Multi-scale analysis of AFM tip and surface interactions

Thoroughly understanding AFM tip-surface interactions is crucial for many experimental studies and applications. It is important to realize that despite its simple appearance, the system of tip and sample surface involves multiscale interactions. In fact, the system is governed by a combination of molecular force (like the van der Waals force), its macroscopic representations (such as surface force) and gravitational force (a macroscopic force). Hence, in the system, various length scales are operative, from sub-nanoscale (at the molecular level) to the macroscopic scale. By integrating molecular forces into continuum equations, we performed a multiscale analysis and revealed the nonlocality effect between a tip and a rough solid surface and the mechanism governing liquid surface deformation and jumping. The results have several significant implications for practical applications. For instance, nonlocality may affect the measurement accuracy of surface morphology. At the critical state of liquid surface jump, the ratio of the gap between a tip and a liquid dome (delta) over the dome height (y(o)) is approximately (n-4) (for a large tip), which depends on the power law exponent n of the molecular interaction energy. These findings demonstrate that the multiscale analysis is not only useful but also necessary in the understanding of practical phenomena involving molecular forces. (c) 2007 Elsevier Ltd. All rights reserved.

Transition waves and nonlinear interactions in the near wake of a circular cylinder

Transition waves and interactions between two kinds of instability-vortex shedding and transition wave in the near wake of a circular cylinder in the Reynolds number range 3 000-10 000 are studied by a domain decomposition hybrid numerical method. Based on high resolution power spectral analyses for velocity new results on the Reynolds-number dependence of the transition wave frequency, i.e. f(t)/f(s) similar to Re-0.87 are obtained. The new predictions are in good agreement with the experimental results of Wei and Smith but different from Braza's prediction and some early experimental results f(t)/f(s) similar to Re-0.5 given by Bloor et nl. The multi-interactions between two kinds of vortex are clearly visualized numerically. The strong nonlinear interactions between the two independent frequencies (f(t), f(s)) leading to spectra broadening to form the coupling mf(s) +/- nf(t) are predicted and analyzed numerically, and the characteristics of the transition are described. Longitudinal variations of the transition wave and its coupling are reported. Detailed mechanism of the flow transition in the near wake before occurrence of the three-dimensional evolution is provided.

Studies on morphogenesis and cellular interactions of Rana grylio virus in an infected fish cell line

A pathogenic virus (RGV), isolated from diseased pig frog Rana grylio with lethal syndrome, was investigated with regard to morphogenesis and cellular interactions in EPC cells, a cell Line from fish. Different stages of virus amplification, maturation and assembly were observed at nucleus, cytoplasm and cellular membranes. The matured virus particles, were not only distributed diffusely in nucleus, cytoplasm and cellular surface, but also aggregated as pseudocrystalline arrays in the cytoplasm. Virions were released by budding from the plasma membranes, or following cell lysis. Various types of cell damage, such as small vacuoles, spherical inclusions, and swollen and empty mitochondria, were also found. Some typical characteristics of RGV, such as the symmetrical shape of the virions, replication process involving both nuclear and cytoplasmic phases, budding release from cellular membrane and intracellular membrane, viromatrix and paracrystalline aggregation in cytoplasm, and its acute pathogenic effects, were observed to be similar to that of other iridoviruses. Therefore, the RGV appears to be a member of the Iridoviridae based on these studies. (C) 1999 Elsevier Science B.V. All rights reserved.

The adsorption of dopamine on gold and its interactions with iron(III) ions studied by microcantilevers

The adsorption of dopamine (DA) molecules on gold and their interactions with Fe3+ were studied by a microcantilever in a flow cell. The microcantilever bent toward the Au side with the adsorption of DA due to the change Of Surface stress induced by the intermolecular hydrogen bonds of DA or the charge transfer effect between adsorbates and the Substrate. The interaction process between DA adsorbates and Fe3+ was revealed by the deflection curves of microcantilever. As indicated by the appearance of a variation during the decline of curves, two steps were observed in the curve at relative high concentrations of Fe3+. In this case, Fe3+ reacted with DA molecules only in the outer layers and the complexes removed with solution. Then Fe3+ reacted further with DA molecules forming the surface complex in the first layer next to the gold. At this stage, the stability Of Surface complexes was time dependent, i.e., unstable initially and stable finally. This may be due to the surface complexes change from mono-dentate to bi-dentate complexes. In another case, i.e., at relative low concentration of Fe3+, only the first step was observed as indicated by the absence of a variation.

