The elastic theory of a single DNA molecule

We study the elastic responses of double-(ds) and single-stranded (ss) DNA at external force fields. A double-strand-polymer elastic model is constructed and solved by path integral methods and Monte Carlo simulations to understand the entropic elasticity, cooperative extensibility, and supercoiling property of dsDNA. The good agreement with experiments indicates that short-ranged base-pair stacking interaction is crucial for the stability and the high deformability of dsDNA. Hairpin-coil transition in ssDNA is studied with generating function method. A threshold force is needed to pull the ssDNA hairpin patterns, stabilized by base pairing and base-pair stacking, into random coils. This phase transition is predicted to be of first order for stacking potential higher than some critical level, in accordance with experimental observations.     

Millimeter and submillimeter wave spectroscopic investigations into the rotation-tunneling spectrum of gGg ethylene glycol, HOCH2CH2OH

The rotation-tunneling spectrum of the second most stable gGg^′ conformer of ethylene glycol (1,2-ethanediol) in its ground vibrational state has been studied in selected regions between 77 and 579 GHz. Compared to the study of the more stable aGg^′ conformer, a much larger frequency range was studied, resulting in a much extended frequency list covering similar quantum numbers, J?55 and K_a?19. While the input data were reproduced within experimental uncertainties up to moderately high values of J and K_a larger residuals remain at higher quantum numbers. The severe mixing of the states caused by the Coriolis interaction between the two tunneling substates is suggested to provide a considerable part of the explanation. In addition, a Coriolis interaction of the gGg^′ ground vibrational state with an excited state of the aGg^′ conformer may also contribute. Relative intensities of closely spaced lines have been investigated to determine the signs of the Coriolis constants between the two tunneling substates relative to the dipole moment components and to estimate the magnitudes of the dipole moment components and the energy difference between the gGg^′ and the aGg^′ conformers. Results of ab initio calculations on the total dipole moment and the vibrational spectrum were needed for these estimates. The current analysis is limited to transitions with quantum numbers J?40 and K_a?6 plus those having J?22 and K_a?17 which could be reproduced within experimental uncertainties. The results are aimed at aiding radioastronomers to search for gGg^′ ethylene glycol in comets and in interstellar space.     

Formation of Supersonic Zones and Local Separation Zones in Transonic Steady-State Flow Past Surface Roughness in the Free Interaction Regime

Within the framework of free interaction theory numerical methods are used to investigate the occurrence of supersonic zones with shocks in the outer inviscid region for flow past roughness in the lower viscous sublayer, with and without the formation of local separation zones.     

Dynamic fractal unifying interaction confirmed with magnetospheric behavior and orbital data

The solar wind makes the magnetosphere to expand and contract as indicated by the expansions and contractions of the auroral oval due to balancing of the dynamic pressure of the ambient space plasma at inner and outer magnetic lines. This self‐similar magnetospheric behavior elucidates the controversial magnetic storm‐substorm relationship and reveals the 3D‐spiral structure of magnetic interaction. The found self‐similarly evolving structure of one seen as fundamental interaction suggests dynamic fractal unifying interaction that builds a firework universe having 3D‐spiral code. The unifying interaction is described with equation drawn in new fundamental dynamic fractal framework. The equation of unifying interaction converges to the inverse square laws and the principle of uncertainty at laboratory scales. The dynamic fractal fundamental framework is made of one 3D‐spirally‐faster‐inward contracting and expanding, oscillating, basic matter. It simply accounts for observed constant speed of light and for the creation of bright and dark bands on a screen behind a tiny slit. The dynamic fractal framework is quantitatively confirmed with the orbital data for the Milky Way Galaxy, the Sun, the Earth, and the triple asteroid system 87 Sylvia. Many testable predictions are also made. The presented new fundamental dynamic fractal framework allows qualitative and quantitative modeling and simplification. © 2007 Wiley Periodicals, Inc. Complexity 12: 61–76, 2007     

