二维高分子链形态的计算机模拟

介绍在“高分子物理实验”教学中新开设的又一个计算机模拟实验，即应用自编的改进型四位置模型，模拟二维空间中的自回避行走链和无规行走链，并验算均方末端距和均方回转半径与聚合度的标度关系，所得结果与de Gennes的理论符合良好。     

虚拟原子探针随机采样法用于氨基酸结构描述及其构效关系研究

考虑药物与蛋白质受体的3类非键作用模式, 利用8类虚拟原子探针和Monte Carlo随机采样技术, 得到了一套新的氨基酸侧链表面静电、立体及疏水势能场(ASSPF)参数. 在此基础上对苦味二肽和血管舒缓激五肽进行了结构表征和QSAR研究, 所建模型复相关系数R2和留一法交互检验复相关系数QLOOCV2分别为0.8457, 0.851和0.7688, 0.7952, 同时分析了肽链不同位置上氨基酸侧链对活性的影响, 取得较好的结果.     

Energy transfer rates and impact sensitivities of two classes nitramine explosives molecules

Some explosives are stable molecules with large energy barriers to chemical reaction, and in shock or impact initiation, a sizable amount of phonon energy must be converted to the molecular internal higher vibrations by multiphonon up pumping. To investigate the relationship between impact sensitivities and energy transfer rates, the number of doorway modes of explosive molecules is estimated by a simple theory in which the rate is proportional to the number of normal mode vibrations. We evaluated frequencies of normal mode vibrations of 13 explosive molecules which are CHNO nitramine-contained and have not been analyzed previously. The number of doorway modes in the regions of 200–700 cm⁻¹ was evaluated by the direct counting method. For more clear investigation of the relationship we have classified these 13 nitramine explosive molecules, by the number of nitramine group they contained, into two groups. There are eight molecules that contained one nitramine group and five molecules that contained poly-nitramine groups. It is found that the number of doorway modes shows a linearly correlation to the impact sensitivities derived from drop hammer tests. This result is in agreement with that of several previous works. Besides, it is also noted in our study that in those nitramine explosives molecules with similar molecular structure (similar number nitramine group they contained) and similar molecular weight, the correlation between the sensitivity and the number of doorway modes is higher. We found that the vibrational frequency of ω corresponds to nitro group motions of every molecule is contributed to the number of doorway modes in the regions of 200–700 cm⁻¹.     

THPep: A machine learning-based approach for predicting tumor homing peptides

In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agents. In this regard, the huge number of therapeutic peptides generated in recent years, demands the need to develop an effective and interpretable computational model for rapidly, effectively and automatically predicting tumor homing peptides. Therefore, a sequence-based approach referred herein as THPep has been developed to predict and analyze tumor homing peptides by using an interpretable random forest classifier in concomitant with amino acid composition, dipeptide composition and pseudo amino acid composition. An overall accuracy and Matthews correlation coefficient of 90.13% and 0.76, respectively, were achieved from the independent test set on an objective benchmark dataset. Upon comparison, it was found that THPep was superior to the existing method and holds high potential as a useful tool for predicting tumor homing peptides. For the convenience of experimental scientists, a web server for this proposed method is provided publicly at http://codes.bio/thpep/.     

Importance of the choice of assumptions and models in the estimation of analytical quality specifications

The validity of any model depends on its ability to imagine the situation or problem to which it is applied. Further, the assumptions made in relation to the model are determining for the actual outcome. Within the field of clinical biochemistry a lot of models for analytical quality specifications, based on a variety of concepts and ’clinical settings’, have been proposed. A hierarchical structure for application of these approaches and models has been agreed on at several occasions in 1999. In this hierarchy, the highest rank is given to evaluation of analytical quality specifications based on ’clinical settings’/’clinical outcome’ models, followed by specifications based on biological variation and on ’clinicians opinions’. This contribution, deals with the problems of combining random and systematic errors and the implications of application of different models to a variety of clinical settings. Received: 1 June, 2002 Accepted: 17 July 2002 Presented at the European Conference on Quality in the Spotlight in Medical Laboratories, 7–9 October 2001, Antwerp, Belgium     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

旋转输液管动力稳定性理论分析北大核心CSCD

基于Lagrange原理和假设模态法建立了旋转输液管的动力学模型.通过降阶升维的方法求解系统的特征值问题,并分析了旋转输液管自由振动特性.得到了不同端部集中质量和转速下,系统特征值随流速升高的演变轨迹.揭示了临界流速随系统参数的变化规律.研究发现,内部流体的流动对旋转输液管动力学特性存在显著影响.在某些参数组合下,系统低阶模态能够形成不同形式的内共振关系.预示了旋转输液管模型蕴含丰富的动力学现象.     

Large cycles in random generalized Johnson graphs

This paper studies thresholds in random generalized Johnson graphs for containing large cycles, i.e. cycles of variable length growing with the size of the graph. Thresholds are obtained for different growth rates.     

Effects of Cone Angles on Nonlinear Vibration Responses of Functionally Graded Shells北大核心CSCD

The nonlinear vibration responses of functionally graded materials (FGMs) shells with different cone angles under external loads were studied. Firstly, the Voigt model was employed to describe the physical properties along the thickness direction of FGMs conical shells. Then, the motion equations were derived based on the 1st-order shear deformation theory, the von Kármán geometric nonlinearity and Hamilton’s principle. Next, the Galerkin method was applied to discretize the motion equations and the governing equations were simplified into a 1DOF nonlinear vibration differential equation under Volmir’s assumption. Finally, the nonlinear motion equations were solved with the harmonic balance method and the Runge-Kutta method, and the amplitude frequency response characteristic curves of the FGMs conical shells were obtained. The effects of different material distribution functions and different ceramic volume fraction exponents on the amplitude frequency response curves of conical shells were discussed. The bifurcation diagrams of conical shells with different cone angles, as well as time process diagrams and phase diagrams for different excitation amplitudes, were described. The motion characteristics were characterized by Poincaré maps. The results show that, the FGMs conical shells present the nonlinear characteristics of hardening springs. The chaotic motions of the FGMs conical shells are restrained and not prone to motion instability with the increase of the cone angle. The FGMs conical shell present a process from the periodic motion to the multi-periodic motion and then to chaos with the increase of the excitation amplitude. © 2022 Editorial Office of Applied Mathematics and Mechanics. All rights reserved.     

带有随机初值的复值Ginzburg-Landau方程的弱平均动力学*

本文研究了无界域上的带有随机初值的复值Ginzburg-Landau方程.首先, 基于解过程的全局适定性, 建立了带有随机初值的Ginzburg-Landau方程的平均随机动力系统.然后, 证明了弱拉回平均随机吸引子的存在唯一性以及随机吸引子的周期性,并将其进一步推广到加权空间L²(?, L²_σ(R)).