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.

Synthesis, structure, and optical properties of a contorted (110)-oriented layered hybrid perovskite: C3H11SN3PbBr4

The < 110 >-oriented perovskite is very rare in the hybrid perovskites family. In this work, an unusual layered < 110 >-oriented hybrid perovskite, which is stabilized by a special organic ligand, 2-(aminoethyl)isothiourea, has been obtained. This ligand combines a primary amine and a formamidine on the two ends of one molecule. Introduction of the special ligand brings about contorted inorganic sheets in the hybrid perovskite structure. The optical properties of the new < 110 >-oriented perovskite were studied.

Bioorganic/inorganic hybrid composition of sponge spicules: Matrix of the giant spicules and of the comitalia of the deep sea hexactinellid Monorhaphis

The giant basal spicules of the siliceous sponges Monorhaphis chuni and Monorhaphis intermedia (Hexactinellida) represent the largest biosilica structures on earth (up to 3 m long). Here we describe the construction (lamellar organization) of these spicules and of the comitalia and highlight their organic matrix in order to understand their mechanical properties. The spicules display three distinct regions built of biosilica: (i) the outer lamellar zone (radius: >300 mu m), (ii) the bulky axial cylinder (radius: <75 mu m), and (iii) the central axial canal (diameter: <2 mu m) with its organic axial filament. The spicules are loosely covered with a collagen net which is regularly perforated by 7-10 mu m large holes; the net can be silicified. The silica layers forming the lamellar zone are approximate to 5 mu m thick; the central axial cylinder appears to be composed of almost solid silica which becomes porous after etching with hydrofluoric acid (HF). Dissolution of a complete spicule discloses its complex structure with distinct lamellae in the outer zone (lamellar coating) and a more resistant central part (axial barrel). Rapidly after the release of the organic coating from the lamellar zone the protein layers disintegrate to form irregular clumps/aggregates. In contrast, the proteinaceous axial barrel, hidden in the siliceous axial cylinder, is set up by rope-like filaments. Biochemical analysis revealed that the (dominant) molecule of the lamellar coating is a 27-kDa protein which displays catalytic, proteolytic activity. High resolution electron microscopic analysis showed that this protein is arranged within the lamellae and stabilizes these surfaces by palisade-like pillars. The mechanical behavior of the spicules was analyzed by a 3-point bending assay, coupled with scanning electron microscopy. The load-extension curve of the spicule shows a biphasic breakage/cracking pattern. The outer lamellar zone cracks in several distinct steps showing high resistance in concert with comparably low elasticity, while the axial cylinder breaks with high elasticity and lower stiffness. The complex bioorganic/inorganic hybrid composition and structure of the Monorhaphis spicules might provide the blueprint for the synthesis of bio-inspired material, with unusual mechanical properties (strength, stiffness) without losing the exceptional properties of optical transmission. (C) 2007 Elsevier Inc. All rights reserved.

Molecular cloning and expression of a novel Kazal-type serine proteinase inhibitor gene from Zhikong scallop Chlamys farreri, and the inhibitory activity of its recombinant domain

Serine proteinase inhibitors (SPIs) play important roles in host physiological and immunological processes in all multicellular organisms. A novel Kazal-type SPI gene was cloned from the Zhikong scallop Chlamys farreri (designated as CfKZSPI) by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfKZSPI was of 1788 nucleotides with a canonical polyadenylation signal sequence AATAAA and a polyA tail, and an open reading frame (ORF) encoding a polypeptide of 509 amino acids with a putative signal peptide of 22 amino acids. The deduced amino acid sequence of CfKZSPI contained 12 tandem Kazal domains with high similarity to other Kazal-type SPIs. The temporal expression of CfKZSPI in hemocytes after Vibrio anguillorum challenge was recorded by quantitative real-time RT-PCR. The relative mRNA expression level of CfKZSPI was up-regulated and reached 43.6-fold at 3 h post-challenge. After a decrease at 6 h, the expression Level increased again and reached 207.8-fold at 12 h post-challenge. The 12th Kazal domain of CfKZSPI was recombined into pET-32a(+) and expressed in Escherichia coli Rosetta-gami (DE3) to investigate its inhibitory activity. The purified recombinant protein (rCf KZSPI-1 2) showed significant inhibitory activity against trypsin but no activity against thrombin. When the molar ratio of inhibitor to trypsin reached 1:1, almost 90% of the enzyme activity could be inhibited, which suggested that one molecule of rCfKZSPI-12 was able to inhibit one molecule of trypsin. Kinetics analysis with Dixon plot showed that the inhibition constant (K-i) of rCfKZSPI-12 to trypsin was 173 nmol L-1. These results indicated that CfKZSPI was a novel Kazal-type SPI with significant inhibitory activity against trypsin, and was suspected to be involved in scallop immune response. (c) 2008 Elsevier Ltd. All rights reserved.

Stiffness behaviour of injection moulded short glass fibre/impact modifier/polypropylene hybrid composites

The stiffness behaviour of injection moulded short glass fibre/impact modifier/polypropylene hybrid composites has been investigated in this work by theoretical predictions and experiments. Predictions from the self-consistent method were found to be in good agreement with test results for the impact modifier/polypropylene blends. By taking into account of the fibre orientation distributions in the skin and core layers, the values of Young's modulus for the skin and core layers were predicted by employing Eshelby's equivalent inclusion method and the average induced strain approach. The prediction of the values of Young's modulus for the whole sample was obtained by applying the simple mixture theory of laminated composites to the predicted results for the skin and core layers. Good correlation between predicted and experimental Young's modulus values were found.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Biological application of multi-component nanowires in hybrid devices powered by F-1-ATPase motors

