A study of fibrous long spacing collagen ultrastructure and assembly by atomic force microscopy

Fibrous long spacing collagen (FLS) fibrils are collagen fibrils that display a banding with periodicity greater than the 67nm periodicity of native collagen. FLS fibrils can be formed in vitro by addition of alpha(1)-acid glycoprotein to an acidified solution of monomeric collagen, followed by dialysis of the resulting mixture. We have investigated the ultrastructure of FLS fibrils formed in vitro using the atomic force microscope (AFM). The majority of the fibrils imaged showed typical diameters of approximately 150nm and had a distinct banding pattern with a approximately 250nm periodicity. However, we have also observed an additional type of FLS fibril, which is characterized by a secondary banding pattern surrounding the primary bands. These results are compared with those obtained in past investigations of FLS ultrastructure carried out using the transmission electron microscope (TEM). The importance of the fibril's surface topography in TEM staining patterns is discussed. Images of FLS fibrils in various stages of assembly have also been collected, and the implications of these images in determining the mechanism of assembly and the formation of the characteristic banding pattern of the fibrils is discussed.     

Fibril stability in solutions of twisted -sheet peptides: a new kind of micellization in chiral systems

The problem of fibril (fibre) formation in chiral systems is explored theoretically being supported by experiments on synthetic de novo 11-mer peptide forming self-assembled -sheet tapes. Experimental data unambiguously indicate that the tapes form fibrils of nearly monodisperse thickness ca . 8-10 nm. Fibril formation and stabilisation are attributed to inter-tape face-to-face attraction and their intrinsic twist, correspondingly. The proposed theory is capable of predicting the fibril aggregation number and its equilibrium twist in terms of molecular parameters of the primary tapes. The suggested novel mechanism of twist stabilisation of finite aggregates (fibrils) is different to the well-known stabilisation of micelles in amphiphilic systems, and it is likely to explain the formation and stability of fibrils in a wide variety of systems including proteinaceous amyloid fibres, sickle-cell hemoglobin fibres responsible for HbS anemia, corkscrew threads found in chromonics in the presence of chiral additives and native cellulose microfibrillar crystallites. The theory also makes it possible to extract the basic molecular parameters of primary tapes (inter-tape attraction energy, helical twist step, elastic moduli) from the experimental data. Received 7 May 1999 and Received in final form 15 February 2000     

Atomic force microscopy investigation of chemically stabilized pericardium tissue

Native and chemically stabilized porcine pericardium tissue was imaged by the contact mode atomic force microscopy (AFM), in air. Chemically stabilized pericardium is used as a tissue-derived biomaterial in various fields of the reconstructive and replacement surgery. Collagen type I is the main component of the fibrous layer of the pericardium tissue. In this study, the surface topography of collagen fibrils in their native state in tissue and after chemical stabilization with different cross-linking reagents: glutaraldehyde (GA), dimethyl suberimidate (DMS) and tannic acid (TA) was investigated. It has been found that chemical stabilization causes considerable changes in the surface topography of collagen fibrils as well as in the spatial organization of the fibrils within the tissue. The observed changes in the D-spacing pattern of the collagen fibril correspond to the formation of intrafibrilar cross-links, whereas formation of interfibrilar cross-links is mainly responsible for the observed tangled spatial arrangement of fibrils and crimp structure of the tissue surface. The crimp structure was distinctly seen for the GA cross-linked tissue. Surface heterogeneity of the cross-linking process was observed for the DMS-stabilized tissue. SDS-PAGE electrophoresis was performed in order to evaluate the stabilization effect of the tissues treated with the cross-linking reagents. It has been found that stabilization with DMS, GA or TA enhances significantly the tissue resistance to SDS/NaCl extraction. The relation between the tissue stability and changes in the topography of the tissue surface was interpreted in terms of different nature of cross-links formed by DMS, GA and TA with collagen.     