AFM, SEM and GIXRD studies of thin films of red polycarbazolyldiacetylenes

In this paper we report the results of a morphological and structural investigation on film properties of a soluble polydiacetylene, the poly[1,6-bis(3,6-dihexadecyl-N-carbazolyl)-2,4-hexadiyne] (polyDCHD-HS). The red films of this polymer, prepared by standard spin-coating techniques, revealed absence of linear dichroism and birefringence in contrast with the ordered mesophases detected by powder X-ray studies. In order to interpret the optical behavior of this polymer, we performed AFM and SEM studies of polyDCHD-HS films spun on hydrophylic and hydrophobic glass substrates. We found the presence of surfaces organized in rod-like particles, more regularly oriented on the hydrophylic substrate. GIXRD studies, carried out on films sufficiently thick to allow the observation of the diffraction pattern, reveled the presence of a lamellar structure with a spacing of 3.22 nm. The low intensity of the diffraction peaks and the isotropic linear optical properties of the films show that the lamellar mesophases are not extended over large areas. These findings were compared with the data obtained from AFM and SEM studies on films of two other polydiacetylenes, the poly[1-(3,6-dihexadexyl-N-carbazolyl)-6-(N-carbazolyl)-2,4-hexadyine] (polya-DCHD) and the poly[1,6-bis(3,6-dipalmitoyl-N-carbazolyl)-2,4-hexadyine] (polyDPCHD), spun on hydrophylic glass substrate. The results confirmed the presence of nodular morphologies which seem to be a general characteristic of this class of materials. The particles organization appears instead related to the chemical nature of the substituents on the carbazolyl rings.     

Bending-torsion vibration of a partially submerged cylinder with an arbitrary cross-section

An analytical method is presented to investigate the bending-torsion vibration characteristics of a cylinder with an arbitrary cross-section and partially submerged in water. The compressibility and the free surface waves of the water are considered simultaneously in the analysis. The exact solution of structure–water interaction is obtained mathematically. Firstly, the analytical expression of the velocity potential of the water is derived by using the method of separation of variables. The unknown coefficients in the velocity potential are determined by the longitudinal and circumferential Fourier expansions along the outer surface of the cylinder and are expressed in the form of integral equations including the unknown dynamic bending deflection and torsional angle of the cylinder. Secondly, the force and torque acting on the cylinder per unit length, provided by the water, are obtained by integrating the water dynamic pressure along the circumference of the cylinder. The general solution of bending-torsion vibration of the cylinder under the water dynamic pressure is derived analytically. The integral equations included in the velocity potential of the water can be solved exactly. Finally, the eigenfrequency equation of cylinder–water interaction is obtained by means of the boundary conditions of the cylinder. Some numerical examples for elliptical columns partially submerged in water are provided to show the application of the present method.     

Adhesion studies of latex film surfaces on the meso- and nanoscale

In this paper the effects of surface roughness and annealing temperature (T) of latex coating films on adhesion are discussed for the different stages of the film formation process. The surface free energy of latex films was assessed in terms of practical work of adhesion (W) (or adherence) using a custom-built adhesion-testing device (ATD), atomic force microscopy (AFM), and contact angle measurements. For preannealed latex films surface roughness averages (R_a) were determined from AFM height images and were related to the values of W obtained from ATD measurements at room temperature. The results obtained using these tests exhibiting surface behavior on different length scales indicate a dependence of the measured adhesion on surface roughness and temperature, as well as on the length scale of the measurements.First preannealed samples were studied, which were obtained by heat treatment above the respective glass transition temperatures (T_g). Increasing the temperature of preannealing resulted in a decrease of the adherence observed in ATD experiments at room temperature. However, on the nanoscale, using AFM, no significant variation of the adherence was observed. This observation can be explained by roughness arguments. Preannealing decreases roughness which results in lower adherence values measured by ATD while for essentially single asperity AFM experiments roughness has an insignificant effect. Specimens were also annealed over a constant period of time (90 min) at different temperatures. At the end of the heat treatment, adhesion was measured at the treatment temperature by ATD. The amplified effect of temperature observed in this case on adherence is attributed to the combination of roughness decrease and increasing test temperature. In a third set of experiments completely annealed samples were studied by ATD as well as by AFM as a function of temperature. With increasing T values ATD showed a decrease in adherence, which is attributed to a decreasing surface free energy of the annealed films at elevated T values. AFM, on the other hand, showed an opposite trend which is assigned to increasing penetration of the tip into the tip/wetting polymer samples versus increasing temperature. Finally, annealing isotherms as a function of time were investigated by ATD in situ at different temperatures. This last set of experiments allowed us to optimize annealing time and temperature to achieve complete curing.     

