基于Toy模型蛋白质折叠预测的多种群微粒群优化算法研究

基于Toy模型的蛋白质折叠结构预测问题是一个典型的NP问题.提出了多种群微粒群优化算法用于计算蛋白质能量最小值.该算法采用了一种新的算法结构,在该结构中,每一代的种群被分为精英子种群、开采子种群和勘探子种群三部分,通过改善种群的局部开采能力和全局勘探能力来提高算法的性能.分别采用Fibonacci蛋白质测试序列和真实蛋白质序列进行了折叠结构预测的仿真实验.实验结果表明该算法能够更精确地进行蛋白质折叠结构预测,为生物科学研究提供了一条有效途径.     

非线性规划在工业产品设计中的应用

目的判断非线性规划方法能否在满足用户使用要求的前提下节约生产加工成本。方法以平板折叠桌作为研究对象,以加工方便作为目标函数,以桌面和桌腿之间的几何关系作为约束条件,建立非线性规划模型,通过MATLAB软件求解得到最优加工方案。结论在给定高为70 cm和圆形桌面直径为80 cm时,平板折叠桌最优加工方案为平板长度158 cm,宽度79.9 cm,厚度3 cm,木条宽度4.7 cm,单侧木条数为17条。     

M型预制袋袋口折合机构运动精度可靠性优化

目的 为提高M型预制袋包装机袋口折合机构轨迹输出点的运动精度,对袋口折合机构进行运动精度可靠性优化。方法 在运动学分析的基础上,用环路增量法建立考虑杆长误差时袋口折合机构的位置误差模型,接着对轨迹输出点进行可靠性分析及蒙特卡洛法验证,通过灵敏度分析确定关键误差影响因素,最后进行运动精度可靠性优化。结果 建立的可靠性模型可以有效地反映杆长误差对机构运动精度的影响,x分量轨迹的可靠度由82.5%提高至92.91%,y分量轨迹可靠度由65.34%提高至89%。结论 经过可靠性优化能够使袋口折合机构运动精度满足设计要求。     

基于确定模式的伪单跳变测试矢量生成技术

提出了一种基于确定模式的伪单跳变测试矢量生成方法,它是在折叠计数器确定模式的基础上,采用LFSR编码折叠计数器种子,通过选定的存储折叠距离来控制测试模式,使得产生的测试矢量之间实现伪单跳变。由于是在确定模式基础上进行的研究,没有改变原来的测试矢量,所以故障覆盖率不会改变,却大大降低了测试功耗。这样既保证了高故障覆盖率,又解决了不同种子所生成的测试矢量之间的重叠冗余。研究结果不仅表明该方案具有很好的数据压缩率,而且证明了该方案的有效性。     

Monte Carlo simulations of systems with complex energy landscapes

Non-traditional Monte Carlo simulations are a powerful approach to the study of systems with complex energy landscapes. After reviewing several of these specialized algorithms we shall describe the behavior of typical systems including spin glasses, lattice proteins, and models for “real” proteins. In the Edwards-Anderson spin glass it is now possible to produce probability distributions in the canonical ensemble and thermodynamic results of high numerical quality. In the hydrophobic-polar (HP) lattice protein model Wang-Landau sampling with an improved move set (pull-moves) produces results of very high quality. These can be compared with the results of other methods of statistical physics. A more realistic membrane protein model for Glycophorin A is also examined. Wang-Landau sampling allows the study of the dimerization process including an elucidation of the nature of the process.     

微型折叠式三维电场传感器

提出一种基于柔性衬底和三维组装方法的新型三维电场传感器.利用柔性衬底的折叠,构建一种互相垂直的新型三维电场传感器,研究了测量空间电场时的耦合,提出解耦算法,标定灵敏度矩阵,实现了空间电场三个方向分量的准确测量;通过一系列的温湿度实验研究了三维结构的形变,证明了三维电场传感器结构稳定可靠.实验结果表明:所研制的三维电场传感器不仅能消除耦合干扰,实现空间电场分量的准确测量,测量误差在3.61％以内;而且通过新的三维组装方法,大大减少了三维电场传感器的质量、体积,折叠工艺简化了三维传感器的组装,有利于批量化生产.     

Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Using Wang–Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse “transition” to a globule state followed by a second “transition” into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of “transitions”. These transitions depend upon the relative interaction strengths and are largely inaccessible to “standard” Monte Carlo methods.     

A Constraint-Based Approach for Deriving 3-D Structures of Cyclic Polypeptides

This paper presents an hybrid algorithm for deriving 3-D structures of cyclic polypeptides. The algorithm combines constraint-based techniques with the most widely used methods for non-cyclic polypeptides. The empirical results demonstrate that the proposed hybrid algorithm outperforms traditional methods especially with respect to running times.     

Genetic Threading

The biological function of proteins is dependent, to a large extent, on their native three dimensional conformation. Thus, it is important to know the structure of as many proteins as possible. Since experimental methods for structure determination are very tedious, there is a significant effort to calculate the structure of a protein from its linear sequence. Direct methods of calculating structure from sequence are not available yet. Thus, an indirect approach to predict the conformation of protein, called threading, is discussed. In this approach, known structures are used as constraints, to restrict the search for the native conformation. Threading requires finding good alignments between a sequence and a structure, which is a major computational challenge and a practical bottleneck in applying threading procedures. The Genetic Algorithm paradigm, an efficient search method that is based on evolutionary ideas, is used to perform sequence to structure alignments. A proper representation is discussed in which genetic operators can be effectively implemented. The algorithm performance is tested for a set of six sequence/structure pairs. The effects of changing operators and parameters are explored and analyzed.     

蛋白质体外折叠技术研究现状与展望

蛋白质折叠技术是生物工程的新“单元操作”。本文阐述了蛋白质体外折叠研究的重要理论意义和应用价值，综述了目前蛋白质体外折叠技术研究进展，最后对蛋白质折叠技术的研究进行了展望。