The Uniaxial Tensile Deformation of Ni Nanowire: Atomic-Scale Computer Simulations

The mechanical deformations of nickel nanowire subjected to uniaxial tensile strain at 300 K are simulated by using molecular dynamics with the quantum corrected Sutten-Chen many-body force field. We have used common neighbor analysis method to investigate the structural evolution of Ni nanowire during the elongation process. For the strain rate of 0.1%/ps, the elastic limit is up to about 11% strain with the yield stress of 8.6 GPa. At the elastic stage, the deformation is carried mainly through the uniform elongation of the distances between the layers (perpendicular to the Z-axis) while the atomic structure remains basically unchanged. With further strain, the slips in the {111} planes start to take place in order to accommodate the applied strain to carry the deformation partially, and subsequently the neck forms. The atomic rearrangements in the neck region result in a zigzag change in the stress-strain curve; the atomic structures beyond the region, however, have no significant changes. With the strain close to the point of the breaking, we observe the formation of a one-atom thick necklace in Ni nanowire. The strain rates have no significant effect on the deformation mechanism, but have some influence on the yield stress, the elastic limit, and the fracture strain of the nanowire.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Magnetic Field Design of the Dipole for Super-FRS at FAIR

The Super-FRS (Super FRagment Separator) is a part of FAIR (Facility for Antiproton and Ion Research), which will be constructed at GSI, Germany by 17 countries. The Super-FRS comprises 24 superferric dipole magnets. The 2D and 3D magnetic field simulations of the prototype magnet are described in this paper. A passive trim slot and four chamfered removable poles are used to satisfy the required field homogeneity which is better than +/-3 x 10(-4) at 1.6 T, 0.8 T and 0.16 T in a wide elliptical useable aperture of 380 mm x 140 mm. Measurement results at various field levels are shown in this paper as well. It can be seen from the comparison of calculation and measurement results that the magnetic designs of the magnet fulfils the requirements.

X-ray crystal structure and molecular mechanics calculations of (2,6-iso-dipropyl-phenylamide) dimethyl (tetra-methylcyclopenta-dienyl) silane titanium dichloride

Crystal and molecular structure of (2.6-dipropylphenylamide) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained from a mixture of ether/hexane as orthorhombic. with a = 12.658 (3) Angstrom. b = 16.62 (3) Angstrom. c = 11.760 (2) Angstrom. V = 2474.2 (9) Angstrom(3). Z = 4, space group Pnma. R = 0.0399; Componud I compose of the pi-bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.

Molecular dynamics simulation of sub-transition for polyethersulfone

Molecular dynamics (MD) simulations of a polyethersulfone (PES) chain are carried out in the amorphous state by using the Dreiding 2.21 force field at four temperatures. Two types of molecular motion, i.e, rotations of phenylene rings and torsions of large segments containing two oxygen atoms, two sulfur atoms, and five phenylene rings on the backbone, are simulated. The modeling results show that the successive phenylene rings should be in-phase cooperative rotations, whereas the successive large segments should be out-of-phase cooperative torsions. By calculating the diffusion coefficient for the phenylene ring rotations, it is found that this rotation contributes to the beta -transition of PES.

Size effects on the melting of nickel nanowires: a molecular dynamics study

The melting process of nickel nanowires are simulated by using molecular dynamics with the quantum Sutten-Chen many-body force field. The wires studied were approximately cylindrical in cross-section and periodic boundary conditions were applied along their length; the atoms were arranged initially in a face-centred cubic structure with the [0 0 1] direction parallel to the long axis of the wire. The size effects of the nanowires on the melting temperatures are investigated. We find that for the nanoscale regime, the melting temperatures of Ni nanowires are much lower than that of the bulk and are linear with the reciprocal of the diameter of the nanowire. When a nanowire is heated up above the melting temperature, the neck of the nanowire begins to arise and the diameter of neck decreases rapidly with the equilibrated running time. Finally, the breaking of nanowire arises, which leads to the formation of the spherical clusters. (C) 2004 Elsevier B.V. All rights reserved.

