用分子动力学模拟甲烷水合物热激法分解

用分子动力学模拟方法研究甲烷水合物热激法分解，系统地研究注入340 K液态水的结构Ⅰ型甲烷水合物的分解机理.模拟显示水合物表层水分子与高温液态水分子接触获得热能，分子运动激烈，摆脱水分子间的氢键束缚，笼状结构被破坏.甲烷分子获得热能从笼中挣脱，向外体系扩散.热能通过分子碰撞从外层传递给内层水分子，水合物逐层分解.对比注入277K液态水体系模拟结果，得出热激法促进水合物分解.

用分子动力学模拟水合物储氢

用分子动力学（MD）模拟方法系统研究了结构Ⅰ型（SⅠ）和结构H型（SH）氢气水合物中氢气的占据情况并确定了氢气水合物的稳定结构：SⅠ水合物氢气分子数小胞中为2，大胞中为3；SH水合物氢气分子数小胞中为2，中胞中为2，大胞中为11．分析了稳定情况下水合物各胞腔内氢气分子之间的径向分布函数（RDF），得出了氢气分子在各胞腔内的稳定位置．由稳定位置得到了稳定结构下氢气水合物的储氢质量分数：SⅠ为5．085％，SH为6．467％．与实验对比得出结论：SH水合物稳定结构下的储氢能力最强．

Boundary conditions at the solid-liquid surface over the multiscale channel size from nanometer to micron

The boundary condition at the solid surface is one of the important problems for the microfluidics. In this paper we study the effects of the channel sizes on the boundary conditions (BC), using the hybrid computation scheme adjoining the molecular dynamics (MD) simulations and the continuum fluid mechanics. We could reproduce the three types of boundary conditions (slip, no-slip and locking) over the multiscale channel sizes. The slip lengths are found to be mainly dependent on the interfacial parameters with the fixed apparent shear rate. The channel size has little effects on the slip lengths if the size is above a critical value within a couple of tens of molecular diameters. We explore the liquid particle distributions nearest the solid walls and found that the slip boundary condition always corresponds to the uniform liquid particle distributions parallel to the solid walls, while the no-slip or locking boundary conditions correspond to the ordered liquid structures close to the solid walls. The slip, no-slip and locking interfacial parameters yield the positive, zero and negative slip lengths respectively. The three types of boundary conditions existing in "microscale" still occur in "macroscale". However, the slip lengths weakly dependent on the channel sizes yield the real shear rates and the slip velocity relative to the solid wall traveling speed approaching those with the no-slip boundary condition when the channel size is larger than thousands of liquid molecular diameters for all of the three types of interfacial parameters, leading to the quasi-no-slip boundary conditions.

溶液中柔性树枝形高分子的分子动力学模拟

树枝形高分子具有几乎完美的分子结构，含有许多末端基团，并拥有特殊的流变行为使其在生物医药、基因治疗、光电材料等领域有广泛的应用前景。探讨树枝形高分子的代数和链节长度对其静态性质和动力学行为的影响规律，将有助于实现树枝形高分子的结构调控，为其广泛应用提供依据和指导。然而，目前系统研究代数和链节长度的研究仍然较少，还遗留很多问题没有得到解决，尤其是树枝形高分子的动力学行为。因此，本论文使用分子动力学的模拟方法探讨了树枝形高分子的静态性质和动力学行为，获得了如下结果： 1. 树枝形高分子的回转半径Rg满足标度律Rg~N1/5(G+1)2/5P2/5（其中树枝形分子的聚合度是N，代数是G，链节长度是P，子代代数是g。）。 2. 随着代数的增加，树枝形高分子的分形维数增加并接近3.0，静态结构因子和硬球的相似，表明其内部结构发生了由类星形向近球形转化。 3. 随着代数和链节长度的增加，出现了“单元”(monomer)密度几乎不变的区域，这是外层子代链节回折的结果。定量计算表明：树枝形分子的回折能力随着链节长度的增加而增强，随着代数的增加而减弱。 4. 树枝形高分子整体的扩散行为和“单元”的运动满足Zimm标度关系。 5. 树枝形分子各子代的运动速度不同，与内层子代相比，外层子代在短时间内扩散较慢，但其松弛较快。借助Stoke-Einstein扩散方程和链节的空间位阻效应，我们解释了子代速度不同的成因。

