一类求解箱式约束优化问题的自适应引力搜索算法

为了改进引力搜索算法求解箱式约束优化问题的性能,提出了一类自适应引力搜索算法,新算法定义了算法停滞系数,当算法陷入停滞时,可以自适应的修改引力参数,帮助算法跳出停滞状态;定义了个体相似系数,当种群陷入局部最优时,通过变异策略改善种群的多样性。数值试验结果表明,新算法有效的平衡了全局开发和局部搜索能力,具有更强的全局寻优能力,适于求解复杂优化问题。     

空间光学成像系统波像差的位相差异估计方法

针对传统光学设计和校正手段无法有效消除空间光学成像系统在轨工作时受各种因素影响使像质变差的问题,提出把均匀设计的思想引入位相差异波前传感技术,对系统在轨工作时的波前畸变进行估计.从而实现了对系统波像差的全局优化估计,放宽了波像差的估计范围,易于实现并行化.通过仿真实验发现,该方法正确估计率高,抗噪声能力强,是进行空间光学成像系统波像差估计的有效方法.     

空间光学成像系统波像差的位相差异估计方法

针对传统光学设计和校正手段无法有效消除空间光学成像系统在轨工作时受各种因素影响使像质变差的问题,提出把均匀设计的思想引入位相差异波前传感技术,对系统在轨工作时的波前畸变进行估计.从而实现了对系统波像差的全局优化估计,放宽了波像差的估计范围,易于实现并行化.通过仿真实验发现,该方法正确估计率高,抗噪声能力强,是进行空间光学成像系统波像差估计的有效方法.     

An evolutionary optimization procedure applied to the synthesis of integrated spot-size converters

An evolutionary algorithm is applied to the synthesis of an integrated spot-size converter. Evolutionary algorithms turned out to be well suited for the solution of very complex problems having strongly non-linear cost functions defined over the solution space. They mostly work faster than other optimization techniques like random search or the Monte-Carlo method because of their parallel search mechanism, also referred to as implicit parallelism. The intrinsic behaviour of the optimization is demonstrated using an example of a spot-size converter that is implemented as a non-periodic segmented waveguide structure. Only a small number of structures have to be evaluated to achieve a coupling loss below 1.3dB that is considered to be very good. A supervising method is proposed, introducing an evolution quality figure. This figure is used to visualize and to qualify the evolution of the algorithm. Based on this figure a termination condition is suggested.     

Molecular phase space transport in water: Non-stationary random walk model

Molecular transport in phase space is crucial for chemical reactions because it defines how pre-reactive molecular configurations are found during the time evolution of the system. Using Molecular Dynamics (MD) simulated atomistic trajectories we test the assumption of the normal diffusion in the phase space for bulk water at ambient conditions by checking the equivalence of the transport to the random walk model. Contrary to common expectations we have found that some statistical features of the transport in the phase space differ from those of the normal diffusion models. This implies a non-random character of the path search process by the reacting complexes in water solutions. Our further numerical experiments show that a significant long period of non-stationarity in the transition probabilities of the segments of molecular trajectories can account for the observed non-uniform filling of the phase space. Surprisingly, the characteristic periods in the model non-stationarity constitute hundreds of nanoseconds, that is much longer time scales compared to typical lifetime of known liquid water molecular structures (several picoseconds).     

Modeling and optimization of non-periodic grating couplers

The higher degree of freedom available for non-periodic gratings (as compared with their periodic counterparts) is investigated. These non-periodic structures may be employed to design novel light couplers with increased functionality. Optimizing such devices requires a complex search in a huge parameter space. The success in the solution of this task depends on the availability of a fast forward solver and a reliable search algorithm. Here, a fast forward solver based on the multiple multipole (MMP) method together with a near-to-far field transformation and a multiple scattering calculation is presented. Thanks to the efficiency of our approach, non-periodic gratings are evaluated with a speed comparable to commonly used periodic grating approximations. This allows our solver to be combined with a heuristic global search scheme, namely an evolutionary algorithm. The procedure is demonstrated with the optimization of a non-periodic grating output coupler that suppresses an unwanted second diffracted order.     