Physical and spectral characterization of the human cyclin A gene and its interactions with anthracycline anticancer drugs

Over expression of cyclin A in human tumors has been linked to cancer by various experimental lines of evidence. However, physical and spectral characterization of the human cyclin A gene and its interactions with anticancer drugs have not been reported. Our gene sequence analysis, singular value decomposition method and melting studies in the presence of antitumor agents, daunomycin, doxorubicin and Hoechst 33258 showed that cyclin A gene had both AT-rich and GC-rich domains. For a ligand with unknown DNA binding specificity, this gene sequence can be used to differentiate its DNA binding preference.

A novel epitaxy of isotactic polypropylene (alpha phase) on PTFE and organic substrates

Isotactic polypropylene in its a modification (alpha iPP) crystallises epitaxially on polytetrafluoroethylene (PTFE) and several hemiacids or salts of substituted benzoic acids via a novel contact plane, namely (110): so far, the only known contact plane involved in alpha iPP homo- and hetero-epitaxies was (010). In spite of its complicated architecture (alternation of antichiral helices with different azimuthal settings), the (110)(alpha iPP) contact plane displays well defined, if not prominent, rows of methyl side chains parallel to the crystallographic (112) direction (at 57 degrees to the c-axis) and approximate to 5.5 Angstrom apart. The matching contact planes of the substrates display linear gratings made of rows of e.g. chlorine atoms or PTFE chains with similar approximate to 5.5 Angstrom inter-row or interchain distances. Various morphologies are observed in iPP thin films crystallised at different cooling rates in the presence of PTFE; they can be analysed in terms of a succession and interplay of successive epitaxies: initial alpha iPP/PTFE heteroepitaxy, followed by alpha iPP/alpha iPP and gamma iPP/alpha iPP homoepitaxies. (C) 1999 Published by Elsevier Science Ltd. All rights reserved.

Miscibility and specific interactions in poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) and poly(P-vinylphenol) blends

The blends of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) (P(HB-co-HV)/poly(p-vinylphenol)(PVPh) were investigated by differential scanning calorimetry (DSC), Fourier transform IR (FT-IR) spectroscopy and high-resolution solid-state C-13 NMR techniques. Single glass transition temperatures existing in the whole composition range indicates that these blends are miscible. The presence of hydrogen bonding between the hydroxyl of PVPh and carbonyl of P(HB-co-HV), shown by FT-IR spectra, is the origin of the miscibility. Furthermore, results obtained by high-resolution solid-state C-13 NMR give more information about the structure of the blends. (C) 1998 Elsevier Science Ltd. All rights reserved.

Gas transport property of homo- and copolyimides from isomeric thiaphthalic dianhydride and oxydianiline

Gas transport properties of home- and copolyimides prepared from 3,3',4,4'- and 2,2',3,3'-thiaphthalic dianhydride (p-TDPA and m-TDPA, respectively) with 4,4-oxydianiline (ODA) were investigated. The fractional free volume of m-TDPA-ODA is larger than that of p-TDPA-ODA, and the chain segmental mobility of the former is lower than that of the latter. The permeability coefficients of m-TDPA-ODA to H-2, CO2, and O-2 are more increased by 48, 69 and 75%, at 30 degrees C and 10 atm, respectively, than those of p-TDPA-ODA; but the permselectivities of m-TDPA-ODA for H-2, CO2, and O-2 toward N-2 are more decreased by 33, 77, and 26%, respectively, than those of p-TDPA-ODA. The permeability coefficients and the diffusion coefficients of the copolyimides can be described by the following equations: log P = Phi(p) log P-p + Phi(m), log P-m and log D-a = D-a = Phi(p) log(D-alpha)(p) + Phi(m) log(D-a)(m), respectively. The variation of the permselectivity is controlled predominantly by diffusivity selectivity. These observations are interpreted in terms of variations in the fractional free volume of polyimides. (C) 1997 John Wiley & Sons, Inc.