Abnormal phenomenon of ac Stark splitting in magneto-optical traps

We experimentally study the ac Stark splitting in D2 line of cold Rb-87 atoms. The frequency span between the Autler-Townes doublets is obviously larger than that derived from theoretical calculation. Two physical effects, which increase the effective Rabi frequency, contribute to the splitting broadening. First, atoms tend to distribute in strong lield places of a inhomogeneous red-detuned light field. Second, atoms reabsorb scattered light when they are huge in number and high in density.

Rashba spin splitting of the minibands of coupled InAs/GaAs pyramid quantum dots

The Rashba spin splitting of the minibands of coupled InAs/GaAs pyramid quantum dots is investigated using the k center dot p method and valence force field model. The Rashba splitting of the two dimensional miniband in the lateral directions is found due to the structure inversion asymmetry in the vertical direction while the miniband in the vertical direction has no Rashba spin splitting. As the space between dots increases, the Rashba coefficients decrease and the conduction-band effective mass increases. This Rashba spin splitting of the minibands will significantly affect the spin transport properties between quantum dots. (C) 2008 American Institute of Physics.

Electronic structure and optical gain of truncated InAs1-xNx/GaAs quantum dots

The shape of truncated square-based pyramid quantum dots (QDs) is similar to that of real QDs in experiments. The electronic band structures and optical gain of InAs1-xNx/GaAs QDs are calculated by using the 10-band k.p model, and the strain is calculated by the valence force field (VFF) method. When the top part of the QD is truncated, greater truncation corresponds to a flatter shape of the QD. The truncation changes the strain distribution and the confinement in the z direction. A flatter QD has a greater C1-HH1 transition energy, greater transition matrix element, less detrimental effect of higher excited transition, and higher saturation gain and differential gain. The trade-off between these properties must be considered. From our results, a truncated QD with half of its top part removed has better overall performance. This can provide guidance to growing QDs in experiments in which the proper growing conditions can be controlled to achieve required properties. (C) 2009 Elsevier Ltd. All rights reserved.

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3143025]

Strain relaxation and band-gap tunability in ternary InxGa1-xN nanowires

The alloy formation enthalpy and band structure of InGaN nanowires were studied by a combined approach of the valence-force field model, Monte Carlo simulation, and density-functional theory (DFT). For both random and ground-state structures of the coherent InGaN alloy, the nanowire configuration was found to be more favorable for the strain relaxation than the bulk alloy. We proposed an analytical formula for computing the band gap of any InGaN nanowires based on the results from the screened exchange hybrid DFT calculations, which in turn reveals a better band-gap tunability in ternary InGaN nanowires than the bulk alloy.

Effects of Sb, N, and period on the electronic properties of GaAs/GaInNAsSb superlattices

We have calculated the bond distributions and atom positions of GaAs/GalnNAsSb superlattices using Keating's semiempirical valence force field (VFF) model and Monte Carlo simulation. The electronic structures of the superlattices are calculated using folded spectrum method (FSM) combined with an empirical pseudopotential (EP) proposed by Williamson et al.. The effects of N and Sb on superlattice energy levels are discussed. We find that the deterioration of the optical properties induced by N can be explained by the localization of the conduction-band states around the N atom. The electron and hole effective masses of the superlattices are calculated and compared with the effective masses of the bulk GaAs and GaInAs.

Electronic properties of GaAs/GayIn1-yNxAs1-y-xSby superlattices

Using Keating's semiempirical valence force field model and Monte Carlo simulation, we calculate the bond distributions and atom positions of GaAs/GaInNAsSb superlattices. The electronic structures of the superlattices are calculated using the folded spectrum method combined with an empirical pseudopotential proposed by Williamson The effects of N and Sb on superlattice energy levels are discussed. The deterioration of the optical properties induced by N is explained by the localization of the conduction-band states around the N atom. The electron and hole effective masses of the superlattices are calculated and compared with the effective masses of the GaAs and GaInAs.

