LCC的分子模型化方法研究进展(1987-1999)

总结了十多年来ＬＣＣ实验室在分子模型化方面的主要研究进展。文章分为６ 个方面： （１） 结构数据库的引进、开发、和推广应用；（２） 支持结构优化的方法研究和软件开发； （３） 虚拟受体模型方法； （４） 用于发现新先导的药效团搜索方法研究和软件开发； （５） 新算法的创立； （６） 科学数据库中结构与性质信息的集成。

An emergency decision support system for the marine pollution

The paper introduces the research progress in an emergency decision support system for marine pollution （EDSS） in China seas and elaborates on the possible role of the Neutron Activation Analysis （NAA） method therein. To deal with the increasingly grave situation of offshore pollution, the EDSS for China seas has been researching and developing. Based on the prediction and analysis of the ocean three-dimensional current field, this system makes an inference on the possible path of diffusion and influencing area of marine pollutants and possible location of pollution source, and in combination with the environmentally sensitive information related to the technical integration of GIS, it puts forward the decision, making support for minimizing the hazard caused by pollutants. This system has been operationalized and running for many years on the Bohai and Huanghai seas＇ Marine Pollutants Prediction and Early-Warning, and it has achieved successful experience for many times in the emergencies of China＇s coastal pollution accidents. At present, the environmental guarantee system directed against heavy metals and radioactive pollutants is in the experimental stage. As the NAA method is especially applicable to the detection of part of heavy metals and radioactive substances, it is of very important practical value for the new system to realize the monitoring, prediction and early-warning of ocean heavy metals and radioactive pollutants.

Finite element simulation and optimal analysis of surfacing on steel orthotropic bridge deck

To analyze the stress state of steel orthotropic deck pavement and provide reference for the design of the overlay, the inner stress state and strain distribution of surfacing under the load of the deformation of the whole bridge structure and tyre load are analyzed by the finite element method of submodeling. Influence of surfacing modulus on the strain state of the overlay is analyzed for the purpose of the optimal design of the overlay structure. Analysis results show that the deformation of the whole bridge structure has no evident influence on the stress state of the overlay. The key factor of the overlay design is the transverse tensile strain in the overlay above the upper edge of web plate of rib. The stress state of the overlay is influenced evidently by the modulus of rigidity transform overlay. And the stress state of the overlay can be optimized and lowered by increasing the modulus and thickness of rigidity transform overlay, The fatigue test has been done to evaluate the fatigue performance and modulus of different deck pavement materials such as epoxy asphalt, SBS modified asphalt, rosphalt asphalt which can provide reference for deck pavement structure design.

表观遗传概念的教学实践与研究

根据高中生物学课程内容要求及人教社2019年版教材有关表观遗传的内容,指导学生开展阅读、观察、比较分析及评价遗传实验图解模型、染色体结构模型及DNA甲基化模型等建模活动,促进学生建立、理解与应用表观遗传概念,全面认识中心法则,认同基因、环境与性状之间关系的复杂性,提高批判性思维能力及建模能力。

Molecular reconstruction model based on structure oriented lumping and group contribution methods

Molecular management is a promising technology to face challenges in the refining industry, such as more stringent requirements for product oil and heavier crude oil, and to maximize the value of every molecule in petroleum fractions. To achieve molecular management in refining processes, a novel model that is based on structure oriented lumping(SOL) and group contribution(GC) methods was proposed in this study. SOL method was applied to describe a petroleum fraction with structural increments, and GC method aimed to estimate molecular properties. The latter was achieved by associating rules between SOL structural increments and GC structures. A three-step reconstruction algorithm was developed to build a representative set of molecules from partial analytical data. First, structural distribution parameters were optimized with several properties. Then, a molecular library was created by using the optimized parameters. In the final step, maximum information entropy(MIE) method was applied to obtain a molecular fraction. Two industrial samples were used to validate the method, and the simulation results of the feedstock properties agreed well with the experimental data.

