基于分子力模型的无线传感器网络定位算法

无线传感器网络中利用节点发送与接收无线信号,确定物体的位置被称为无线传感器网络节点定位,它是无线传感器网络的一个重要研究领域.基于测距的无线传感器网络定位算法,其关键步骤是通过接收信号的强弱来估计信标节点与未知节点的距离.提出了一种基于分子力模型的WSN定位算法,本算法也是基于测距思想,其中,引入排斥力和吸引力的概念,并假设未知节点处于平衡状态,这两种力此时合力为零.算法求解使用迭代算法.论文实验证明,所提算法的时间复杂度和空间复杂度较小,且具备较好的定位精度.

力场/溶剂水模型对EGFRvⅢ抗原-MR1(scFv)抗体复合物的MM-PBSA计算精度的影响与实验验证

以表皮生长因子Ⅲ型突变体(EGFRvⅢ)抗原多肽与其抗体(MR1)及其人源化突变体的复合物结构为出发点,采用分子动力学中的6种常用力场及3种常用溶剂水模型,分别对上述抗原-抗体复合物进行100ns的分子动力学模拟与分子力学和连续介质模型计算自由能(MM-PBSA),并在实验上利用等温滴定量热(ITC)仪测定了抗原和抗体相互作用的热力学参数.通过在结构变化、能量变化及野生型与突变体比较等几个方面进行综合分析,给出了最佳的计算模型.对不同力场及水模型计算精度等相关问题进行了探讨.

苯环5位取代磺酰脲类化合物的水解动力学及三维定量构效关系初步研究

研究了除草活性较好的9个新型苯环5位取代的磺酰脲类化合物(A^I)分别在酸性、中性及碱性水溶液中的水解情况.采用HPLC-MS对水解产物进行分离鉴定,推测了水解产物的结构及水解路径.采用比较分子力场(Co MFA)方法,对化合物的结构与水解半衰期之间的关系进行了三维定量构效关系(3D-QSAR)研究.结果表明,苯环5位取代的苯磺酰脲类化合物的水解遵循一级动力学反应,容易发生酸性条件下的水解,水解反应第一步主要为酸催化下磺酰脲桥的断裂,形成5位取代的苯磺酰胺和氨基杂环.苯环5位取代的苯磺酰胺进一步发生5位酰胺基的水解,最后得到化合物c(6-氨基糖精)和d(糖精).苯环5位经修饰改造后,在相同条件下,其水解速度明显高于改造前的母体化合物单嘧磺酯和甲磺隆.苯环5位为酰胺基取代的化合物的水解速度随酰胺基上烷基碳原子数的增加及烷基体积的增大而降低.经计算所得的Co MFA模型能够对该系列化合物的水解半衰期进行较好的预测.

Analysis to the Driving Force Model and Driving Factor on the Utilized Changes of Cultivated Land in Gonghe County

Using gradually regression analysis to establish the driving force model of utilized change of cultivated land in Gonghe County, and using path analysis, correlation analysis, partial correlation analysis and system dynamics method to inspect the effect of driving changing on cultivated land change under different change situations. Driving factors, action mechanism and process of utilized change of cultivated land were analyzed from the county territory scale level. At last, some corresponding policies and measures were put forward.

Simulation study on non-linear effects of initial melt temperatures on microstructures during solidification process of liquid Mg_7Zn_3 alloy

The non-linear effects of different initial melt temperatures on the microstructure evolution during the solidification process of liquid Mg7Zn3 alloys were investigated by molecular dynamics simulation, The microstructure transformation mechanisms were analyzed by several methods. The system was found to be solidified into amorphous structures from different initial melt temperatures at the same cooling rate of 1×10^12 K/s, and the 1551 bond-type and the icosahedron basic cluster （12 0 12 0 ） played a key role in the microstructure transition. Different initial melt temperatures had significant effects on the final microstructures. These effects only can be clearly observed below the glass transition temperature Tg; and these effects are non-linearly related to the initial melt temperatures, and fluctuated in a certain range. However, the changes of the average atomic energy of the systems are still linearly related with the initial melt temperatures, namely, the higher the initial melt temperature is, the more stable the amorphous structure is and the stronger the glass forming ability will be.

