Self-assembly and structure transformations in living polymers forming fibrils

The classical isodesmic one-dimensional model for equilibrium polymerization is generalized in order to describe self-assembly in systems forming fibrils. The model was applied to peptide solutions forming -sheet tapes which can further aggregate into stacks of various thickness: double tapes and fibrils (several double tapes stacked together). We found that in some cases the model yields several step-like transitions as the concentration increases: first from monomers to single or double tapes, and then to fibrils. The abruptness of the first transition is controlled by the free energy penalty for transformation of a peptide from random coil to a straight -strand conformation (the latter is characteristic for tapes). If both single and double tapes are allowed, the length of the aggregates after the first transition can be very large with high scission energies. For very low energies of attraction between double tapes, the transition from double tapes to fibrils happens separately (above the first transition), and it is even more abrupt and produces extremely long fibrils. The theoretical findings are used to extract the characteristic molecular parameters for the self-assembly of the de novo peptide DN1 forming polymeric -sheets in water. Received 28 June 1999     

The interplay between surface micro-topography and -mechanics of type I collagen fibrils in air and aqueous media: An atomic force microscopy study

Calf skin type I collagen fibrils were regenerated from acidic solution and imaged with contact mode atomic force microscopy in air, water, and buffer solution. When imaged in air at a contact force of 20-150 nN, collagen fibrils exhibited a distinct transverse banding pattern with a period of 65 nm, consisting of high ridges and shallow grooves. The force dependence of the images suggests that such banding pattern is attributed to the transverse contraction of the fibril upon dehydration during sample preparation, which reflects the tangential mass density across the fibril. Imaging in water and phosphate buffer solution at a contact force of 15-80 nN revealed hydrated collagen fibrils with smooth surfaces. The rigidity of the collagen fibrils decreased considerably upon hydration. Scanning the cantilever tip in an aqueous medium at a contact force of 90-280 nN enabled us to probe subunit arrangement in the bulk region of the collagen fibril. The results indicate that the molecular assembly in the hydrated fibril is akin to that in the intact form. The image resolution was improved by stabilizing the collagen molecules through crosslinking with glutaraldehyde, which served to resolve microfibril-like structure on the fibril surface. Received 28 March 2000 and Received in final form 15 June 2001     

Unfolding and Fibrillogenesis of Insulin: Temperature,Pressure and Chemistry

Protein folding or unfolding can lead to the population of intermediates or partially unfolded conformations that have a high aggregation tendency. Some of these states associate in vivo to form fibrillar structures. These fibrils are the hallmark of molecular diseases such as Alzheimer's disease. It has been suggested that in vitro fibril formation is a generic property of all proteins. Insulin has been chosen as a model protein to study the process of fibrillation with Fourier-transform infrared spectroscopy. It is found that the formation of fibrils is preceded by amorphous aggregation. We also investigated the effect of hydrostatic pressure on insulin fibrils. The observed spectral changes are interpreted in terms of fibril dissociation into protofilaments. Preliminary results indicate that pressure is an interesting tool to characterize the interactions that maintain the fibril structure.     

Structural phase transition in FeBO under pressure

Using the density functional theory the structural and magnetic properties of iron borate under high pressure have been studied. At about P = 22.7 GPa a first order phase transition to the phase described by the same space group Rc has been found. The phase transition is accompanied by a 9% volume change of the unit cell, a four times decrease of the magnetic moment on Fe, an increase of the charge density at Fe, and a disappearance of the energy gap in the electronic density of states. Received 21 September 2001 and Received in final form 6 January 2002 Published online 6 June 2002     

Elasticity theory of a twisted stack of plates

We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a macroscopic elasticity theory of DNA to four. We derive an effective twist-stretch energy in terms of the macroscopic stretch along and relative excess twist about the DNA molecular axis. In addition to the bulk stretch and twist moduli found previously, we obtain a twist-stretch modulus with the following remarkable properties: 1) it vanishes when the radius of the helical curve following the geometric center of each plate is zero, 2) it vanishes with the elastic constant K₂₃ that couples compression normal to the plates to a shear strain, if the plates are perpendicular to the molecular axis, and 3) it is nonzero if the plates are tilted relative to the molecular axis. This implies that a laminated helical structure carved out of an isotropic elastic medium will not twist in response to a stretching force, but an isotropic material will twist if it is bent into the shape of a helix. Received: 4 July 1997 / Received in final form: 16 October 1997 / Accepted: 21 October 1997     

A chiral axial next nearest neighbour xy-model for antiferroelectric liquid crystals