In this paper, construction of hybrid device by integrating nanowires with F1-ATPase motors is described. The nickel nanowires and multi-segment nanowires, including gold and nickel, were fabricated by electrochemical deposition in nanoporous templates. The nickel nanowires functionalized by biotinylated peptide can be assembled directly onto F1-ATPase motors to act as the propellers. If the multicomponent nanowires, including gold and nickel, were selectively functionalized by the thiol group modified ssDNA and the synthetic peptide, respectively, the biotinylated F1- ATPase motors can be attached to the biotinylated peptide on nickel segment of the nanowires. Then, the multi-component nanowires can also be used as the propellers, and one may observe the rotations of the multi-component nanowires driven by F1-ATPase motors. Therefore, introduction of multiple segments along the length of a nanowire can lead to a variety of multiple chemical functionalities, which can be selectively bound to cells and special biomolecules. This method provides an insight for the construction of other hybrid devices with its controlling arrangement of different biomolecule on designed nanometer scale structures.

Elastic Waves in a Hybrid Multilayered Piezoelectric Plate

An analytical-numerical method is presented for analyzing dispersion and characteristic surface of waves in a hybrid multilayered piezoelectric plate. In this method, the multilayered piezoelectric plate is divided into a number of layered elements with three-nodal-lines in the wall thickness, the coupling between the elastic field and the electric field is considered in each element. The associated frequency dispersion equation is developed and the phase velocity and slowness, as well as the group velocity and slowness are established in terms of the Rayleigh quotient. Six characteristic wave surfaces are introduced to visualize the effects of anisotropy and piezoelectricity on wave propagation. Examples provide a full understanding for the complex phenomena of elastic waves in hybrid multilayered piezoelectric media.

Impact response and failure mechanisms of ultrahigh modulus polyethylene fiber composites and polyethylene fiber-carbon fiber hybrid composites

The impact response and failure mechanisms of ultrahigh modulus polyethylene (UHMPE) fiber composites and UHMPE fiber-carbon fiber hybrid composites have been investigated. Charpy impact, drop weight impact and high strain rate impact experiments have been performed in order to study the impact resistance, notch sensitivity, strain rate sensitivity and hybrid effects. Results obtained from dynamic and quasi-static measurements have been compared. Because of the ductility of UHMPE fibers, the impact energy absorption of UHMPE fiber composites is very high, thereby leading to excellent damage tolerance. By hybridizing with UHMPE fibers, the impact properties of carbon fiber composites can be greatly improved. The impact and shock failure mechanisms of these composites are discussed.

Thermal Strain Analysis of a Flip-Chip Package by a Modified Hybrid Method

介绍一种可用于微电子封装局部应变场分析的实验/计算混合方法,该方法结合了有限元的整体/局部模型和实时的激光云纹干涉技术,利用激光云纹干涉技术所测得的应变场来校核有限元整体模型的计算结果,并用整体模型的结果作为局部模型的边界条件,对实验难以确定的封装结构局部位置的应力、应变场进行分析.用这种方法对可控坍塌倒装封装结构在热载荷作用下焊球内的应变场分布进行了分析,结果表明该方法能够提供封装结构内应力-应变场分布的准确和可靠的结果,为微电子封装的可靠性分析提供重要的依据. For the reliability analysis of electronic packages, strains in very localized areas, such as an interconnection or a corner, need to be determined. In this paper, a modified hybrid method of global/local modeling and real time moire interferometry is presented. In this method, a simplified, coarsely meshed global model is developed to get rough information about the deformation of the microelectronic package. In order to make sure the global model has been reasonably simplified and the material properties ...

Essential and Non-Essential Work of Fracture of PI/SiO2 Hybrid Thin Films

Essential work of fracture (EWF) analysis is used to study the effect of the silica doping level on fracture toughness of polyimide/silica (PI/SiO2) hybrid films. By using double-edge-notched-tension (DENT) specimens with different ligament lengths, it seems that the introduction of silica additive can improve the specific essential work of fracture (w (e) ) of PI thin films, but the specific non-essential work of fracture (beta w (p) ) will decease significantly as the silica doping level increasing from 1 to 5 wt.%, and even lower than that of neat PI. The failure process of the fracture is investigated with online scanning electron microscope (SEM) observation and the parameters of non-essential work of fracture, beta and w (p) , are calculated based on finite element (FE) method.

Hybrid Finite Compact-WENO Schemes for Shock Calculation

Hybrid finite compact (FC)-WENO schemes are proposed for shock calculations. The two sub-schemes (finite compact difference scheme and WENO scheme) are hybridized by means of the similar treatment as in ENO schemes. The hybrid schemes have the advantages of FC and WENO schemes. One is that they possess the merit of the finite compact difference scheme, which requires only bi-diagonal matrix inversion and can apply the known high-resolution flux to obtain high-performance numerical flux function; another is that they have the high-resolution property of WENO scheme for shock capturing. The numerical results show that FC-WENO schemes have better resolution properties than both FC-ENO schemes and WENO schemes. In addition, some comparisons of FC-ENO and artificial compression method (ACM) filter scheme of Yee et al. are also given.

A Constrained Particle Dynamics for Continuum-Particle Hybrid Method in Micro- and Nano-Fluidics

A hybrid method of continuum and particle dynamics is developed for micro- and nano-fluidics, where fluids are described by a molecular dynamics (MD) in one domain and by the Navier-Stokes (NS) equations in another domain. In order to ensure the continuity of momentum flux, the continuum and molecular dynamics in the overlap domain are coupled through a constrained particle dynamics. The constrained particle dynamics is constructed with a virtual damping force and a virtual added mass force. The sudden-start Couette flows with either non-slip or slip boundary condition are used to test the hybrid method. It is shown that the results obtained are quantitatively in agreement with the analytical solutions under the non-slip boundary conditions and the full MD simulations under the slip boundary conditions.

A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved.