Research on Optimization of Fe Clusters Structure Based on Structural Clustering Niche Differential Evolution Algorithm

团簇被称之为“物质第五态”。它是材料科学的新起点，在许多领域都有着广泛的应用。团簇的稳态结构对其独特的物理和化学等性质起到了至关重要的作用，因而受到许多学者的广泛关注。由于团簇的大小在几埃到几百埃之间，尺寸非常小，用实验设备很难合成和直接观测。因此用理论研究的方法来探究团簇的稳态结构显得十分重要。但是寻找团簇的稳态结构十分困难，除了基态结构之外，还存在成千上万的亚稳态结构。目前团簇优化问题已被学者证明为NP难问题，因此用传统的优化方法难以获得最优解，于是使得基于进化算法的全局优化方法得到了广泛应用。 本文以Fe团簇作为研究对象，采用Finnis-Sinclair势来描述原子间的相互作用，以能...The cluster is known as the material fifth state. It has been widely used in many fields, such as physics, chemistry, biology, and engineering. And the cluster is regarded as the new start of the material science. The stable structures of clusters have attracted increasing attention because they play a vital role in their unique physical and chemical properties. The size of cluster is ranged from ...学位：工程硕士院系专业：航空航天学院_工程硕士(控制工程)学号：2322013115337

The improvement research on multi-objective optimization algorithm based on non-dominated sorting

多目标优化问题（MOP）在许多科学研究和工程设计当中普遍存在，此类问题求解十分复杂但又十分重要。尽管传统多目标优化算法已经有了长足的发展，但遗存的问题依然很多，需要改进。 进化多目标优化算法将传统方法中的加权策略改为以种群为单位的进化策略，取得了更理想的优化的效果，NSGA-II就是其中的佼佼者。在此次研究中本人在NSGA-II的基础上提出了一种基于随机交叉算子、变异算子的算法RCVO-NSGA-II（RandomCrossVariationOperator-nondominatedsortinggeneticalgorithmII）用于解多目标优化问题。RCVO-NSGA-II随机采用模拟...Multiobjective optimization problem is common existing in many scientific researches and engineering design and the solution of this kind of problem is very complicated and important. Although the development of the traditional multi-objective optimization algorithm have made great progress, but a lot of problems are need to be improved. Evolutionary multi-objective optimization algorithm change ...学位：工程硕士院系专业：信息科学与技术学院_工程硕士(计算机技术)学号：X201222101

The use of a physiologically based pharmacokinetic model to evaluate deconvolution measurements of systemic absorption

BACKGROUND: An unknown input function can be determined by deconvolution using the systemic bolus input function (r) determined using an experimental input of duration ranging from a few seconds to many minutes. The quantitative relation between the duration of the input and the accuracy of r is unknown. Although a large number of deconvolution procedures have been described, these routines are not available in a convenient software package. METHODS: Four deconvolution methods are implemented in a new, user-friendly software program (PKQuest, ). Three of these methods are characterized by input parameters that are adjusted by the user to provide the "best" fit. A new approach is used to determine these parameters, based on the assumption that the input can be approximated by a gamma distribution. Deconvolution methodologies are evaluated using data generated from a physiologically based pharmacokinetic model (PBPK). RESULTS AND CONCLUSIONS: The 11-compartment PBPK model is accurately described by either a 2 or 3-exponential function, depending on whether or not there is significant tissue binding. For an accurate estimate of r the first venous sample should be at or before the end of the constant infusion and a long (10 minute) constant infusion is preferable to a bolus injection. For noisy data, a gamma distribution deconvolution provides the best result if the input has the form of a gamma distribution. For other input functions, good results are obtained using deconvolution methods based on modeling the input with either a B-spline or uniform dense set of time points

Interactive drug-design: using advanced computing to evaluate the induced fit effect

This thesis describes the efforts made to provide protein flexibility in a molecular modelling software application, which prior to this work, was operating using rigid proteins and semi flexible ligands. Protein flexibility during molecular modelling simulations is a non-­‐trivial task requiring a great number of floating point operations and it could not be accomplished without the help of supercomputing such as GPGPUs (or possibly Xeon Phi). The thesis is structured as follows. It provides a background section, where the reader can find the necessary context and references in order to be able to understand this report. Next is a state of the art section, which describes what had been done in the fields of molecular dynamics and flexible haptic protein ligand docking prior to this work. An implementation section follows, which lists failed efforts that provided the necessary feedback in order to design efficient algorithms to accomplish this task. Chapter 6 describes in detail an irregular – grid decomposition approach in order to provide fast non-­‐bonded interaction computations for GPGPUs. This technique is also associated with algorithms that provide fast bonded interaction computations and exclusions handling for 1-­‐4 bonded atoms during the non-­‐bonded forces computation part. Performance benchmarks as well as accuracy tables for energy and force computations are provided to demonstrate the efficiency of the methodologies explained in this chapter. Chapter 7 provides an overview of an evolutionary strategy used to overcome the problems associated with the limited capabilities of local search strategies such as steepest descents, which get trapped in the first local minima they find. Our proposed method is able to explore the potential energy landscape in such a way that it can pick competitive uphill solutions to escape local minima in the hope of finding deeper valleys. This methodology is also serving the purpose of providing a good number of conformational updates such that it is able to restore the areas of interaction between the protein and the ligand while searching for optimum global solutions

Stochastics global optimization methods and their applications in Chemical Engineering

Ph.DDOCTOR OF PHILOSOPH

Modified Intelligent Water Drops with perturbation operators for atomic cluster optimization

A modified version of the Intelligent Water Drops algorithm (MIWD) was developed then used to determine the most stable configurations of Lennard-Jones (LJ), Binary Lennard-Jones (BLJ) and Morse Clusters. The algorithm is unbiased in that it uses no a priori cluster geometry information or cluster seeds. Results for LJ clusters show that the algorithm is effective and efficient in rediscovering all clusters up to size N = 104 with better success rates specially on difficult clusters compared to previous best methodologies reported in literature. Results on more difficult systems, such as the Binary Lennard Jones clusters up to size 50 (with 5 different atomic size ratios) and Morse clusters up to size 60 (with 2 interparticle range potentials), also showed the ability of MIWD to handle more complex systems. MIWD was then applied to predict the most stable structures of Janus clusters up to size 50 and on size 100 using a LJ potential model with a modulated angular term suited for two-patched Janus particles. Results show that MIWD is able to find well-structured geometries of Janus clusters. It is believed that this has been the first time that a nature-inspired stochastic algorithm and a variant of the IWD algorithm has been applied to the configurational optimization of Janus clusters