The epitaxial sexiphenyl (0 0 1) monolayer on TiO2(1 1 0): A grazing incidence X-ray diffraction study

A para-sexiphenyl monolayer of near up-right standing molecules (nominal thickness of 30 Å) is investigated in-situ by X-ray diffraction using synchrotron radiation and ex-situ by atomic force microscopy. A terrace like morphology is observed, the step height between the terraces is approximately one molecular length. The monolayer terraces, larger than 20 μm in size, are extended along the [0 0 1] direction of the TiO₂(1 1 0) substrate i.e. along the Ti-O rows of the reconstructed substrate surface. The structure of the monolayer and its epitaxial relationship to the substrate is determined by grazing incidence X-ray diffraction. Extremely sharp diffraction peaks reveal high crystalline order within the monolayer, which was found to have the bulk structure of sexiphenyl. The monolayer terraces are epitaxially oriented with the (0 0 1) plane parallel to the substrate surface (out-of-plane order). Four epitaxial relationships are observed. This in-plane alignment is determined by the arrangement of the terminal phenyl rings of the sexiphenyl molecules parallel to the oxygen rows of the substrate.     

Interaction of metals with an organic semiconductor: Ag and In on PTCDA

The interaction of Ag and In with a thin film of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) was studied by near-edge X-ray absorption fine structure (NEXAFS). Upon Ag deposition on a PTCDA film of 20 nm thickness the relative intensities and lineshapes, as well as the angular dependence of the spectra remains unchanged, illustrating the formation of a chemically unreactive Ag/PTCDA interface. On the other hand, the adsorption of 0.3 nm In strongly decreases the intensity of the π^* resonances in C and O K-edge NEXAFS spectra. This is attributed to a strong charge transfer between In and PTCDA, leading to a redistribution of the charge in the molecule. However, the absence of a strong shift or new features and negligible dependence of peak intensities corresponding to π^* resonances on the In thickness indicate that the interaction between In and PTCDA is not accompanied by a covalent bond formation.     

Study of nitrogen ion implantation and diffusion phenomena on thin chromium layers followed by the atomic force microscopy and secondary ion mass spectroscopy techniques characterization

This research investigates the effect of ion implantation dosage level and further thermal treatment on the physical characteristics of chromium coatings on Si(1 1 1) substrates. Chromium films had been exposed to nitrogen ion fluencies of 1 × 10¹⁷, 3 × 10¹⁷, 6 × 10¹⁷ and 10 × 10¹⁷ N⁺ cm⁻² with a 15 keV energy level. Obtained samples had been heat treated at 450 °C at a pressure of 2 × 10⁻² Torr in an argon atmosphere for 30 h. Atomic force microscopy (AFM) images showed significant increase in surface roughness as a result of nitrogen ion fluence increase. Secondary ion mass spectroscopy (SIMS) studies revealed a clear increased accumulation of Cr₂N phase near the surface as a result of higher N⁺ fluence. XRD patterns showed preferred growth of [0 0 2] and [1 1 1] planes of Cr₂N phase as a result of higher ion implantation fluence. These results had been explained based on the nucleation-growth of Cr₂N phase and nitrogen atoms diffusion history during the thermal treatment process.