Hydration of nucleic acid components in dependence on nucleotide composition and relative humidity: a Monte Carlo simulation

What role does the nucleotide composition play in the process of formation of hydrated environment of nucleic acids? Can one estimate the hydration of nucleic acids on the level of their components? In order to resolve these questions we have completed an extensive computer simulation of the hydration of nucleic acids components - deoxynucleoside monophosphates distinguished by nucleotide composition. The energetic characteristics of systems containing deoxynucleoside monophosphates and water clusters of various dimensions are received. Our results demonstrate that deoxynucleoside monophosphates containing guanine and/or cytosine residues hydrated more strongly because of formation of more hydrogen bonds with water molecules in small water clusters, i.e. at low values of relative humidity. With increasing of number of water molecules in a water cluster the energetic preference of deoxynucleoside monophosphates containing guanine and/or cytosine residues decreases, and for water clusters corresponding to a state of a dilute aqueous solution the hydration of all types of deoxynucleoside monophosphates does not differ in a great degree. Deoxynucleoside monophosphates containing guanine and/or cytosine residues cause the greater destruction of the water structure compensated by the greater interaction with the nearest water molecules for all levels of relative humidity. Received 25 December 2001 and Received in final form 22 March 2002 Published online 13 September 2002     

Gaussian Effective Potential and superconductivity

The Gaussian Effective Potential in a fixed transverse unitarity gauge is studied for the static three-dimensional U(1) scalar electrodynamics (Ginzburg-Landau phenomenological theory of superconductivity). In the broken-symmetry phase the mass of the electromagnetic field (inverse penetration depth) and the mass of the scalar field (inverse correlation length) are both determined by solution of the coupled variational equations. At variance with previous calculations, the choice of a fixed unitarity gauge prevents from the occurrence of any unphysical degree of freedom. The theory provides a nice interpolation of the experimental data when approaching the critical region, where the standard mean-field method is doomed to failure. Received 18 November 2002 / Received in final form 26 March 2003 Published online 20 June 2003 RID="a" ID="a"e-mail: giuseppe.angilella@ct.infn.it     

Shapes of nearly cylindrical, axisymmetric bilayer membranes

Shapes of nearly cylindrical sections of axisymmetric phospholipid membranes are studied theoretically. Describing the shape of such sections by their deviation from a reference cylinder, the well-established shape equation for axisymmetric bilayer membranes is expanded in terms of this deviation, and it is then solved analytically. The phase diagram shows the resulting stationary shapes as functions of system parameters and external conditions, i.e., the pressure difference across the membrane, the membrane tension, the difference between the tensions of the two monolayers, and the axial force acting on the vesicle. The accuracy of the approximate analytical solution is demonstrated by comparison with numerical results. The obtained analytical solution allows to extend the analysis to include shapes where numerical methods have failed. Received 27 September 2000 and Received in final form 26 March 2001     

Vertical water distribution during the drying of polymer films cast from aqueous emulsions

We present a systematic study of the vertical uniformity of water distribution during the drying of waterborne colloidal films, testing the predictions of a Peclet number Pe defined for this system. Pe indicates the relative contributions of water evaporation and Brownian diffusion in determining the concentration profile in the vertical direction (i.e. normal to the substrate). When Pe < 1, the water concentration in films cast from an alkyd emulsion is found via magnetic-resonance profiling to be uniform with depth, which is consistent with expectations. When Pe > 1, a gradient in the water concentration develops, with less water near the interface with air. The water profiles reveal that the alkyd particles do not coalesce immediately upon contact in close-packing. At later times, a concentrated surface layer develops, but particles are not coalesced in this layer to form a continuous “skin”, but rather the structure is likely to be that of a biliquid foam. Received 20 March 2002 and Received in final form 12 June 2002     

Adsorption of anionic polyelectrolytes to dioctadecyldimethylammonium bromide monolayers

