Efficiency of simulated annealing for peptides with increasing geometrical restrictions

Simulated annealing (SA) is a popular global minimizer that can conveniently be applied to complex macromolecular systems. Thus, a molecular dynamics or a Monte Carlo simulation starts at high temperature, which is decreased gradually, and the system is expected to reach the low-energy region on the potential energy surface of the molecule. However, in many cases this process is not efficient. Alternatively, the low-energy region can be reached more effectively by minimizing the energy of selected molecular structures generated along the simulation pathway. The efficiency of SA to locate energy-minimized structures within 5 kcal/mol above the global energy minimum is studied as applied to three peptide models with increasing geometrical restrictions: (1) The linear pentapeptide Leu-enkephalin described by the ECEPP potential, (2) a cyclic hexapeptide described by the GROMOS force field energy E_GRO alone, and (3) the same cyclic peptide with E_GRO combined with a restraining potential based on 31 proton–proton restraints obtained from nuclear magnetic resonance (NMR) experiments. The efficiency of SA is compared to that of the Monte Carlo minimization (MCM) method of Li and Scheraga, and to our local torsional deformations (LTD) method for the conformational search of cyclic molecules. The results for the linear peptide show that SA provides a relatively weak guidance towards the most stable energy region; as expected, this guidance increases for the cyclic peptide and the cyclic peptide with NMR restraints. However, in general, MCM and LTD are significantly more efficient than SA as generators of low-energy minimized structures. This suggests that LTD might provide a better search tool than SA in structure determination of protein regions for which a relatively small number of restraints are provided by NMR. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1659–1670, 1999     

Breaking Data Encryption Standard with a Reduced Number of Rounds Using Metaheuristics Differential Cryptanalysis

This article presents the author’s own metaheuristic cryptanalytic attack based on the use of differential cryptanalysis (DC) methods and memetic algorithms (MA) that improve the local search process through simulated annealing (SA). The suggested attack will be verified on a set of ciphertexts generated with the well-known DES (data encryption standard) reduced to six rounds. The aim of the attack is to guess the last encryption subkey, for each of the two characteristics Ω. Knowing the last subkey, it is possible to recreate the complete encryption key and thus decrypt the cryptogram. The suggested approach makes it possible to automatically reject solutions (keys) that represent the worst fitness function, owing to which we are able to significantly reduce the attack search space. The memetic algorithm (MASA) created in such a way will be compared with other metaheuristic techniques suggested in literature, in particular, with the genetic algorithm (NGA) and the classical differential cryptanalysis attack, in terms of consumption of memory and time needed to guess the key. The article also investigated the entropy of MASA and NGA attacks.     

模拟体液法制备纳米级羟基磷灰石

用模拟体液法制备纳米羟基磷灰石(hydroxyapatite,HAP or HA)粉体。研究了反应温度、反应浓度和反应时间对合成的影响。结果发现,制备纳米级羟基磷灰石的最佳工艺条件为:反应温度60℃,浓度为15倍的模拟体液(simulate body fluid,SBF),反应时间为10h。在此工艺条件下制备的羟基磷灰石粉体的微观形貌为球形颗粒,平均颗粒直径为30 nm。     

基于模拟退火算法的宽角度X射线超反射镜设计研究

应用于硬X射线波段的宽带多层膜光学元件———宽角度X射线超反射镜的设计可以归结为一个连续变量的多维多极值的全局优化问题。缺少一种有效的全局优化方法是阻碍解决这一难题的一个关键。模拟退火算法是一种简单而且通用的全局优化算法。结合光学多层膜的设计原理提出了利用模拟退火算法来进行宽角度X射线超反射镜设计的新方法。结合已有的方法选择了W和C作为膜层的膜对材料,设计出Cu的Kα线处角度范围0.9°~1.1°反射率达到20%的宽角度X射线超反射镜。并在此基础上采用改进的自适应模拟退火算法实现了Cu的Kα线处宽角度X射线超反射镜的理想设计结果。设计结果表明了模拟退火算法在多层膜最优化设计领域的正确性和有效性。     

Sunlight- or UVA-Light-Mediated Synthesis of Hydroxamic Acids from Carboxylic Acids

The development of light-mediated methods for synthetic applications is increasingly attracting high interest. We present herein a new photochemical protocol for the synthesis of hydroxamic acids, which constitute an important class of medicinal agents, mainly due to their anticancer properties. The method is mediated by UVA-light or sunlight and its key point is the generation of a charge transfer complex by the interaction of 4-dimethylaminopyridine with a halomethane. Various carboxylic acids were directly coupled with O-protected hydroxylamines, upon irradiation with either LED 370 nm or solar light. A detailed study of the mechanism was carried out by the employment of direct infusion–high resolution mass spectrometry (DI-HRMS), providing experimental evidence for the formation of various activated species, which may lead to the desired product. The light-mediated protocol was applied in the synthesis of the drugs Vorinostat and Bufexamac.