Molecular modeling study of the effect of base methylation on internal interactions and motions in DNA and implication to B-Z conformation change

Methylation in the bases of DNA is known to induce B-Z conformation change. In this work, molecular mechanics and normal mode analysis are used to probe how certain methylation affects the internal interactions and thermodynamic motions in the DNA double helixes in both B and Z conformations, and its implication to B-Z conformation change. By molecular modeling with Insight II, two cases involving cytosine C5 and guanine C8 methylation on both B and Z-form DNA duplex d(CGCGCG)2 are studied in comparison with the corresponding unmethylated duplexes. The internal interaction energies computed based on a molecular mechanics force field and the entropies due to internal motions computed according to a normal mode analysis are in fare agreement with respective observed thermodynamic quantities. The analysis on the computed individual energy terms suggests that the observed B-Z conformation change induced by methylation is primarily driven by enthalpic factors. A combination of changes in Van der Waals interaction, electrostatic interaction and hydrogen bonding likely contributes to the change of enthalpy that favors Z-conformation in the methylated states.

Homology modeling and evolutionary trace analysis of superoxide dismutase from extremophile Acidithiobacillus ferrooxidans

The gene sod in Acidithiobacillusferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional （3D） molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Glyl03 and Glul61 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.

Construction of a macromolecular structural model of Chinese lignite and analysis of its low-temperature oxidation behavior

The aim of this paper is to analyze the change in the active structure of lignite during the process of lowtemperature oxidation by constructing a molecular structure model for lignite. Using quantum computation combined with experimental results of proximate analysis, ultimate analysis, Fourier transform infrared spectroscopy(FTIR) and X-ray photoelectron spectroscopy(XPS), a structural model for the large molecular structure was constructed. By analyzing the bond lengths in the model molecule, the evolution law for the active structure of lignite was predicted for the process of low-temperature oxidation. In low-temperature oxidation,alkanes and hydroxyls are the primary active structures observed in lignite, though ether may also react. These active functional groups react with oxygen to release heat, thereby speeding up the reaction between coal and oxygen. Finally, the content of various functional groups in the process of lignite low-temperature oxidation was analyzed by infrared analysis, and the accuracy of the model was verified.

Modeling of segregation in magnetized fluidized bed with binary mixture of Geldart-B magnetizable and nonmagnetizable particles

For the magnetized fluidized bed(MFB)with the binary mixture of Geldart-B magnetizable and nonmagnetizable particles,the magnetically induced segregation between these two kinds of particles occurs at high magnetic field intensities(H),leading to the deterioration of the fluidization quality.The critical intensity(H_(ms))above which such segregation commences varies with the gas velocity(U_g).This work focuses on establishing a segregation model to theoretically derive the H_(ms)–U_g relationship.In a magnetic field,the magnetizable particles form agglomerates.The magnetically induced segregation in essence refers to the size segregation of the binary mixture of agglomerates and nonmagnetizable particles.Consequently,the segregation model was established in two steps:first,the size of agglomerates(d_A)was calculated by the force balance model;then,the H_(ms)–U_g relationship was obtained by substituting the expression of d_Ainto the basic size segregation model for binary mixtures.As per the force balance model,the cohesive and collision forces were 1_2 orders of magnitude greater than the other forces exerted on the agglomerates.Therefore,the balance between these two forces largely determined d_A.The calculated d_A increased with increasing H and decreasing U_g,agreeing qualitatively with the experimental observation.The calculated H_(ms)–U_ g relationship agreed reasonably with the experimental data,indicating that the present segregation model could predict well the segregation behavior in the MFB with the binary mixture.