We describe a chiral axial next nearest neighbour xy-model to account for the various subphases exhibited by antiferroelectric liquid crystals made of chiral rod-like molecules. The assumed form of the interlayer interactions is based on physical processes which are discussed. Using a discrete model, the predicted sequence of transitions is SmA-SmC-SmC-FI_H-FI_I-FI_L-SmC ^* A, where FI stands for a ferriphase, as seen in many compounds. The ferri and SmC phases are characterized by relatively large angles between the c-vectors of successive layers and occur only when the compounds have high optical purity. The calculated field induced structures exhibit a plateau of the apparent tilt angle at , where is the tilt angle of the molecules in the ferriphase. The conoscopic figures in the presence of a field and ellipsometric parameters in the absence of a field have also been generated, which agree extremely well with the experimental results. Recent anomalous X-ray scattering studies prove the xy-character of the configurations, though the commensurate structures that are found in the ferriphase require an extension of the model to include lock-in terms. Received 23 August 1999     

Electric birefringence study of an amyloid fibril system: The short end of the length distribution

In this article, a system of amyloid fibrils, based on the protein β-lactoglobulin, is studied by transient electric birefringence. Single pulses of an electric field were applied to the solution, and the initial rise and subsequent decay of birefringence analysed. The decay takes place on a range of relaxation times, and therefore contains information about the length distribution of fibrils in the system. The information can be extracted using theories of the electric polarisability of polyelectrolyte rods, since the fibrils are an example of these. Despite the long-standing complications of such theories, useful quantitative information about the system can still be obtained. Using the Fixman model of polyelectrolyte polarisability, we obtain a measurement of the short end of the length distribution which shows the fibril concentration as a function of length rising linearly from 0.02-2 μm. The short end of the length distribution was unobtainable in our previous study using rheo-optics (S.S. Rogers et al., Macromolecules 38, 2948 (2005)), but reasonable agreement between the two techniques shows they are complementary.     

A multispectrum fitting procedure to deduce molecular line parameters: Application to the 3-0 band of 12 C 16 O

To deduce accurate infrared molecular line parameters (positions at zero pressure, pressure-shifting and pressure-broadening coefficients, collisional narrowing coefficients, and intensities) from rovibrational spectra, an automatic method based upon a multispectrum fitting procedure has been set up, able to treat simultaneously several laboratory Fourier transform spectra. A validation of this method, using absorption spectra of the 3-0 vibrational band of CO around 6 350 cm^-1, already used to measure line intensities and self-broadening coefficients, is presented, and the advantages of the method are pointed out. The self-collisional narrowing of CO was observed and determined for the first time in Fourier transform spectra: β = 0.028±0.004 cm^-1 atm^-1 at about 296 K. Received 21 September 2000 and Received in final form 15 January 2001     

Simple model for attraction between like-charged polyions

We present a simple model for the possible mechanism of appearance of attraction between like charged polyions inside a polyelectrolyte solution. The attraction is found to be short ranged, and exists only in the presence of multivalent counterions. It is produced by the correlations in layers of condensed counterions surrounding each polyion and is only weakly temperature dependent. We find the attraction to be maximum at zero temperature and dimish as the temperature is raised. The attraction is only possible if the number of condensed counterions exceeds the threshold, , where is the valence of counterions and Z is the polyion charge. Received 10 March 1999 and Received in final form 20 April 1999     

Pseudo-gap and possible Spin-Peierls transition in the vanadium oxide VOSb 2 O 4

We report on the magnetic susceptibility and electron spin resonance measurements on polycrystalline samples of the vanadium oxide VOSb₂O₄, a quasi-one-dimensional S = 1/2 Heisenberg system. The susceptibility vanishes at zero temperature, but there is no cusp at the onset of the susceptibility drop, and the ESR linewidth exhibits an increase characteristic of a phase transition at a much lower temperature. We show that this behaviour is consistent with the formation of a pseudo-gap in a spin-Peierls system in the adiabatic limit. Received 7 February 2001 and Received in final form 24 April 2001     

Cusp satellite bands in the spectrum of molecule

We report measurements and a theoretical explanation of the cusp-shaped satellite bands in the blue wing of the cesium D₂ resonance line which have been observed for the first time. The bands are identified as transitions where the upper state dissociates into the 6 ²P _3/2 + 6 ² S _1/2 atomic asymptote. The experiment has been performed using a standard absorption setup, computer controlled data acquisition and computer data processing. We have shown that the peculiar shape of the difference-potential curve is solely responsible for the spectrum containing the cusp-shaped satellite bands. The appearance of these satellite bands has been discussed and explained relating the theory of satellite bands to the catastrophe theory. The shape of the line wing and of the satellite bands have been calculated using the Fourier transform technique. To ensure a more stringent comparison between the experimental and the theoretical spectrum, we have analyzed and compared the derivatives of the measured and the calculated satellite band shape. On the contrary to the customary direct comparison between the measured and the calculated absorption coefficient, the derivative clearly shows all differences and resemblances between satellite band profiles. The degree of coincidence of the experimentally observed and the theoretically calculated satellite band shape can be used as an ultimate check on the assessment of the quality of potential-energy curves involved in the formation of satellite bands. Received: 1 October 1997 / Revised: 14 January 1998 / Accepted: 24 February 1998     