Monolayers of dioctadecyldimethylammonium bromide (DODA) at the air/water interface were used as model for charged surfaces to study the adsorption of anionic polyelectrolytes. After spreading on a pure water surface the monolayers were compressed and subsequently transferred onto a polyelectrolyte solution employing the Fromherz technique. The polyelectrolyte adsorption was monitored by recording the changes in surface pressure at constant area. For poly(styrene sulfonate) and carboxymethylcellulose the plot of the surface pressure as function of time gave curves which indicate a direct correlation between the adsorbed amount and surface pressure as well as a solely diffusion controlled process. In the case of rigid rod-like poly(p-phenylene sulfonate)s the situation is more complicated. Plotting the surface pressure as function of time results in a curve with sigmoidal shape, characterized by an induction period. The induction period can be explained by a domain formation, which can be treated like a crystallization process. Employing the Avrami expression developed for polymer crystallization, the change in the surface pressure upon adsorption of rigid rod-like poly(p-phenylene sulfonate)s can be described. Received 1st July 2000 and Received in final form 7 December 2000     

Collisional broadening and shifting of ammonia absorption lines at 790 nm

By using a diode laser spectrometer based on a commercial heterostructure diode laser operating in free-running mode, line shape parameters of some ammonia ro-vibrational overtones at 790 nm have been measured at room temperature. These weak absorption lines have been detected by using the wavelength modulation spectroscopy technique with second-harmonic detection. The broadening and shifting coefficients have been obtained for ten absorption lines by fitting the collected second-harmonic absorption features and varying the pressure of different buffer gases. Received 13 February 2002 / Received in final form 18 September 2002 Published online 17 December 2002 RID="a" ID="a"e-mail: alex@ifam.pi.cnr.it     

Coupled longitudinal and transverse stimulated Brillouin scattering in single-mode optical fibers

Due to their finite numerical aperture, both longitudinal and transverse stimulated Brillouin scattering can occur in single-mode fibers. We discuss the role of the fiber structure and propose a coherent model accounting for both effects. We show experimentally and numerically that, in some cases, the perturbative cladding Brillouin scattering (CBS) can severely affect the dynamics of SBS Brillouin fiber lasers. New dynamical regimes of long-fiber Brillouin ring lasers are presented, including stable trains of modulated pulses. Received 17 September 2001 / Received in final form 5 March 2002 Published online 28 June 2002     

Spike autosolitons and pattern formation scenarios in the two-dimensional Gray-Scott model

We performed an extensive numerical study of pattern formation scenarios in the two-dimensional Gray-Scott reaction-diffusion model. We concentrated on the parameter region in which there exists a strong separation of length and/or time scales. We found that the static one-dimensional autosolitons (stripes) break up into two-dimensional radially-symmetric autosolitons (spots). The traveling one-dimensional autosolitons (wave fronts) can be stable or undergo breakup. The static two-dimensional radially-symmetric autosolitons may break up and self-replicate leading to the formation of space-filling patterns of spots, wave fronts, or spatio-temporal chaos due to the competition of self-replication and annihilation of spots upon collision. Received 6 November 2000 and Received in final form 27 February 2001     

Adhesion between an elastic body and a randomly rough hard surface

I have developed a theory of adhesion between an elastic solid and a hard randomly rough substrate. The theory takes into account that partial contact may occur between the solids on all length scales. I present numerical results for the case where the substrate surface is self-affine fractal. When the fractal dimension is close to 2, complete contact typically occurs in the macro-asperity contact areas, while when the fractal dimension is larger than 2.5, the area of (apparent) contact decreases continuously when the magnification is increased. An important result is that even when the surface roughness is so high that no adhesion can be detected in a pull-off experiment, the area of real contact (when adhesion is included) may still be several times larger than when the adhesion is neglected. Since it is the area of real contact which determines the sliding friction force, the adhesion interaction may strongly affect the friction force even when no adhesion can be detected in a pull-off experiment. Received 3 April 2002     

Nanoparticles superficial density of charge in electric double-layered magnetic fluid: A conductimetric and potentiometric approach

We analyze potentiometric and conductimetric measurements simultaneously performed on Electric Double-Layer Magnetic Fluid based on cobalt ferrite nanoparticles, in order to obtain the pH-dependence of the particle surface charge density. We propose a mechanism for the charging of the particle surface. This model considers the ferrofluid solution as a mixture of strong and weak diprotic acids. We show how an exact analytical treatment involving proton transfer between the particle surface and the bulk solution allows the construction of a speciation diagram of the charged superficial sites. The saturation value of the superficial density of charge is found to be equal to 0.326 ± 0.065 C m^-2. Received 9 May 2001 and Received in final form 17 July 2001     