What can a chemist learn from nature’s macrocycles? – A brief, conceptual view

Macrocyclic natural products often display remarkable biological activities, and many of these compounds (or their derivatives) are used as drugs. The chemical diversity of these compounds is immense and may provide inspiration for innovative drug design. Therefore, a database of naturally occurring macrocycles was analyzed for ring size, molecular weight distribution, and the frequency of some common substructural motifs. The underlying principles of the chemical diversity are reviewed in terms of biosynthetic origin and natures strategies for diversity and complexity generation in relation to the structural diversity and similarities found in the macrocycle database. Finally, it is suggested that synthetic chemists should use not only natures molecules, but also natures strategies as a source of inspiration. To illustrate this, the biosynthesis of macrocycles by non-ribosomal peptide synthetases and terpene and polyketide cyclases, as well as recent advances of these strategies in an integrated synthesis/biotechnology approach are briefly reviewed.     

周期优势结构提炼与搜索路径强化结合提升换热网络结构进化能力

针对强制进化随机游走算法（RWCE）在优化后期会陷入局部最优而使搜索能力下降的问题,提出周期优势结构提炼与搜索路径强化结合策略.首先对系统种群初步优化,每隔一定周期进行一次优势个体提炼,然后采用多重路径复制的方法将这些优势个体给其他个体,最后根据搜索机制遍布整个求解域.以优势个体为中心进行多重路径搜索策略,提高了局部寻优精度,增加了种群多样性,进而增强了全局搜索能力,优化效率和质量得以提高.     

Collective resonance model of energy exchange in 3D nonequipartitioned beams

Energy exchange between the longitudinal and transverse degrees of freedom of nonequipartitioned bunched beams (non-neutral plasmas) is investigated by means of 3D simulation. It is found that collective instability may lead to energy transfer in the direction of equipartition, without full progression to it, in certain bounded regions of parameter space where internal resonance conditions are satisfied, in good agreement with stability charts from an earlier derived 2D Vlasov analysis. Nonequipartitioned stable equilibria, however, exist in relatively wide regimes of parameter space. This provides evidence that such regimes may be safely used in the design of future high-intensity linacs.     

A geometry optimization framework for photonic crystal design

The performance of photonic crystal devices can depend strongly on their geometry. Alas, their fundamental physics offers relatively little by way of pointers in terms of optimum shapes, so numerical design search techniques must be used in an attempt to determine high performance layouts. We discuss strategies for solving this type of optimization problem, the main challenge of which is the conflict between the enormous size of the space of potentially useful designs and the relatively high computational cost of evaluating the performance of putative shapes. The optimization technique proposed here operates over increasing levels of fidelity, both in terms of the resolution of its non-parametric shape definition and in terms of the resolution of the numerical analysis of the performance of putative designs. This is a generic method, potentially applicable to any type of electromagnetic device shape design problem. We also consider a methodology for assessing the robustness of the optima generated through this process, investigating the impact of manufacturing errors on their performance. As an illustration, we apply this technology to the design of a two-dimensional photonic crystal structure; the result features a large complete band gap structure and a topology that is different from previously published designs.     

Profiling the immune responses of human patients treated with recombinant streptokinase after myocardial infarct

The SPOT synthesis of peptide arrays on continuous cellulose membranes should be generally applicable in the analysis of sequential antibody binding sites using the enzyme-substrate or other standard detection protocols. The use of total serum is limited by the occurrence of high background levels. This may be overcome if affinity purified antibodies or sera with high antibody titers are used, which allows work at high dilutions and a consequent reduction of background level. Here we demonstrate the mapping of antigenic regions located on recombinant streptokinase SK-2 (Heberkinase) using cellulose-bound peptide scans and human total sera from patients treated with SK-2 (Heberkinase). Streptokinase (SK) is a 47 kDa protein produced by various strains of hemolytic streptococci and is a potent activator of the fibrinolytic enzyme system in humans. SK is in widespread clinical use to treat acute infarction because of its function as an activator of vascular fibrinolysis. Since streptococcal infections are common, normal individuals are immunized with SK and antibodies (Abs) to SK can be detected in most of them. This therapy generates significant T-cell responses to SK and the neutralizing capacity of the Abs rises significantly. Neutralizing Abs reduces the efficiency of thrombolytic therapy and may cause allergic reactions. The widespread use of SK in humans makes its antigenicity an important clinical problem. In this regard the study of the immunodominant regions of SK becomes an important aspect for the improvement of this thrombolytic agent.     

