Jakob Bohr

Role of attractive forces in tapping tip force microscopy

We present experimental and numerical results demonstrating the drastic influence of attractive forces on the behaviour of the atomic force microscope when operated in the resonant tapping tip mode in an ambient environment. It is often assumed that tapping is related to repulsive interaction. In contrast, we find that in general the attractive forces are the most dominant interaction in this mode of operation. We show that attractive forces in combination with the repulsive elastic type of forces cause points of instability in the parameter space constituted by: the cantilever swing amplitude, the frequency bias point, and the distance between the fixed end of the cantilever and the sample. These points of instability can result in disturbances during image acquisition on hard elastic surfaces.

Protein secondary structure and homology by neural networks The α-helices in rhodopsin

Neural networks provide a basis for semiempirical studies of pattern matching between the primary and secondary structures of proteins. Networks of the perceptron class have been trained to classify the amino‐acid residues into two categories for each of three types of secondary feature: α‐helix or not, β‐sheet or not, and random coil or not. The explicit prediction for the helices in rhodopsin is compared with both electron microscopy results and those of the Chou‐Fasman method. A new measure of homology between proteins is provided by the network approach, which thereby leads to quantification of the differences between the primary structures of proteins.

Prediction of protein secondary structure at 80% accuracy.

Secondary structure prediction involving up to 800 neural network predictions has been developed, by use of novel methods such as output expansion and a unique balloting procedure. An overall performance of 77.2%–80.2% (77.9%–80.6% mean per‐chain) for three‐state (helix, strand, coil) prediction was obtained when evaluated on a commonly used set of 126 protein chains. The method uses profiles made by position‐specific scoring matrices as input, while at the output level it predicts on three consecutive residues simultaneously. The predictions arise from tenfold, cross validated training and testing of 1032 protein sequences, using a scheme with primary structure neural networks followed by structure filtering neural networks. With respect to blind prediction, this work is preliminary and awaits evaluation by CASP4. Proteins 2000;41:17–20.

Magnetic rare earth superlattices

Abstract Advances in molecular beam epitaxy deposition techniques have recently made it possible to grow, an atomic plane at a time, single crystalline superlattices composed of alternating layers of a magnetic rare earth, such as Gd, Dy, Ho, or Er, and metallic Y, which has an identical chemical structure. The primary goal of this article is to review the new and interesting magnetic structures which have been discovered in these novel superlattice systems and to consider what implications the observed phases have on our understanding of the underlying microscopic magnetic interactions. In particular, the effects of the artificial periodicity or compositional modulation, finite layer thickness, and epitaxial strain on the resulting long range magnetic order of Gd-Y, Dy-Y, Ho-Y, Er-Y, and Gd-Dy superlattices are described.

Microwave enhanced kinetics observed in ORD studies of a protein

Microwaves are shown to affect the kinetics of conformational changes of the protein beta-lactoglobulin. Microwaves can accelerate conformational changes in the direction towards the equilibrium state. This applies both for the folding and the unfolding processes. Cold denaturing thermal unfolding of the proteins is accelerated by negative temperature gradients. Microwave irradiation of the protein solution heated it by about 0.3 degree, and hence the observed acceleration of denaturing is therefore non-thermal.

DIFFRACTION STUDIES OF RARE EARTH METALS AND SUPERLATTICES

We review the results of X-ray scattering studies of the rare earth metals and present related new results for superlattices and thin slabs. In rare earth crystals we have observed weak structural modulations which accompany the magnetic ordering. The wave length of this modulation can be derived from a spin-slip model in accordance with symmetry considerations. X-ray scattering of both the charge and magnetization density modulations allow for highly accurate determination of the magnetic wave vector. The physical basis of our discussion is given in the context of lattice modulations. The implications of these results for the understanding of magnetic structure of rare earth superlattices are also discussed in the light of recent neutron diffraction studies of holmium-yttrium superlattices. The effect of the finite size of the magnetic block in a superlattice is considered and it is shown that significantly different behavior than in bulk is expected. In particular it is found that for thin slabs the ferromagnetic phase has the lowest energy.

Phase Transformation in Solid C60/C70: An Electron Microscopy Study

Crystals of icosahedral C60/C70 clusters have been studied using electron diffraction and high-resolution electron microscopy. The as-grown crystals are found to be hexagonally close packed but with a lot of stacking defects. Under electron irradiation they transform into a face-centred cubic structure. Evidence is provided for a close mixture of C60 and C70.

Molecular ordering of ethanol at the calcite surface.

To produce biominerals, such as shells, bones, and teeth, living beings create organic compounds that control the growth of the solid phase. Investigating the atomic scale behavior of individual functional groups at the mineral-fluid interface provides fundamental information that is useful for constructing accurate predictive models for natural systems. Previous investigations of the activity of coccolith-associated polysaccharides (CAP) on calcite, using atomic force microscopy (AFM) [Henriksen, K., Young, J. R., Bown, P. R., and Stipp, S. L. S. Palentology 2004, 43 (Part 3), 725-743] and molecular dynamics (MD) modeling [Yang, M., Stipp, S. L. S., and Harding, J. H. Cryst. Growth Des. 2008, 8 (11), 4066-4074], have suggested that OH functional groups control polysaccharide attachment. The purpose of this work was to characterize, using X-ray reflectivity (XR) combined with molecular dynamics (MD) simulations, the structuring on calcite of a layer of the simplest carbon chain molecule that contains an OH group, ethanol (CH(3)-CH(2)-OH). We found evidence that EtOH forms a highly ordered structure at the calcite surface, where the first layer molecules bond with calcite. The ethanol molecules stand up perpendicularly at the interface or nearly so. As a consequence, the fatty, CH(3) ends form a new surface, about 6 Å from the termination of the bulk calcite, and beyond that, there is a thin gap where ethanol density is low. Following is a more disordered layer that is two to three ethanol molecules thick, about 14 Å, where density more resembles that of bulk liquid ethanol. The good agreement between theory and experiment gives confidence that a theoretical approach can offer information about behavior in more complex systems.

Magnetic rare-earth superlattices (invited)

The magnetic structures of several single‐crystal, magnetic rare‐earth superlattice systems grown by molecular‐beam epitaxy are reviewed. In particular, the results of recent neutron diffraction investigations of long‐range magnetic order in Gd‐Y, Dy‐Y, Gd‐Dy, and Ho‐Y periodic superlattices are presented. In the Gd‐Y system, an antiphase domain structure develops for certain Y layer spacings, whereas modified helical moment configurations are found to occur in the other systems, some of which are commensurate with the chemical superlattice wavelength. References are made to theoretical interaction mechanisms recently proposed to account for the magnetic states of these novel materials.

A symmetry principle for epitaxial rotation

Two-dimensional and three-dimensional crystals adsorbed on crystalline substrate are often observed to be rotated, in the plane of the interface, by some apparently arbitrary angle relative to high-symmetry directions of the substrate. In cases where the lattice mismatch between adsorbate and substrate can be varied, it is frequently found that the rotation angle varies with the mismatch. Theoretical explanations for this epitaxial rotation have focused on the elastic properties and on commensurate structures. Here, an alternative explanation is proposed, based on finite-size effects. The adsorbate rotations that result from such considerations agree exactly with a simple symmetry principle which, it is argued, underlies the phenomenon of epitaxial rotation.