Co-ion dependence of DNA nuclease activity suggests hydrophobic cavitation as a potential source of activation energy

The source of the activation energy that allows cutting of DNA by restriction enzymes is unclear. A systematic study of the cutting efficiency of the type-II restriction endonuclease EcoRI, with varying background electrolyte ion pair and buffer reported here, shows only a modest dependence of efficiency on cation type. Surprisingly, efficiency does depend strongly on the presumed indifferent anion of the background salt. What emerges is that competition between the background salt anion and the buffer anion for the enzyme and DNA surfaces is crucial. The results are unexpected and counterintuitive from the point of view of conventional electrolyte theory. However, taken together with recent developments in surface chemistry, the results do fall into place and could also suggest a novel mechanism for enzyme activity as an alternative to metal-activated hydrolysis: microscopic cavitation in a hydrophobic pocket might be the source of activation energy. Received 19 June 2000 and Received in final form 17 October 2000     

Momentum transfer theory of ion transport under the influence of resonant charge transfer collisions: the case of argon and neon ions in parent gases

Transport properties of ion swarms in presence of Resonant Charge Transfer (RCT) collisions are studied using Momentum Transfer Theory (MTT). It was shown that, not surprisingly, RCT collisions may be represented as a special case of elastic scattering. Using the developed MTT we tested a previously available anisotropic set of cross-sections for Ar+Ar ⁺ collisions by making the comparisons with the available data for the transverse diffusion coefficient. We also developed an anisotropic set of Ne+Ne ⁺ integral cross-sections based on the available data for mobility, longitudinal and transverse diffusion. Anisotropic sets of cross-sections are needed for Monte Carlo simulations of ion transport and plasma models. Received 16 June 2002 / Received in final form 2nd August 2002 Published online 24 September 2002 RID="a" ID="a"e-mail: vrhovac@phy.bg.ac.yu RID="b" ID="b"e-mail: zoran@phy.bg.ac.yu     

The osmotic coefficient of rod-like polyelectrolytes: Computer simulation, analytical theory, and experiment

The osmotic coefficient of solutions of rod-like polyelectrolytes is considered by comparing current theoretical treatments and simulations to recent experimental data. The discussion is restricted to the case of monovalent counterions and dilute, salt-free solutions. The classical Poisson-Boltzmann solution of the cell model correctly predicts a strong decrease in the osmotic coefficient, but upon closer look systematically overestimates its value. The contribution of ion-ion-correlations are quantitatively studied by MD simulations and the recently proposed DHHC theory. However, our comparison with experimental data obtained on synthetic, stiff-chain polyelectrolytes shows that correlation effects can only partly explain the discrepancy. A quantitative understanding thus requires theoretical efforts beyond the restricted primitive model of electrolytes. Received 25 July 2000 and Received in final form 4 December 2000     

Induced bubble shape oscillations and their impact on the rise velocity

When a 2-4 mm diameter bubble rising with constant velocity hits a thin wire, bubble shape oscillations can be induced. As a consequence also the bubble rise velocity strongly oscillates. With the help of a force balance we show that these velocity oscillations are an added-mass effect. Received 9 April 2002 / Received in final form 11 July 2002 Published online 14 October 2002 RID="a" ID="a"e-mail: lohse@tn.utwente.nl     

