QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Hybrid Qm/Mm Simulation Of The Hydration Phenomena Of Dipalmitoylphosphatidylcholine Headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous Solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated. (C) 2008 Elsevier Inc. All rights reserved.

Phase Transformation Accommodated Plasticity In Nanocrystalline Nickel

Based on detailed x-ray diffraction and transmission electron microscopy we have found body-centered-cubic (bcc) Ni upon room-temperature rolling of nanocrystalline (nc) face-centered-cubic (fcc) Ni. The bcc phase forms via the Kurdjumov-Sachs (KS) martensitic transformation mechanism when the von Mises equivalent strain exceeds similar to 0.3, much higher than accessible in tensile testing. The fcc and bcc phases keep either the KS or the Nishiyama-Wasserman orientation relationship. Our results provide insights into the deformation physics in nc Ni, namely, the fcc-to-bcc phase transformation can also accommodate plasticity at large plastic strains. (C) 2008 American Institute of Physics.

Microstructural evolution and formation of nanocrystalline intermetallic compound during surface mechanical attrition treatment of cobalt

Nanocrystalline intermetallic Co3Fe7 was produced on the surface of cobalt via surface mechanical attrition (SMA). Deformationinduced diffusion entailed the formation of a series of solid solutions. Phase transitions occurred depending on the atomic fraction of Fe in the surface solid solutions: from hexagonal close-packed (<4% Fe) to face-centered cubic (fcc) (4-11% Fe), and from fcc to body-centered cubic (>11% Fe). Nanoscale compositional probing suggested significantly higher Fe contents at grain boundaries and triple junctions than grain interiors. Short-circuit diffusion along grain boundaries and triple junctions dominate in the nanocrystalline intermetallic compound. Stacking faults contribute significantly to diffusion. Diffusion enhancement due to high-rate deformation in SMA was analyzed by regarding dislocations as solute-pumping channels, and the creation of excess vacancies. Non-equilibrium, atomic level alloying can then be ascribed to deformation-induced intermixing of constituent species. The formation mechanism of nanocrystalline intermetallic grains on the SMA surface can be thought of as a consequence of numerous nucleation events and limited growth. (C) 2007 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Experimental laws of cratering for hypervelocity impacts of spherical projectiles into thick target

It is shown in this paper that the laws of cratering in a thick target under hypervelocity impact by a spherical projectile can be approximately expressed by the so-called iso-deviation law and a 2/3 power law. Moreover, hypervelocity impact should be characterized by the isotropic expansion of a crater. In the special case, when the projectile and target are of the same material, the laws mentioned above reduce to the result of a semi-spherical crater and the energy criterion. Generally speaking, a semi-spherical crater and the energy criterion are both approximations, which only take projectile density and target strength into account, and can be used for a rough estimation on the order of magnitude. The inconsistency in various fitted power laws in the literature was also clarified and explained in the paper.

Preliminary-results of gaas single-crystal growth under high gravity conditions

GaAs single crystals have been grown under high gravity conditions, up to 9g0, by a recrystallization method with decreasing temperature. The impurity striations in GaAs grown under high gravity become weak and indistinct with smaller striation spacings. The dislocation density of surcharge-grown GaAs increases with increase of centrifugal force. The cathodoluminescence results also show worse perfection in the GaAs grown at high gravity than at normal earth gravity.

The catastrophic change of steady flow in collapsible tubes

Based on a general background we have developed a mechanical model of the catastrophic change of steady flow in collapsible tubes and got the critical conditions for the catastrophic change analyzing the effects of viscosity, gravity and the longitudinal gradient of external pressure. Several simple flows have been discussed. Furthermore, we conducted three types of model experiments, Results agree with the theoretical critical conditions qualitatively.

装药弹体侵彻混凝土厚靶中的炸药摩擦起爆模型

基于炸药的热爆炸理论,采用炸药的热点温度(也称为临界起爆温度)作为起爆判据,分析了装药弹体在侵彻混凝土厚靶过程中的炸药安全性问题,建立了炸药摩擦起爆的热传导模型.对模型进行了量纲一化分析,得出量纲一热流率幅值Qm与炸药和弹壳界面量纲一温度峰值T′max的关系,以及可在实际工程中应用的临界量纲一控制参数Qmc,同时得到了反映摩擦产生的热量在炸药与弹壳间分配比例关系的量纲一参数ΚⅠ.结果表明,炸药装药和弹壳接触面间的强摩擦是形成热点、从而导致炸药早炸的一个重要因素.