Exploring the chemical space of peptides for drug discovery: a focus on linear and cyclic penta-peptides

Peptide and peptide-like structures are regaining attention in drug discovery. Previous studies suggest that bioactive peptides have diverse structures and may have physicochemical properties attractive to become hit and lead compounds. However, chemoinformatic studies that characterize such diversity are limited. Herein, we report the physicochemical property profile and chemical space of four synthetic linear and cyclic combinatorial peptide libraries. As a case study, the analysis was focused on penta-peptides. The chemical space of the peptide and N-methylated peptides libraries was compared to compound data sets of pharmaceutical relevance. Results indicated that there is a major overlap in the chemical space of N-methylated cyclic peptides with inhibitors of protein–protein interactions and macrocyclic natural products available for screening. Also, there is an overlap between the chemical space of the synthetic peptides with peptides approved for clinical use (or in clinical trials), and to other approved drugs that are outside the traditional chemical space. Results further support that synthetic penta-peptides are suitable compounds to be used in drug discovery projects.     

Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands

A novel heuristic using an iterative select-and-purge strategy is proposed. It combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme. This approach aims to the de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them. The algorithm performs an unbiased stochastic exploration of the sample space, acting as a binary classifier when analyzing the entire peptides population. It uses a novel and effective criterion for weighting the likelihood of a given peptide to form an association complex with a particular ligand molecule based on amino acid sequences. The exploratory analysis relies on chemical information of peptides composition, sequence patterns, and association free energies (docking scores) in order to converge to those peptides forming the association complexes with higher affinities. Statistical estimations support these results providing an association probability by improving predictions accuracy even in cases where only a fraction of all possible combinations are sampled. False positives/false negatives ratio was also improved with this method. A simple rigid-body docking approach together with the proper information about amino acid sequences was used. The methodology was applied in a retrospective docking study to all 8000 possible tripeptide combinations using the 20 natural amino acids, screened against a training set of 77 different ligands with diverse functional groups. Afterward, all tripeptides were screened against a test set of 82 ligands, also containing different functional groups. Results show that our integrated methodology is capable of finding a representative group of the top-scoring tripeptides. The associated probability of identifying the best receptor or a group of the top-ranked receptors is more than double and about 10 times higher, respectively, when compared to classical random sampling methods.     

Phase transition and thermodynamic properties of Sr under high pressure

We have performed the first-principles and classical molecular dynamics simulations to investigate the phase diagram and thermodynamic properties of Sr under high pressure and temperature. The obtained solid phase diagram of Sr, based on the quasi-harmonic approximation (QHA), is greatly supported by the available experimental data under low pressure. From the coexistence-phase molecular dynamics simulations, we also obtained the high-pressure melting curve of Sr which shows good agreement with the experiment. While, the experimentally observed β-Sn structure of Sr-III was found to be mechanically unstable according to our phonon dispersion calculations and evolutionary algorithm structure searches. We find that α-U phase (space group Cmcm) is energetically favorable and is the good candidate of Sr-III.     

HIV蛋白酶多肽抑制剂的理论研究

艾滋病病毒的发现距今已有二十多年的历史了.它仍然以很快的速度在全球范围速蔓延.研发抗艾滋病药物是当代药学的重大课题之一.在以往研究的基础上,我们利用分子叠合和分子对接这两种分子模拟手段,把从PDB数据库中得到的与HIV蛋白酶结合的12个肽类分子和已经上市的抗艾滋病的药物Saquinavir做比较.根据结构相同或相近的分子具有相同的活性原理,运用分子叠合初部判断分子活性,特别是药效团的特征比对揭示了分子活性的原因,为进一步的药物设计奠定了良好的基础.进而采用分子对接的分子模拟方法对这12个肽类分子的活性构象进行了深入的分析,预测出了这12个分子对HIV病毒蛋白酶的不同抑制作用.研究发现:P01、P05、P09、P12可能与已知药物Saquinavir在与HIV蛋白酶结合时具有相似的活性,其中P9的活性最强,有望成为抗HIV药物的理想前体,为下一步的HIV药物的设计研究提供了理论依据.     