Local structure of calcium silicate melts from classical molecular dynamics simulation and a newly constructed thermodynamic model

The distributions of local structural units of calcium silicate melts were quantified by means of classical molecular dynamics simulation and a newly constructed structural thermodynamic model. The distribution of five kinds of Si-O tetrahedra Qi from these two methods was compared with each other and also with the experimental Raman spectra, an excellent agreement was achieved. These not only displayed the panorama distribution of microstructural units in the whole composition range, but also proved that the thermodynamic model is suitable for the utilization as the subsequent application model of spectral experiments for the thermodynamic calculation. Meanwhile, the five refined regions mastered by different disproportionating reactions were obtained. Finally, the distributions of two kinds of connections between Qi were obtained, denoted as Qi-Ca-Qj and Qi-[Ob]-Qj, from the thermodynamic model, and a theoretical verification was given that the dominant connections for any composition are equivalent connections.

Thermodynamic model of lead oxide activity in PbO-CaO-SiO_2-FeO-Fe_2O_3 slag system

According to the ion and molecule coexistence theory, a thermodynamic model of lead oxide activity in PbO-CaO-SiO2-FeO-Fe2O3 slag system was established at the temperature of 1273-1733 K. The activities of Pb O in slag were calculated, and their equal activity curves were plotted. The influences of slag basicity Q, iron oxide rate R and temperature T on activity NPb O and activity coefficient γPbO were also investigated. Results show that the calculated values of γPb O are in good agreement with the reported experimental data, showing that the model can wholly embody the slag structural characteristics. NPbO departures positively from Raoult values, and increases with increasing Pb O content in slag but changes little with T. γPbO increases with increasing Q, and goes through the maximum with increasing R for basic slag（Q0.3）. Results can be applied to the thermodynamic research and operational optimization of modern lead smelting technologies.

Computer Simulation of Thin Film Wrinkling on Elastic Substrate

Numerous theoretical and experimental efforts have been made to explain the dependence of the static wrink^h~g morphology on the materials＇ physical properties, whereas the dy- namic wrinkling process remains elusive. In the present work, we design a wrinkling model consisting of a soft substrate and a graphene-like rigid thin film to investigate this dynamic process. The simulation shows that the whole wrinkling process includes three stages. At the incubation and wrinkling stages, the stress along the horizon direction of the soft substrate transfers to the stiff film. However, at the equilibrium stage, the stress of the rigid film slowly transfers back to the substrate although the total energy still decreases. It is found that the stress of the substrate concentrates at the top surface, especially at the trough, whereas the stress distribution of the film depends on direction. In the perpendicular direc- tion, the stress at the wave＇s equilibrium position surpasses that at the crest and trough and, oppositely, the stress concentrates at the crest and trough in the horizon direction. Present model reproduces both wrinkling and delamination patterns and can be a powerful tool to deeply understand the structure deformation of material induced by stress release.

A Molecular Thermodynamic Model for Interfacial Tension in Surfactant-Oil-Water System

An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular ther-modynamic model has been proposed. The interfacial tension of surfactant-oil-water systems can be calculated from the surface tensions of pure oil and water by this model. The interfacial tension data for sodium dodecyl sulphate-heptane-water system, polyoxyethylene n-octylphenol-heptane-water system and hexadecyl trimethyl ammonium bromide-heptane-water system have been correlated. By using the adjustable parameters obtained, the interfacial tensions of these systems at other temperatures have been predicted. Both the correlated and the predicted values are satisfactory.