Precise measurement of hyperfine coupling in CH F based on nuclear spin conversion

A new method is proposed for the experimental determination of the hyperfine coupling in molecules. The method is based on the level-crossing effect in the spin isomer conversion in alternating electric fields. An experiment performed with the ¹³CH₃F molecules has revealed the strength of the off-diagonal in K () nuclear spin-spin coupling kHz, which is only by kHz larger than the theoretical value calculated on the basis of the molecular structure. Received 25 January 2000 and Received in final form 11 May 2000     

Nuclear effects and higher twists in F3 structure function

We analyze the CCFR collaboration iron target data on the xF₃ structure function making particular emphasis on the extraction of the higher twist contributions from the data. Corrections for nuclear effects are applied in order to extract data on the structure function of the isoscalar nucleon. Our analysis confirms the observation made earlier, that the higher twist terms depend strongly on the level to which QCD perturbation theory analysis is applied. We discuss the impact of nuclear effects on the higher twist term as well as on the QCD scale parameter extracted from the fit to data. Received: 4 August 2000 / Accepted: 17 September 2000     

Dynamics of isolated twin boundary in (TMTSF)

Intermittent and irregular motion of isolated twin boundary (kink) in organic crystal (TMTSF)₂PF₆ was studied at room temperature. Both the local velocity and the time of intermission are determined not only by external stress and temperature but also by the time (t w) elapsed after the backward passage and before the following forward one. When the kink moves after longer t w, its velocity becomes smaller and the time of intermission longer. Both tend to saturate for t w longer than 10² s. This result indicates that some disorder is induced in the lattice by the backward motion and it is relaxed during t w. We also found that the effect of the backward motion of one kink on its following motion is equivalent quantitatively to that of the forward motion of the pair-created counterpart. Received: 14 April 1998 / Received in final form and Accepted: 1st September 1998     

Formation of cold Cs ground state molecules through photoassociation in the pure long-range state

We report on the formation of translationally cold Cs₂ ground state molecules through photoassociation in the 1_u attractive molecular state below the 6 s _1/2 +6 p _3/2 dissociation limit. The cold molecules are obtained after spontaneous decay of photoassociated molecules in a MOT and in a dark SPOT. We also used polarized atoms, in the f =3, m f =+3Zeeman ground state. Purely asymptotic and adiabatic calculations including hyperfine interaction and rotation are in excellent agreement with observed structures. As expected, the 1_u state is actually a pure long-range state, consisting of paired atoms, uniquely linked by the first terms of the multipole expansion of the electrostatic interaction. A temperature of 20 K has been measured for the molecular cloud. Received 19 July 1999     

Effects of properties of the surfactant on its aggregate behavior

The effects of the solvent-surfactant interaction, chain length and stiffness of surfactants on the formation of aggregates and the aggregation degree of surfactants in the two-dimension solution have been investigated using discontinuous molecular-dynamics simulations. When the tail-water repulsion increases or the head-water attraction decreases, the aggregation degree increases. Increasing the chain length and raising the stiffness of surfactants lead to the increment of the aggregation degree. Received 25 July 2001 and Received in final form 7 May 2002     

Encapsulation of filaments of a self-assembling bicopper complex in polymer nanowires

We report on the preparation conditions and the characterization by calorimetry and small-angle neutron scattering of a molecular composite material obtained via the heterogeneous nucleation of the fibrils of a thermoreversible gel. This physical process allows encapsulation of monomolecular filaments of a self-assembling bicopper complex into nanosized polymer fibrils. Due to the existence of 1-D arrangements of copper atoms, this material may possess unusual magnetic properties (spin ladders). Received 20 January 1999 and Received in final form 14 May 1999     

Pattern formation in the reaction with anisotropic lateral adsorbate-adsorbate interactions

We present Monte Carlo simulations of the formation of (1×2) islands in the case of the 2 A + B ₂ → 2 AB reaction occurring via the Langmuir-Hinshelwood mechanism on a square lattice under steady-state conditions. The model employed takes into account the effect of anisotropic lateral B-B interactions on the rates of B diffusion and elementary reaction events. The results obtained with qualitatively realistic ratio of the rate of elementary reaction steps indicate that the average island size depends on the details of diffusion and reaction dynamics in a similar way as in the earlier studied case of the simplest A + B reaction running via the Eley-Rideal mechanism. Received 4 January 2002 and Received in final form 2 April 2002 Published online 25 June 2002