基于散射量子行走的完全图上结构异常搜索算法

完全图K_N 上某个顶点连接到图G将破坏其对称性. 为加速定位这类结构异常, 基于散射量子行走模型设计搜索算法, 首先给出了算法酉算子的定义, 在此基础上利用完全图的对称性, 将算法的搜索空间限定为一个低维的坍缩图空间. 以G为一个顶点的情况为例, 利用硬币量子行走模型上的研究结论简化了坍缩图空间中酉算子的计算, 并借助矩阵扰动理论分析算法演化过程. 针对星图S_N 上结构异常的研究表明, 以星图中心节点为界将整个图分为左右两个部分, 当且仅当两部分在N→∞时具有相同的特征值, 搜索算法可以获得量子加速. 本文说明星图上的分析方法和结论可以推广至完全图的坍缩图上. 基于此, 本文证明无论完全图连接的图G结构如何, 搜索算法均可在O(√N) 时间内定位到目标顶点, 成功概率为1-O(1√N), 即量子行走搜索该类异常与经典搜索相比有二次加速.     

An improved genetic algorithm with dynamic topology

The genetic algorithm(GA) is a nature-inspired evolutionary algorithm to find optima in search space via the interaction of individuals. Recently, researchers demonstrated that the interaction topology plays an important role in information exchange among individuals of evolutionary algorithm. In this paper, we investigate the effect of different network topologies adopted to represent the interaction structures. It is found that GA with a high-density topology ends up more likely with an unsatisfactory solution, contrarily, a low-density topology can impede convergence. Consequently, we propose an improved GA with dynamic topology, named DT-GA, in which the topology structure varies dynamically along with the fitness evolution. Several experiments executed with 15 well-known test functions have illustrated that DT-GA outperforms other test GAs for making a balance of convergence speed and optimum quality. Our work may have implications in the combination of complex networks and computational intelligence.     

Luus-Jaakola optimization procedure for multilayer optical coatings

Designing multilayer optical coatings is a difficult optimization problem because of the huge size of the search space. In the present paper, the Luus-Jaakola (LJ) optimization procedure, a new optimization algorithm, is employed to model multilayer optical coatings in the X-ray domain. With this algorithm it is not necessary to specify initially the number of layers present in a design. Only an upper limit needs to be defined. The algorithm has been used to maximize the reflectivity over a range of incident angles at a fixed wavelength, and over a wavelength range at a fixed incident angle. The results show that the LJ algorithm can be effectively applied to the design of multilayer optical coatings resulting in fewer layers than obtained using alternative optimization methods.     

Optimization of ultra-fast interactions using laser pulse temporal shaping controlled by a deterministic algorithm

Femtosecond laser pulse temporal shaping techniques have led to important advances in different research fields like photochemistry, laser physics, non-linear optics, biology, or materials processing. This success is partly related to the use of optimal control algorithms. Due to the high dimensionality of the solution and control spaces, evolutionary algorithms are extensively applied and, among them, genetic ones have reached the status of a standard adaptive strategy. Still, their use is normally accompanied by a reduction of the problem complexity by different modalities of parameterization of the spectral phase. Exploiting Rabitz and co-authors’ ideas about the topology of quantum landscapes, in this work we analyze the optimization of two different problems under a deterministic approach, using a multiple one-dimensional search (MODS) algorithm. In the first case we explore the determination of the optimal phase mask required for generating arbitrary temporal pulse shapes and compare the performance of the MODS algorithm to the standard iterative Gerchberg–Saxton algorithm. Based on the good performance achieved, the same method has been applied for optimizing two-photon absorption starting from temporally broadened laser pulses, or from laser pulses temporally and spectrally distorted by non-linear absorption in air, obtaining similarly good results which confirm the validity of the deterministic search approach.