Deformation Twinning in Nanocrystalline NI

Deformation twinning is observed upon large plastic deformation in nanocrystalline (nc) Ni by transmission electron microscopy examinations. New and compelling evidence has been obtained for several twinning mechanisms that operate in nc grains, with the gain boundary emission of partial dislocations determined as the most proficient. Deformation twinning in nc Ni is discussed in comparison with molecular dynamics simulation results, based on generalized planar fault energy curves.

Plastic Deformation Of Nanocrystalline Nickel

A high-resolution electron microscopy study has uncovered the plastic behavior of accommodating large strains in nanocrystalline (NC) Ni subject to cold rolling at liquid nitrogen temperature. The activation of grain-boundary-mediated-plasticity is evidenced in NC-Ni, including twinning and formation of stacking fault via partial dislocation slips from the grain boundary. The formation and storage of 60A degrees full dislocations are observed inside NC-grains. The grain/twin boundaries act as the barriers of dislocation slips, leading to dislocation pile-up, severe lattice distortion, and formation of sub-grain boundary. The vicinity of grain/twin boundary is where defects preferentially accumulate and likely the favorable place for onset of plastic deformation. The present results indicate the heterogeneous and multiple natures of accommodating plastic strains in NC-grains.

Inherent Shear-Dilatation Coexistence In Metallic Glass

Shear deformation can induce normal stress or hydrostatic stress in metallic glasses [ Nature Mater. 2 ( 2003) 449, Intermetallics 14 ( 2006) 1033]. We perform the bulk deformation of three-dimensional Cu46Zr54 metallic glass (MG) and Cu single crystal model systems using molecular dynamics simulation. The results indicate that hydrostatic stress can incur shear stress in MG, but not in crystal. The resultant pronounced asymmetry between tension and compression originates from this inherent shear-dilatation coexistence in MG.

Growth of deformation twins in room-temperature rolled nanocrystalline nickel

Deformation twinning has been observed in room-temperature rolled nanocrystalline Ni. The growth of the deformation twins via the emission of partial dislocations from a grain boundary has been examined in detail. Partial dislocations on neighboring slip planes may migrate for different distances and then remain in the grain interior, leading to the formation of a steplike twin boundary TB . With continued twin growth, the TBs become gradually distorted and lose their coherent character due to accumulated high stresses. Moreover, we propose that microtwins may form near such TBs due to the emission of partial dislocations from the TB.

Tobramycin与16S rRNA A位点复合物的分子动力学模拟

采用分子动力学方法(Molecular dynamics,MD)对托普霉素(Tobramycin)与16S rRNA的A位点复合物的特异性识别机制进行了理论模拟研究,模拟时间为3.6 ns. 结果表明,A位点中波动最大的部位是两个环外碱基A1492和A1493;tobramycin的环Ⅰ和环Ⅱ是其最保守的结构单元,可能参与了Tobramycin与16S rRNA的A位点之间的特异性识别. 另外,发现一个残存时间为3.6 ns的"结构化"水分子,它桥接了Tobramycin环Ⅱ的N3与环Ⅰ的N6′之间的氢键,稳定了Tobramycin的结构;Tobramycin周围水合密度较高的位点出现在环Ⅰ和环Ⅱ附近,这也正是晶体结构中形成较多水媒介氢键及动力学模拟中结构化水分子出现的位置. 动力学模拟证实Tobramycin与16S rRNA间的结合是大量氢键及水分子相互作用的结果,这有助于设计和开发以Tobramycin为基础,具有高亲和力及特异性的16S rRNA抑制剂.

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.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.