Subspace Barzilai and Borwein)最小非负二乘与自适应Tikhonov正则化相结合的驻留时间快速求解方法。同时,在一次收敛中采用双去除函数优化螺旋线轨迹下光学元件的加工,保证中心区域与全口径面形精度一致。仿真表明该算法与常用Lawson-Hanson最小非负二乘法相比,计算精度一致且求解效率大幅提高。对Φ600mm以彗差为主的光学表面模拟加工,峰谷(PV)值和均方根(RMS)值从初始的2.712λ与0.461λ中心区域全局一致收敛到0.306λ和0.0199λ(λ=632.8nm)。因此,提出的算法能够在有效保证面形收敛精度的同时快速获得稳定可靠的驻留时间分布,为磁流变抛光应用于大口径光学元件提供有力支持。