Second-harmonic generation in Ge20As25S55 glass irradiated by an electron beam

Second-harmonic generation was observed in Ge(20)AS(25)S(55) chalcogenide glass irradiated by an electron beam. The second-harmonic intensity increased with increasing electron-beam current and accelerating voltage. The second-harmonic generation in Ge20As25S55 glass was caused by the space-charge electrostatic field that was generated by irradiation of an electron beam. Second-order nonlinearity chi ((2)) as great as 0.8 pm/V was obtained. The results of measurements of thermally stimulated depolarization current indicated that the glass was poled in the thin layers of its surface (several micrometers) and that the nonlinearity was stable. (C) 2001 Optical Society of America.

Ultrafast non-linear optical properties of Ge20As25Se55 chalcogenide films

The non-resonant third-order non-linear optical properties of amorphous Ge20As25Se55 films were studied experimentally by the method of the femtosecond optical heterodyne detection of optical Kerr effect. The real and imaginary parts of complex third-order optical non-linearity could be effectively separated and their values and signs could be also determined, which were 6.6 x 10(-12) and -2.4 x 10(-12) esu, respectively. Amorphous Ge20As25Se55 films showed a very fast response in the range of 200 fs under ultrafast excitation. The ultrafast response and large third-order non-linearity are attributed to the ultrafast distortion of the electron orbitals surrounding the average positions of the nucleus of Ge, As and Se atoms. The high third-order susceptibility and a fast response time of amorphous Ge20As25Se55 films makes it a promising material for application in advanced techniques especially in optical switching. (c) 2005 Elsevier B.V. All rights reserved.

Femtosecond optical Kerr effect study of Ge(10)AS(40)S(30)Se(20) film

The results of the femtosecond optical heterodyne detection of optical Kerr effect at 805 nm with the 80 fs ultrafast pulses in amorphous Ge10As40S30Se20 film is reported in this paper. The film shows an optical non-linear response of: 200 fs under ultrafast 80 fs-pulse excitation and the values of real and imaginary parts of non-linear susceptibility chi((3)) were 9.0 X 10(-12) and -4.0 X 10(-12) esu, respectively. The large third-order non-linearity and ultrafast response are attributed to the ultrafast distortion of the electron orbits surrounding the average positions of the nucleus of Ge, As, S and Se atoms. This Ge10As40S30Se20 chalcogenide glass would be expected as a promising material for optical switching technique. (c) 2005 Elsevier Ltd. All rights reserved.

Non-resonant third-order non-linear optical properties of amorphous GeSe2 film

The real and imaginary parts of third-order susceptibility of amorphous GeSe2 film were measured by the method of the femtosecond optical heterodyne detection of optical Kerr effect at 805 nm with the 80 fs ultra fast pulses. The results indicated that the values of real and imaginary parts were 8.8 x 10(-12) esu and -3.0 x 10(-12) esu, respectively. An amorphous GeSe2 film also showed a very fast response within 200 fs. The ultra fast response and large third-order non-linearity are attributed to the ultra fast distortion of the electron orbits surrounding the average positions of the nucleus of Ge and Se atoms. (c) 2005 Elsevier B.V. All rights reserved.

Ultrafast optical Kerr effect in amorphous Ge10As40S30Se20 film induced by ultrashort laser pulses

The results of the femtosecond optical heterodyne detection of optical Kerr effect at 805 am with the 80 fs ultrafast pulses in amorphous Ge10As40S30Se20 film is reported in this Letter. The film shows an optical nonlinear response of 200 fs under ultrafast 80 fs-pulse excitation, and the values of real and imaginary parts of nonlinear susceptibility chi((3)) were 9.0 x 10(-12) esu and -4.0 x 10(-12) esu respectively. The large third-order nonlinearity and ultrafast response are attributed to the ultrafast distortion of the electron orbits surrounding the average positions of the nucleus of Ge, As, S and Se atoms. This Ge10As40S30Se20 chalcogenide glass would be expected as a promising material for optical switching technique.

Low loss waveguide in Nd3+-doped silicate glass fabricated by carbon ion implantation

Low loss index enhanced planar waveguides in Nd3+-doped silicate glass were fabricated by 3.0 MeV C+ ion implantation. The enhancement of the refractive index confined the light propagating in the waveguide. The prism-coupling method was used to measure dark modes in the waveguide. The effective refractive indices of the waveguide were obtained based on the dark modes. The moving fiber method was applied to measure the waveguide propagation loss. Loss measured in non-annealed samples is about 0.6 dB/cm. And the waveguide mode optical near-field output at 633 nm was presented. (c) 2005 Elsevier B.V. All rights reserved.