抑制人乳腺癌细胞MCF-7生长的查尔酮类化合物的三维定量构效关系研究

目的:通过研究抑制人乳腺癌细胞MCF-7生长的查尔酮类化合物的三维定量构效关系(3D-QSAR),为查尔酮类抗肿瘤药物的研发提供理论基础。方法:分析55个查尔酮类化合物的结构和活性(pIC_(50))值,进行分子叠合后,采用比较分子力场分析(CoMFA)模型考察化合物的立体场和静电场,比较分子相似性指数分析(CoMSIA)模型考察化合物的立体场、静电场、疏水场、氢键供体场和氢键受体场,确立最优取代基团并进行预测。结果:CoMFA模型显示立体场、静电场对化合物活性有影响,CoMSIA模型显示疏水场、静电场、立体场对化合物活性影响显著。分子叠合后,在公共骨架上的R_1、R_2取代基附近引入亲水性基团,R_1、R_4取代基区域引入具有一定负电荷的基团,减少R_2取代基上的位阻并在R_2、R_4引入正电荷基团,可明显增加查尔酮类化合物的活性。按此结果设计了2种新的化合物,其pIC_(50)分别达到了5.538、5.589(CoMFA法)和5.552、5.628(CoMSIA法)。结论:3D-QSAR可准确分析查尔酮类化合物抑制人乳腺癌细胞MCF-7生长活性的结构特征,可为新药的开发研究提供理论指导。

Homology modeling and docking studies of IscS from extremophile Acidithiobacillus ferrooxidans

The gene iscS-3 from ,4cidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral 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 further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5＇-phosphate（PLP） and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS（P-I） and cysteine-PLP-IscS（C-P-I） complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glul05, Glu79, Ser203 and Hisl80 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein IscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.

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 Thermodynamic Model for Polyelectrolyte Solutions with Added Salts

A molecular thermodynamic model of polyelectrolyte developed previously was extended to polyelectrolyte solutions with added salts.Thermodynamic properties,such as activity coefficients of polyelectrolytes or added salts and osmotic coefficients of solvent, of a number of aqueous mixtures of polyelectrolytes and salts are analyzed with the proposed model.Successful correlation is obtained in the range of moderate or higher polyion concentration.For the same sample,thermodynamic properties of polyelectrolytes with and without simple electrolytes can be predicted mutually using parameters from regression data.

Dynamics Studies on Molecular Diffusion in Zeolites

A review about the applications of molecular dynamics(MD)simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.

Molecular Dynamics Simulations of Self-diffusion Coefficients of Exponential-six Fluids

Self-diffusion coefficients of exponential-six fluids are studied using equilibrium molecular dynamics simulation technique. Mean-square displacements and velocity autocorrelation functions are used to calculate self-diffusion coefficients through Einstein equation and Green-Kubo formula. It has been found that simulation results are in good agreement with experimental data for liquid argon which is taken as exponential-six fluid. The effects of density, temperature and steepness factor for repulsive part of exponential-six potential on self-diffusion coefficients are also investigated. The simulation results indicate that the self-diffusion coefficient of exponential-six fluid increases as temperature increases and density decreases. In addition, the larger self-diffusion coefficients are obtained as the steepness factor increases at the same temperature and density condition.

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.

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.

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.

Glass Formation of n-Butanol： Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=1204.10 K, which is in good agreement with experimental results 1104-1 K.

Lagrangian model of zooplankton dispersion:numerical schemes comparisons and parameter sensitivity tests

This paper presents two comparisons or tests for a Lagrangian model of zooplankton dispersion:numerical schemes and time steps.Firstly,we compared three numerical schemes using idealized circulations.Results show that the precisions of the advanced Adams-Bashfold-Moulton(ABM) method and the Runge-Kutta(RK) method were in the same order and both were much higher than that of the Euler method.Furthermore,the advanced ABM method is more efficient than the RK method in computational memory requirements and time consumption.We therefore chose the advanced ABM method as the Lagrangian particle-tracking algorithm.Secondly,we performed a sensitivity test for time steps,using outputs of the hydrodynamic model,Symphonie.Results show that the time step choices depend on the fluid response time that is related to the spatial resolution of velocity fields.The method introduced by Oliveira et al.in 2002 is suitable for choosing time steps of Lagrangian particle-tracking models,at least when only considering advection.