The further understanding of chain topology effect on the properties of single polymer in good solvent: Special behaviors of single tadpole chain

Chain topology strongly affects the static and dynamic properties of polymer melts and polymers in dilute solution. For different chain architectures, such as ring and linear polymers, the molecular size and the diffusion behavior are different. To further understand the chain topology effect on the static and dynamic properties of polymers, we focus on the tadpole polymer which consists of a cyclic chain attached with one or more linear tails. It is found that both the number and the length of linear tails play important roles on the properties of the tadpole polymers in dilute solution. For the tadpole polymers with fixed linear tail length and number, with increasing the degree of polymerization of tadpole polymers, a transition from linear-like to ring-like behavior is observed for both the static and dynamic properties.

Application of a New Cyclic Guanidinium Ionic Liquid on Dye-Sensitized Solar Cells (DSCs)

A new cyclic guanidinium ionic liquid OGI (1,3-dimethyl-2-N ''-methyl-N ''-octylimidazoguanidinium iodide) has been used as a quasi-solid-state electrolyte for dye-sensitized solar cells (DSCs), and 6.38% conversion efficiency was achieved at AM 1.5 simulated sunlight (9.81 mW cm(-2)). Further gelation with SiO2 nanoparticles afforded the solid-state electrolyte, which presented overall conversion efficiency of 5.85%. The diffusion properties of these OGI-based electrolytes were investigated. In the meantime, the optimal structure and ion-pairing interaction in OGI have been proposed by density functional theoretical calculation (DFT) at the B3LYP/6-21G(d,p) level.

Daunomycin binding to detergent micelles: A model system for evaluating the hydrophobic contribution to drug-DNA interactions

The interaction of daunomycin with sodium dodecyl sulfate and Triton X-100 micelles was investigated as a model for the hydrophobic contribution to the free energy of DNA intercalation reactions. Measurements of visible absorbance, fluorescence lifetime, steady-state fluorescence emission intensity, and fluorescence anisotropy indicate that the anthraquinone ring partitions into the hydrophobic micelle interior. Fluorescence quenching experiments using both steady-state and lifetime measurements demonstrate reduced accessibility of daunomycin in sodium dodecyl sulfate micelles to the anionic quencher iodide and to the neutral quencher acrylamide. Quenching of daunomycin fluorescence by iodide in Triton X-100 micelles was similar to that seen with free daunomycin. Studies of the energetics of the interaction of daunomycin with micelles by fluorescence and absorbance titration methods and by isothermal titration calorimetry in the presence of excess micelles revealed that association with sodium dodecyl sulfate and Triton X-100 micelles is driven by a large negative enthalpy. Association of the drug with both types of micelles also has a favorable entropic contribution, which is larger in magnitude for Triton X-100 micelles than for sodium dodecyl sulfate micelles.

Channel formation and intermediate range order in sodium silicate melts and glasses

Kargl, Florian; Meyer, A.; Horbach, J.; Kob, W., (2004) 'Channel formation and intermediate range order in sodium silicate melts and glasses', Physical Review Letters 93(2) pp.027801 RAE2008

Pesquisa computacional de inibidores de fatores de virulência de bacillus anthracifs

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Multiscale numerical modelling of crack propagation in two-dimensional metal plate

A novel multiscale model of brittle crack propagation in an Ag plate with macroscopic dimensions has been developed. The model represents crack propagation as stochastic drift-diffusion motion of the crack tip atom through the material, and couples the dynamics across three different length scales. It integrates the nanomechanics of bond rupture at the crack tip with the displacement and stress field equations of continuum based fracture theories. The finite element method is employed to obtain the continuum based displacement and stress fields over the macroscopic plate, and these are then used to drive the crack tip forward at the atomic level using the molecular dynamics simulation method based on many-body interatomic potentials. The linkage from the nanoscopic scale back to the macroscopic scale is established via the Ito stochastic calculus, the stochastic differential equation of which advances the tip to a new position on the macroscopic scale using the crack velocity and diffusion constant obtained on the nanoscale. Well known crack characteristics, such as the roughening transitions of the crack surfaces, crack velocity oscillations, as well as the macroscopic crack trajectories, are obtained.