Influence of Molecular Sieve Supported Metal Oxides on the Desulfurization in Catalytic Cracking of Sulfur-containing Model Compounds and Hydrocarbons

Zn, La, Zr, Sn and Ti loaded molecular sieves were prepared by impregnation method. Conversions of benzothiophene and dibenzothiophene over the metal oxides modified ultra stable zeolite Y(USY), ZSM-5, β and MSU-2 molecular sieve catalysts were investigated by means of micro-activity test (MAT) experiments. The results showed that Zn and La loaded catalysts were better than the other metals, and ZSM-5 with lower SiO2/Al2O,3 mole ratio showed better results than those with higher SiO2/Al2O3 as far as desulfurization reaction is considered. A comparison of the desulfurization activities of the La/Zri-USY catalyst with USY catalyst indicated that the bimetal loaded USY catalyst gave good products selectivity when sulfur containing heavy oil was used as the feedstock. The sulfur content in gasoline fraction was decreased by 25%, and there was no loss in the Research Octane Number.

Integrated Process for Production of Surfactin(III)Modeling of Adsorption Column

The study is focused on modeling of separation process and optimization.An adsorption separation process is simulated.The surfactin production process by Bacillus subtilis ATCC 21332 followed by surfactin adsorption in a fixed-bed column packed with commercial active carbon is studied in laboratory.The adsorption column achieves high surfactin recovery(94%)by up-flow methanol elution at 25°C.The adsorption column is simulated with a complex one-dimensional plug flow dispersion model coupled with nonlinear adsorption equilibrium,based on the assumption that the adsorption of surfactin is monomolecular layer and no micelle is formed.The molecular diffusion coefficient of surfactin in water solution with electric neutrality is estimated to be 0.428×10 -5 cm 2 ·s -1 by molecular dynamics simulation.The model developed can describe the complex interplay of adsorption kinetics,fluid dynamics,and mass-transfer phenomena based on the assumption of no radial temperature and concentration gradients,and is of adequate precision.The work involved in this paper is valuable for the optimization of the production process of surfactin.

Calculation of Environmental Capacity of Petroleum Hydrocarbon in Jiaozhou Bay

The method has been established to calculate the environmental capacity (ECO), surplus environment capacity (SECO) of water with respect to marine petroleum hydrocarbons associated with oil (PHAOs) and the self-purification capacity (SPCO) of main self-purification process to PHAOs in the Jiaozhou Bay, China, according to the dynamic model for distribution of marine PHAOs among multiphase environments. The variation of concentration of PHAOs in the Jiaozhou Bay is well simulated by the dynamic model. Based on the model, the ECo, SECo of water with respect to PHAOs in the Jiaozhou Bay were calculated during the last 10 years under the first-class and second-class quality standard requirement, according to SPCO of main self-purification process to PHAOs. The results show that about 200 tons of PHAOs could be discharged into the Jiaozhou Bay for maintaining the first class seawater quality standard, and about 600 tons of PHAOs for the second class seawater quality standard later.

Molecular Simulations of FCC Dry Gas Components Adsorption in Zeolite Y

Adsorption of FCC dry gas components, hydrogen(H_2), nitrogen(N_2), methane(CH_4), ethane(C_2H_6) and ethylene(C_2H_4) in zeolite Y was studied by performing the Grant Canonical Monte Carlo(GCMC) simulations at 298K and 823K and under a pressure range up to 10 MPa. Simulation results were analyzed using the Langmuir model, which presented fitting of dry gas components adsorption to be suggested as the monolayer adsorption. C_2H_4 presented most single adsorption amount, which reached 7.63 mol/kg at 298K under a pressure of 200kPa. Thermodynamic parameters of the Gibbs free energy change, enthalpy change and entropy change were analyzed based on adsorption equilibrium constant obtained from the GCMC simulations. The results suggested that it was more favorable for C_2H_4 to be adsorbed in zeolite Y. Adsorption molecules were in ordered arrangement in the zeolite, and C_2H_4 exhibited a more orderly arrangement than other components. Additionally, a competition in the adsorption of a mixture of dry gas components was found, and supercages were the priority adsorption space. The competition was favorable to CH_4 and C_2H_6, and the competitive power was affected by temperature.

Fermi Resonances and Vibrational Spectrum of a Polyatomic Molecule XY4： an Algebraic Approach

A U(2) algebraic model is introduced for the spectrum of a molecule XY4, where the interactions between the stretch and bend modes are described by Td symmetric Fermi resonance terms. The presented algebraic model in a limit corresponds to another model in recent literature. The vibrational spectrum of methane (CH4) measured recently with modern spectroscopy techniques is employed to test those models. The obtained standard deviation between the observed and the calculated vibrational energy levels in the algebraic model is smaller than that in the corresponding model.

Selective Adsorption of Sulfur Compounds in Model Gasoline Containing Olefins by Modified Zeolites

The effects of olefins were quantified by measuring the decreased amount of thiophenes removed by modified zeolites with an increasing olefin concentration in model fuels （300 ppm） via fixed-bed adsorption technique at room temperature and atmosphere pressure. The influence of olefins on adsorptive desulfurization of model fuel had been investigated by FT-IR techniques, which revealed that the protons in the zeolites were the sites responsible for the adsorption of olefins. On the CeY zeolite, in the presence of strong hydroxyl species in the zeolites, the adsorbed olefin compounds can attach to the protons molecularly via electrophilic interaction and undergo the opening of the C=C bonds depending on the acidity of the zeolites. The reduced desulfurization performance of CeY zeolite was attributed to the direct occupation of the absorbent＇s active sites by olefins. In contrast to the CeY zeolite, the NiY zeolites were unable to react directly with pure olefins. However the sulfur compounds and olefins adsorbed on the protons may subsequently undergo olefin alkylation reactions, which can block the zeolite pores and then prevent sulfide molecules from having access to super-cages to contact with the metal cations. This work demonstrates also that the NiY zeolites exhibit excellent performance for selective adsorption desulfurization of model fuel containing olefin compounds.

Phonon Dispersion and Thermodynamics Properties of CaF_2 via Shell Model Molecular Dynamics Simulations

The phonon and thermodynamics properties of face-centered cubic CaF2 at high pressure and high temperature are investigated by using the shell model interatomic pair potential within General Utility Lattice Program （GULP）. The phonon dispersion curves and the corresponding density of state （PDOS） in this work are consistent with the experimental data and other theoretical results. The transverse optical （TO） and longitudinal optical （LO） mode splitting as well as heat capacity at constant volume Cv and entropy S versus pressure and temperature are also obtained.

化学信息集成系统CASAC 3

概述了实验室目前正在开发的计算机化学集成系统CASAC 3。CASAC3集成了本实验室多年的研究成果;综合了化学信息数据库、分子模型化方法及3D分子搜索技术。为未来的研究提供了一个综合易用的平台。

π-Conjugated Unit-Dependent Optical Properties of Linear Conjugated Oligomers

The optical properties of three linear conjugated oligomers （F-P, F-P-F, and P-F-P-F-P）, where phenothiazine （P） and fluorene （F） groups arrange alternately, are investigated. With the enhancement of the π-conjugated system, their absorption and emission bands both gradually red shift, and their two-photon properties are also improved. Meanwhile, their fluorescence dynamic traces are analyzed with continuous rate distribution model, exhibiting that their decay rates gradually accelerate and the rate distribution width become narrower. The quantum chemical calculation offers their molecular structures and transition mechanism, showing that the enhancement of π-conjugated system should be responsible for tile improvement of two-photon properties.

Size influence on the fluorescence decay time of ZnS:Mn^(2+) nanocrystals

ZnS:Mn2+ nanocrystals(NCs) with particle size from 1.9 nm to 3.2 nm are synthesized via chemical precipitation method with different [S2-]/[Zn2+] ratios.The size-dependent decay for Mn emission exhibits a double exponential behavior.And two lifetime values,in millisecond time domain,can both be shortened with size increasing,which is attributed to enhanced interaction between host and Mn2+ impurity.A molecular structure model is proposed to interpret the tendency of two lifetime components,which is correlated to the number of S vacancy(Vs) defects around Mn2+.