Compatibility and specific interactions in poly(beta-hydroxybutyrate) and poly(p-vinylphenol) blends

The miscibility and specific interactions in poly (beta-hydroxybutyrate) (PHB)/poly(p-vinylphenol) (PVPh) blends were studied by differential scanning calorimetry(DSC) , fourier transform infrared(FTIR) spectrometer and high resolution solid state C-13 NMR, A single composition-dependent glass transition temperatures were obtained by DSC which indicate the blends of PHB/PVPh were miscible in the melt state, The experimental glass transition temperatures were fitted quite well with those obtained from Couchman-Karasz equation. The FTIR study shows that the strong intermolecular hydrogen bonding exists in blends of PHB with strong proton acceptor and PVPh with strong proton donor and is the origin of its compatibility. The CPMAS C-13 NMR spectra also show that the strong hydrogen bonding exists in PHB/PVPh blends. From the T-1 rho(H) relaxation time it follows that the blends of PHB/PVPh(40/60, 20/80) studied are completely homogeneous on the scale of about 3.2 nm.

Interactions of thiamine monophosphate (TMP) with one- and two-dimensional polymeric halogenomercurate anions. Crystal structures of (TMP)(Hg2Br5)center dot 0.5H(2)O and (TMP)(2)(Hg3I8)

An investigation into the interactions between thiamine monophosphate (TMP) and anions has resulted in the preparation and X-ray characterization of the compounds (TMP)(Hg2Br5).0.5H(2)O (1) and (TMP)(2)(Hg3I8) (2). In each compound the TMP molecule exists as a monovalent cation in the usual F conformation. The halogenomercurate anions occur in two-dimensional (2-D) network in 1 or one-dimensional (1-D) chain in 2. In both 1 and 2, the structures consist of alternating cationic sheets of the hydrogen-bonded TMP molecules and anionic sheets of the polymeric halogenomercurate anions. The TMP molecule binds to the polymeric anions through the characteristic 'anion bridge I', C(2)-H..X...pyrimidinium (X = Br in 1 and 1 in 2), and electrostatic interactions between electropositive S(1) and halogen atoms. The 'anion bridge II' of the type N(4'1)-H...X...thiazolium (X = phosphate group) plays a role in stabilizing the molecular conformation. The biological implication of the host-guest-like complexation between TMP and polymeric anions is discussed.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

The co-evolutionary relationship between bitterling fishes and freshwater mussels: insights from interspecific comparisons

Hypothesis: In parasites that use hosts for offspring development, adults may base oviposition decisions on a range of host traits related either to host quality or the co-evolutionary relationship between parasite and host. We examined whether host quality or co-evolutionary dynamics drive the use of hosts in the bitterling-mussel relationship. Organisms: Six species of bitterling fish (Acheilognathinae) and eight species of freshwater mussels (Unionidae, Corbiculidae) that are used by bitterling for oviposition. Site of experiments: Experimental tanks in Wuhan, China, at the site of the natural distribution of the studied species. Methods: Three experiments that controlled for host accessibility and interspecific interactions were conducted to identify host preferences among bitterling fishes and their mussel hosts. We started with a broad interspecific comparison. We then tested bitterling behavioural choices, their temporal stability, and mussel host ejection behaviour of the eggs of generalist and specialist bitterling species. Finally, we measured host mussel quality based on respiration rate and used published studies on mussel gill structure to infer mussel suitability as hosts for bitterling eggs. Results: We found significant interspecific differences among bitterling species in their use of mussel hosts. Bitterling species varied in their level of host specificity and identity of preferred hosts. Host preferences were flexible even among apparently specialized species and fishes switched their preferences adaptively when the quality of individuals of preferred host species declined. Mussels varied considerably in their response to oviposition through egg ejections. Host preference by a generalist bitterling species correlated positively with host quality measured as the efficiency of the mussel gills to extract oxygen from inhaled water. Host ability to eject bitterling eggs correlated positively with their relative respiration rate, probably due to a higher velocity of water circulating in the mussel gill chamber.