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3143025]

两个冠醚分子在简正坐标分析及NRCC程序在微机上的移植

本文用加拿大国立研究院(National Research Council of Canada) Fuhrer等人编制的FORTRAN语言程序（以下简称NRCC程序），对两个冠醚类化合物进行了简正坐标分析，这两个化合物分子是二氧六环(C_4H_8O_2)和12－冠－4(C_8H_(16)O_4)。作者用Synder和Zerbi提出的一般价力场，计算了二氧六环的36个简正振动频率，精化四次后的结果误差为14.04 cm~(-1)，得到了二氧六环的精化力场和势能分析矩阵；做了12－冠－4－的中红外光谱(3200-5000cm~(-1))。远红外光谱(500-70cm~(-1))和拉曼光谱(3200-50 cm~(-1)，从而归属出12－冠－4的78个简正振动频率实验值；利用二氧六环的精化力场作为初始力场，计算了12－冠－4的简正振动频率，对78个简正振动频率进行了精化计算，精化三次后的结果误差为13.99 cm~(-1)，精化后得到12－冠－4的精化力场和势能分布矩阵；将NRCC程序以BASIC语言移至TRS-80微型机上，对二氧六环进行了计算，结果良好，首次给出二氧六环一般价力场的势能分布。一、对二氧六环的处理 二氧六环分子式C_4H_8O_2，合14个原子，有3N－6＝36个简正振动频率。分子结构系由二个乙氧基(-CH_2-CH_2-O-)单元组成的含有四个碳，两个氧的六元环，平衡态分子为椅式构象，属于C_(2h)点群，36个简正振动频率分为四个对称类Ag、Au、Bg和Bu，分布是：Ag 10个，Bg 8个，Au 9个，Bu9个。二氧六环的分子结构及坐标示意图见28而图5，定义了14个伸缩内坐标，26个弯曲内坐标，6个扭曲内坐标，共46个，C－C键长1.54A，C-O键长1.41 A，C－H键长1.096A，键角都用109°28'。用CART程序（NRCC程序之一）计算二氧六环14个原子的笛卡尔坐标，用GMAT程序（NRCC程序之二）计算其B矩阵和G矩阵，用FPERT程序（NRCC程序之三）计算其简正振动频率、精化力场，计算用一般价力场，引入V矩阵对称化，将46个坐标化为46个（内）对称坐标，10个多余坐标在FPERT程序计算中除去。二、对12－冠－4的处理 12－冠－4分子式C_8H_(16)O_4，含28个原子，共3N－6＝78个简正振动频率，分子结构为四个乙氧基(-CH_2-CH_2-O-)单元组成的含八个碳、四个氧的12元环，自由分子的12－冠－4属于C点群。结构数据引自Groth的X光衍射分数和坐标，自己编制了BASIC语言程度将分数坐标化为笛卡尔坐标，用GMAT程序计算B矩阵和G矩阵，FPERT程序计算78个简正振动频率、精化力场、计算势能分布矩阵，引入U矩阵将92个内坐标化为92个对称坐标，14个多余坐标在FPERT程序中自动除去。三、结果 势能分布矩阵给出分子的振动归属，对这两个冠醚类分子的3N－6个简正振动频率，可以划分为五个振动区域。1．C－H伸缩振动区（3000－2800 cm~(-1)） 在该区中，二氧六环有八个值：2974、2966、2854和2867 cm~(-1)各两个，12－冠－4有16个值：2935、2923、2915和2907 cm~(-1)各两个，2860 cm~(-1)8个，高于2900 cm~(-1)者为反对称伸缩振动，低于2900 cm~(-1)者为对称伸缩振动。2．亚甲基弯曲振动之一(1500-1400 cm~(-1)) 该区的主要振动是亚甲基剪式振动(Scissor)，其它振动小于10％二氧六环在该区有四个频率：1443、1461、1451和1457 cm~(-1)，12－冠－4有八个频率：1466、1450、1450和1405 cm~(-1)各两个。3．亚甲基弯曲振动区二(1400-1200 cm~(-1))该区的主要振动模式为亚甲基的颤动(wag)、卷曲(twist)和摆动(rock)振动，其它振动小于13％。二氧六环在该区有八个频率：1334、1303、1396、1216、1367、1264、1377和1296 cm~(-1)，12－冠－4有十六个频率：1388、1363、……1229 cm~(-1)（其中1288、1307cm~(-1)非简并，其余皆两重简并）。4．环的骨架伸缩振动区(1200-600 cm~(-1))该区振动模式复杂，除环的骨架伸缩振动外，还有亚甲基的wag、twist、rock以及环的骨架弯曲振动，而且这些振动的势能分布值都不小。二氧六环在该区有十一个频率，从1127至610 cm~(-1)，12－冠－4有二十个频率，从1135至184 cm~(-1)且大都是二重简并的。5．低频区(600-50cm~(-1))这两个分子在低频区的势能分布略有差别。二氧六环在该区有五个频率：503、486、427、276和224 cm~(-1)，主要振动模式为骨架弯曲振动和扭曲振动，C－O、C－C的扭曲振动在三个最低频率中分布占10－30％。12－冠－4在该区有18个频率，除570和547cm~(-1)处，都是二重简并的，六个最低频率的振动模式完全属于C－O、C－C键的扭曲振动，其它振动小于10％，所以200 cm~(-1)以下可称为12－冠－4的扭曲振动区，在600－200cm~(-1)之间的12个频率主要是骨架的弯曲振动，也有一定量的亚甲基wag、twist、rock振动。12－冠－4的简正坐标分析尚未有人做过。二氧六环的计算结果与Snyder和Zerbi的分析相吻合，12－冠－4和二氧六环两分子势能分布的相对一致性证明了对12－冠－4的简正坐标分析基本是正确的。本文比较了二分子的力常数和振动频率，探讨了环的大小对振动光谱的影响。四、NRCC程序简介 NRCC程序由CART、GMAT和FPERT三个程序组成，即可联一起运用，亦可分开独立进行运算。该程序功能强，所占内存大，适于大、中型计算机使用。CART程序之名字取自Cartisian Co-or-dinates的前四个字母，功能系由分子结构参数（键长、键角）计算分子内各原子的笛卡尔坐标。GMAT程序之名字取自G matrix的前四个字母，功能系由分子内各原子的笛卡尔坐标，原子质量和内坐标定义计算分子内各原子的坐标交换矩阵B和Wilson振动动能矩阵G。FPERT程序之名字取自F Perturbation的前五个字母，功能系由分子振动功能矩阵G、势能常数即力常数矩阵F计算分子的简正振动频率和势能分布矩阵，再通过实验频率精化势能矩阵F。NRCC程序可对含30个原子、60个内坐标的分子进行简正坐标分析，扩充后容量增大一倍。该程序可选用一般价力场(General Valence Force Field, 简称GVFF)和UBS力场(Urey-Bradley-Shimanouchi Force Field)，简称UBSFF或UBFF)。可选用对称化U矩阵，可自行决定力场精化次数和阻尼常数以限制精化结果的收敛性。五、NRCC程序在TRS－80微型机上移植试尝（该部分曾在第三届长春夏季化学讨论会上宣读）针对NRCC程序占内存空间大、难以在微型机上实现的情况，作者将NRCC程序改编为BASIC语言，改变程序的原来结构，形成一组BASIC语言程序：CART／BAS、GMAT／BAS和VIFR／BAS，改编后的BASIC程序在TRS－80微型机调试通过，TRS－80机字长8位，New Dos系统内存32K。改写后的程序只保持了原程序的基本原理，在内存，语句上改动很大，以适于微型机使用。数据在程序中直接嵌入，利于修改替换，且BASIC语言简单易学，便于操作。CART／BAS程序可计算含30个原子以内的分子的笛卡尔坐标，GMAT／BAS程序可计算含20个原子、45个内坐标的分子的G矩阵，VIFR／BAS程序可计算含15个原子的分子的简正振动频率。利用这组程序，作者以二氧六环分子为例做了一些试尝运算，误差14.4 cm~(-1)，相对误差1.8%，结果较理想。