The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Influences of local polymer-solvent π-π-interaction on dynamics of phenyl ring rotation and its role on photophysics of conjugated polymer

In this report, the role of local polymer-solvent π-π-interaction on rotational dynamics of phenyl rings of poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylenevinylene] (MEH-PPV) is examined by utilizing nuclear magnetic resonance (NMR) spectroscopy. We have found that an aromatic solvent can couple strongly with the phenyl rings via favorable local π-π-interaction, causing a restriction of the ring rotation. The dynamic process takes place at much faster rate in a non-aromatic solvent. NMR line shape analysis indicates the existence of two side chain configurations with relatively long life-time in toluene and pyridine while a single time-averaged configuration is detected in chloroform and tetrahydrofuran. Addition of chloroform or cyclohexane to a solution of MEH-PPV in toluene is accompanied by an increase of the rotational dynamics. This indicates that the expansion or collapse of main chain upon varying solvent quality play a minor role on the rotational dynamics. The relationship between the dynamics of ring rotation and photophysics of MEH-PPV in solution is discussed.     

钙钛矿型CaSiO_3解压缩和重压缩过程的分子动力学模拟

用分子动力学模拟方法 (MD)研究了 3 0 0K时钙钛矿型CaSiO3 ,从高压到负压的解压缩过程 .MD模拟获得的P V关系与实验数据相近 ,与已报道的MD模拟数据基本一致 ,所得体积模量也在实验数据分布范围内 .减压缩和重压缩的MD模拟数据与实验结果相似 .钙钛矿型CaSiO3 解压缩成非晶态时 ,存在两个结构破坏阶段 :破坏硅氧八面体和破坏钙氧二十面体 .当钙氧二十面体被破坏后 ,重压缩不能得到钙钛矿型结构 .只要钙氧二十面体未被破坏 ,重压缩可恢复钙钛矿型结构 .本研究得到的结果尚未见相关报道 .由MD模拟数据计算了CaSiO3 系统的红外光谱 ,分析这些数据可知钙钛矿型CaSiO3 解压缩非晶化是一个二阶软模相变 .研究表明钙钛矿型CaSiO3 结构存在一个等容的亚稳极限 ,其解压缩非晶化是一个受动力学控制的亚稳状态 .     

Dynamic Study of Gemini Surfactant and Single-chain Surfactant at Air／Water Interface

Molecular dynamics (MD) simulation are used to study the properties of gemini surfactant of ethyl-α,ω-bis(dodecyldimethylammonium bromide) (C12C2C12) and dodecyl-trimethylammonium bromide (DTAB) at the air/water interface, respectively. In the two systems,t he surfactant concentrations are both 28 wt.%, and other conditions are also the same. After reaching the thermodynamic equilibrium, the concentration profiles, the radial distributions functions (RDF) and the mean squared displacement (MSD) are investigated. The results reveal that the surface activity of C12C2C12 surfactant is higher than DTAB surfactant.     

大肠杆菌有限生长的微量热及非线性动力学研究

The finite growth of Escherichia coli was studied by using a LKB 2277 BioActivity Mollitor. We found that the finite growth is a nonliear dynamic process. The nonlinear dynamic behaviour in the finite growth process and the nonlinear dynamic models describing the process were discovered and established. The curve of logistic map corresponding to the finite growth thermogram of Escherichia coli was obtained and the nonlinear dynamic parameters were calculated by means of a computer. Moreover, we also discussed the nonlinear dynamic characters of Escherichia colt in its finite growth process.     

Molecular dynamics studies on octadecylammonium chloride at the air/liquid interface

Molecular dynamics simulations on surfactant octadecylammonium chloride at the air/liquid interface were performed. It was found that the alkyl chains of octadecylammonium would change to order with increasing the concentration of octadecylammonium at the air/liquid interface. Some functions, such as the concentration distributions, the radial distribution function and the mean squared displacement (MSD) were evaluated to investigate the structural properties of interface. We found that the salts can affect octadecylammonium aggregate at the interface: (1) univalent ions, such as chloride and sodium ions, affect slightly the structure of monolayer and (2) bivalent ions, such as sulfate or calcium ions, affect greatly, especially for the bivalent negative ions.     

Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors

The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by -substituted indomethacin ethanolamide inhibitors.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.