Morphologies of diblock copolymer thin films before and after crystallization

Spin-coated thin films of about 100nm of low-molecular-weight hydrogenated poly(butadiene-b- ethyleneoxide) (PB_h-PEO) diblock copolymers have been crystallized at various constant temperatures. Crystallization has been observed in real time by light microscopy. Detailed structural information was obtained by atomic force microscopy, mainly enabled by the large viscoelastic contrast between amorphous and crystalline regions. The behavior in thin films is compared to the bulk properties of the polymer. Crystallization started from an annealed microphase separated melt where optical microscopy indicated a lamellar orientation parallel to the substrate. A small difference in the length of the crystallizable block produced significantly different crystallization behavior, both in the bulk and in thin films. For thin films of the shortest diblock copolymer (45% PEO content) and for an undercooling larger than about 10 degrees, crystallization created vertically oriented lamellae. These vertical lamellae could be preferentially aligned over several micrometers when crystallization occurred close to a three-phase contact line. Annealing at temperatures closer to the melting point or keeping the sample at room temperature for several months allowed the formation of a lamellar structure parallel to the substrate. A tentative interpretation based on kinetically caused chain folding and relaxation within the crystalline state, with implications on general aspects of polymer crystallization, is presented. Received 19 March 1999 and Received in final form 14 December 1999     

Influence of saline and pH on collagen type I fibrillogenesis in vitro: fibril polymorphism and colloidal gold labelling

We have produced different collagen type I fibrils by in vitro fibrillogenesis of acetic acid-soluble collagen within the pH range 2.5-9.0, in the presence and absence of 150 mM NaCl. The varying relatively stable molecular assemblies and polymorphic fibrillar end-products produced after 24 h incubation have been assessed and compared by the TEM study of specimens negatively stained with uranyl acetate. In the presence of 150 mM NaCl, the assembly of collagen at low pH (2.5) leads to the formation of initial molecular aggregates that progressively link together at slightly higher pH (5.0) to form sub-fibrils and spindle-shaped D-banded bundles of sub-fibrils. At pH 6.0 these D-banded bundles aggregate into larger spindle-shaped fibrils with lateral misalignment of the D-banding across the bundle. However, at pH 7.0 and 8.0, in the presence of 150 mM NaCl, the characteristic parallel-sided mature D-banded collagen type I fibres are formed. At pH 9.0 more loosely formed parallel-sided D-banded collagen fibrils are present, within which the spindle-shaped sub-fibrils can be defined by negative staining more convincingly than at pH 7-8. In the presence of 50 mM buffer at pH 2.5, but absence of 150 mM NaCl, collagen type I forms disorganized periodic initial molecular aggregates, which have a tendency to link together to form sub-fibrils. Flexuous collagen type I sub-fibrils predominate at pH 5.0, alongside large spindle-shaped fibrils that possess a regular transverse approximately 10 nm periodicity, with an oblique approximately 67 nm periodicity, significantly different to the D-banding periodicity. At pH 7.0 and pH 8 in the absence of saline loosely-formed flexuous and spindle-shaped fibres co-exist, with underlying sub-fibrils visible, but at pH 9.0 only disorganized flexuous fibrillar aggregates are present. Colloidal gold labelling of the characteristic D-banded collagen type I fibrils with 5 nm and 2 nm chemically reactive gold particles reveals a periodic labelling pattern, which is not apparent with 10 nm and 15 nm gold particles, due to steric hindrance. The flexuous and spindle-shaped collagen fibrils also bind 2 nm gold particles in a specific manner. In all cases, the specific chemisorption of gold onto the collagen fibrils is probably determined by the availability of repeating amino acid side chains of the collagen molecules along the fibril surface. The controlled production of varying stable collagen type I fibrillogenesis products is likely to be of value within numerous areas of biotechnology, biology and medicine, including experimental biomineralization.     

An experimental confirmation of longitudinal electrodynamic forces

According to the conventional views of electromagnetic theory, as these are expressed in the Lorentz force law, all the forces which act on a current carrying metallic conductor are perpendicular to the current streamlines. However, over the years, from Ampère through Maxwell until the present day, there have been persistent claims that when current flows in a metallic conductor, there are mechanical forces acting along current streamlines which subject the conductor to tensile stress, and which are therefore capable of performing work in the direction of current flow. The problem of substantiating these claims has always lain in the difficulty of designing an experiment in which the effects are unambiguously demonstrated. The present paper describes an experiment which to a large extent removes these ambiguities, and which provides a compelling novel demonstration of forces acting along current streamlines. A force calculation based on Ampère's original electrodynamic force law is found to be consistent with the observed behaviour. Received 15 November 2000 and Received in final form 12 March 2001