Modelling the adsorption and imaging of C60 molecules on a graphite substrate

The adsorption of a C60 monolayer on a graphite substrate was modelled via molecular dynamics simulation covering a significant period of 160 picoseconds. The final configuration of C60s agrees closely with that observed in a scanning tunnelling microscopy (STM) experiment. Clusters of adsorbed molecules were then selected and their STM-like images were computed via the Keldysh Green function method.

Development of complex classical force fields through force matching to ab initio data: Application to a room-temperature ionic liquid

Recent experimental neutron diffraction data and ab initio molecular dynamics simulation of the ionic liquid dimethylimidazolium chloride ([dmim]Cl) have provided a structural description of the system at the molecular level. However, partial radial distribution functions calculated from the latter, when compared to previous classical simulation results, highlight some limitations in the structural description offered by force fieldbased simulations. With the availability of ab initio data it is possible to improve the classical description of [dmim]Cl by using the force matching approach, and the strategy for fitting complex force fields in their original functional form is discussed. A self-consistent optimization method for the generation of classical potentials of general functional form is presented and applied, and a force field that better reproduces the observed first principles forces is obtained. When used in simulation, it predicts structural data which reproduces more faithfully that observed in the ab initio studies. Some possible refinements to the technique, its application, and the general suitability of common potential energy functions used within many ionic liquid force fields are discussed.

Evidence of Short-Range Screening in Shock-Compressed Aluminum Plasma

We have investigated the angular variation in elastic x-ray scattering from a dense, laser-shock-compressed aluminum foil. A comparison of the experiment with simulations using an embedded atom potential in a molecular dynamics simulation shows a significantly better agreement than simulations based on an unscreened one-component plasma model. These data illustrate, experimentally, the importance of screening for the dense plasma static structure factor.

Phase Behaviour, Interactions, and Structural Studies of (Amines+Ionic Liquids) Binary Mixtures

We present a study on the phase equilibrium behaviour of binary mixtures containing two 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}imide-based ionic liquids, [Cnmim] [NTf2] (n=2 and 4), mixed with diethylamine or triethylamine as a function of temperature and composition using different experimental techniques. Based on this work, two systems showing an LCST and one system with a possible hourglass shape are measured. Their phase behaviours are then correlated and predicted by using Flory–Huggins equations and the UNIQUAC method implemented in Aspen. The potential of the COSMO-RS methodology to predict the phase equilibria was also tested for the binary systems studied. However, this methodology is unable to predict the trends obtained experimentally, limiting its use for systems involving amines in ionic liquids. The liquid-state structure of the binary mixture ([C2mim] [NTf2]+diethylamine) is also investigated by molecular dynamics simulation and neutron diffraction. Finally, the absorption of gaseous ethane by the ([C2mim][NTf2]+diethylamine) binary mixture is determined and compared with that observed in the pure solvents.

Pinning down the solid-state polymorphism of the ionic liquid [bmim][PF6]

The solid-state polymorphism of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF6], has been investigated via low-temperature and high-pressure crystallisation experiments. The samples have been characterised by single-crystal X-ray diffraction, optical microscopy and Raman spectroscopy. The solid-state phase behaviour of the compound is confirmed and clarified with respect to previous phase diagrams. The structures of the previously reported gamma-form, which essentially exhibits a G'T cation conformation, as well as those of the elusive beta- and alpha-forms, are reported. Crystals of the beta-phase are twinned and the structure is heavily disordered; the cation conformation in this form is predominantly TT, though significant contributions from other less frequently encountered conformers are also observed at low temperature and high pressure. The cation conformation in the alpha-form is GT; the presence of the G'T conformer at 193 K in this phase can be eliminated on cooling to 100 K. Whilst X-ray structural data are overall in good agreement with previous interpretations based on Raman and NMR studies, they also reveal a more subtle interplay of intermolecular interactions, which give rise to a wider range of conformers than previously considered.