Henrik Bohr

Large scale biomimetic membrane arrays

AbstractTo establish planar biomimetic membranes across large scale partition aperture arrays, we created a disposable single-use horizontal chamber design that supports combined optical–electrical measurements. Functional lipid bilayers could easily and efficiently be established across CO2 laser micro-structured 8u2009×u20098 aperture partition arrays with average aperture diameters of 301u2009±u20095xa0μm. We addressed the electro-physical properties of the lipid bilayers established across the micro-structured scaffold arrays by controllable reconstitution of biotechnological and physiological relevant membrane peptides and proteins. Next, we tested the scalability of the biomimetic membrane design by establishing lipid bilayers in rectangular 24u2009×u200924 and hexagonal 24u2009×u200927 aperture arrays, respectively. The results presented show that the design is suitable for further developments of sensitive biosensor assays, and furthermore demonstrate that the design can conveniently be scaled up to support planar lipid bilayers in large square-centimeter partition arrays.n FigureFluorescent image of a large 24u2009×u200924 rectangular bilayer array

An update of the DEF database of protein fold class predictions

An update is given on the Database of Expected Fold classes (DEF) that contains a collection of fold-class predictions made from protein sequences and a mail server that provides new predictions for new sequences. To any given sequence one of 49 fold-classes is chosen to classify the structure related to the sequence with high accuracy. The updated prediction system is developed using data from the new version of the 3D-ALI database of aligned protein structures and thus is giving more reliable and more detailed predictions than the previous DEF system.

Color-symmetric superconductivity in a phenomenological QCD model

In this paper, we construct a theory of the NJL type where superconductivity is present, and yet the superconducting state remains, in the average, color symmetric. This shows that the present approach to color superconductivity is consistent with color singletness. Indeed, quarks are free in the deconfined phase, but the deconfined phase itself is believed to be a color singlet. The usual description of the color superconducting state violates color singletness. On the other hand, the color superconducting state here proposed is color symmetric in the sense that an arbitrary color rotation leads to an equivalent state, with precisely the same physical properties.

Exact solutions to a schematic nuclear quark model and colorless superconductivity

Exact solutions are found to the equations of a standard nuclear quark model exemplified by the Bonn model which is defined in terms of an effective pairing force. We show, by symmetry arguments, that, in general, the ground state of this model is not color neutral. In particular, color-neutral states have, in general, higher energy than the ground state. A novel BCS-type formalism, which is able to describe exactly color symmetrical BCS states, is used to show that the model admits, but only as excited states, color-neutral superconductivity. Therefore, such a model, with just a pairing force, is unrealistic as a model for the color-neutral confined phase which prevails at normal nuclear densities. Finally, the paper shows that there exists a color-neutral superconducting phase independently of whether the model is based on the pairing force or a more realistic three-body string force.

EXCITED STATE PROCESSES IN PHOTOSYNTHESIS MOLECULES

A study of electronic processes in the chlorophyll and carothenoid molecules of the photo-reaction center II is presented with the focus on the electronic excitations and charge transfer in the photosynthetic process. Several novel ideas are mentioned especially concerning the electron replenishment and nuclear vibrational excitations. The study is build mainly on numerical quantum calculations of electronic structures of molecules in the photo-reaction center.

Protein-induced bilayer perturbations: Lipid ordering and hydrophobic coupling.

The host lipid bilayer is increasingly being recognized as an important non-specific regulator of membrane protein function. Despite considerable progress the interplay between hydrophobic coupling and lipid ordering is still elusive. We use electron spin resonance (ESR) to study the interaction between the model protein gramicidin and lipid bilayers of varying thickness. The free energy of the interaction is up to -6kJ/mol; thus not strongly favored over lipid-lipid interactions. Incorporation of gramicidin results in increased order parameters with increased protein concentration and hydrophobic mismatch. Our findings also show that at high protein:lipid ratios the lipids are motionally restricted but not completely immobilized. Both exchange on and off rate values for the lipid<-->gramicidin interaction are lowest at optimal hydrophobic matching. Hydrophobic mismatch of few A results in up to 10-fold increased exchange rates as compared to the optimal match situation pointing to the regulatory role of hydrophobic coupling in lipid-protein interactions.

IMPLICATIONS OF RELATIVISTIC CONFIGURATIONS AND BAND STRUCTURES IN THE PHYSICS OF BIO-MOLECULES AND SOLIDS

Beyond the second row of elements in the Mendeleev periodic table, the consideration of the relativistic effect is important in determining proper configurations of atoms and ions, in many cases. Many important quantities of interest in determining physical and chemical properties of matter, such as the effective charge, root mean square radii, and higher moments of radii used in many calculations, e.g. in the determinations of legend stabilization bond energies depend on whether the treatment is relativistic or not. In general, these quantities for a given l-orbital having two different j-values, e.g. and , differ from each other, hence, making it necessary to treat them as separate orbitals. This also necessitates characterizing bands with their j-values in many instants and not l-values, particularly for “d” and f-orbitals. For example, in Au, and are to be dealt with as two distinct bands. The observed enhancement of laser induced field emission in W, which is not understood in terms of non-relativistic band-structures, can be explained in terms of the expected relativistic band structure. Spin-orbit coupling, which is the manifestation of the relativistic effect, is a prime factor in facilitating intersystem crossing in bio-molecules.

Condensed matter physics of biomolecule systems in a differential geometric framework

In this contribution biomolecular systems are analyzed in a framework of differential geometry in order to derive important condensed matter physics information. In the first section lipid bi-layer membranes are examined with respect to statistical properties and topology, e.g. a relation between vesicle formation and the proliferation of genus number. In the second section differential geometric methods are used for analyzing the surface structure of proteins and thereby understanding catalytic properties of larger proteins.