Expression pattern and developmental behaviour of cellular nucleic acid-binding protein (CNBP) during folliculogenesis and oogenesis in fish

In vertebrates, folliculogeneis establishes an intricate system for somatic cell-oocyte interaction, and ultimately leads to the acquisition of their respective competences. Although the formation process and corresponding interactions are strikingly similar in diverse organisms, knowledge of genes and signaling pathways involved in follicle formation is very incomplete and the underlying molecular mechanisms remain enigmatic. CNBP has been identified for more than ten years, and the highest level of CNBP transcripts has been observed in adult zebrafish ovary, but little is known about its functional significance during folliculogeneis and oogenesis. In this study, we clone CNBP cDNA from gibel carp (Carassius auratus gibelio), and demonstrate its predominant expression in gibel carp ovary and testis not only by RTPCR but also by Western blot. Its full-length cDNA is 1402 bp, and has an ORF of 489 nt for encoding a peptide of 163 aa. And its complete amino acid sequence shared 68.5%-96.8% identity with CNBPs from other vertebrates. Based on the expression characterization, we further analyze its expression pattern and developmental behaviour during folliculogeneis and oogenesis. Following these studies, we reveal an unexpected discovery that the CagCNBP is associated with follicular cells and oocytes, and significant distribution changes have occurred in degenerating and regenerating follicles. More interestingly, the CagCNBP is more highly expressed in some clusters of interconnected cells within ovarian cysts, no matter whether the cell clusters are formed from the original primordial germ cells or from the newly formed cells from follicular cells that invaded into the atretic oocytes. It is the first time to reveal CNBP relevance to folliculogeneis and oogenesis. Moreover, a similar stage-specific and cell-specific expression pattern has also been observed in the gibel carp testis. Therefore, further studies on CNBP expression pattern and developmental behaviour will be of significance for understanding functional roles of CNBP during gametogenests. (c) 2005 Elsevier B.V. All rights reserved.

Narrowing of band gap and low-temperature spin glass behavior of FeNi co-doped ZnO nanowires

This letter reports on the Raman, optical and magnetic properties of FeNi co-doped ZnO nanowires prepared via a soft chemical solution method. The microstructural investigations show that the NiFe co-dopants are substituted into wurtzite ZnO nanostructure without forming any secondary phase. The co-doped nanowires show a remarkable reduction of 34 nm (267.9 meV) in the optical band gap, while suppression in the deep-level defect transition in visible luminescence. Furthermore, these nanowires exhibit ferromagnetism and an interesting low-temperature spin glass behavior, which may arise due to the presence of disorder and strong interactions of frustrated spin moments of Ni and Fe co-dopants on the ZnO lattice sites. Copyright (C) EPLA, 2009

Spin precession and electron spin polarization wave in [001]-grown quantum wells

We theoretically study the spatial behaviors of spin precessions modulated by an effective magnetic field in a two-dimensional electron system with spin-orbit interaction. Through analysis of interaction between the spin and the effective magnetic field, we find some laws of spin precession in the system, by which we explain some previous phenomena of spin precession, and predict a controllable electron spin polarization wave in [001]-grown quantum wells. The shape of the wave, like water wave, mostly are ellipse-like or circle-like, and the wavelength is anisotropic in the quantum wells with two unequal coupling strengths of the Rashba and Dresselhaus interactions, and is isotropic in the quantum wells with only one spin orbit interaction.