[Show abstract][Hide abstract] ABSTRACT: The question of the value of the pitch angle of DNA is visited from the
perspective of a geometrical analysis of transcription. It is suggested that
for transcription to be possible, the pitch angle of B-DNA must be smaller than
the angle of zero-twist. At the zero-twist angle the double helix is maximally
rotated and its strain-twist coupling vanishes. A numerical estimate of the
pitch angle for B-DNA based on differential geometry is compared with numbers
obtained from existing empirical data. The crystallographic studies shows that
the pitch angle is approximately 38 deg., less than the corresponding
zero-twist angle of 41.8 deg., which is consistent with the suggested principle
[Show abstract][Hide abstract] ABSTRACT: A viscous tree arises when two plates sandwiching a fluid are being separated. By experimental investigations of such self-organized trees it is revealed that they originate from the competition for space between viscous fingers. Scaling properties are addressed and a computer simulation based on a phenomenological model is presented. If the two plates are separated rapidly (or in vacuum) cavitation appears leading to the formation of a foam. Cavitation is suggested as a possible mechanism for the formation of large-scale structure in the Universe.
[Show abstract][Hide abstract] ABSTRACT: In the present work we have applied the method of the EPR spin probes which allows performing simultaneously EPR and magnetization measurements to the investigation of magnetism of the Gd stearate Langmuir–Blodgett (LB) films. For this purpose we have prepared and studied by the EPR technique the Gd and Y stearate LB films. Placing the small BDPA crystal on the film surface we have found that for the Gd LB sample the effective g-value of the radical's resonance depends on the film orientation in respect to the external magnetic field direction. The relative shift of the EPR signal corresponded to the magnetization of the film along the field direction. Such effect has not been observed for the Y stearate LB film. The data obtained give an experimental proof for the room temperature magnetic ordering in the gadolinium stearate LB film.
Materials Science and Engineering C 12/2002; 22(2):201-207. · 2.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Comparative structural study of gadolinium stearate Langmuir–Blodgett (LB) films formed by monolayer deposition from either aqueous gadolinium acetate or gadolinium chloride solutions have been carried out. Structure of the films was characterized by X-ray diffraction, Fourier transform infrared spectroscopy, high-energy electron diffraction, atomic force microscopy and scanning electron microscopy. It was found that when subphase pH had a value at which all monolayer stearic acid molecules were ionized and bound with Gd3+ cations (pH>5), the LB films deposited from gadolinium acetate and gadolinium chloride subphases had substantially different structure. The gadolinium stearate LB films formed with gadolinium acetate subphase were highly ordered and consisted of hexagonal layers with unit cell parameter a≈4.8 Å and interlayer spacing d≈49 Å. LB films formed with GdCl3 subphase under the same conditions (salt concentration, pH) were characterized by a rather disordered structure where along with hexagonal phase, a monoclinic phase with the interlayer parameter d≈40 Å was present. The reason of this phenomenon is discussed. The data obtained indicate that the control of multivalent metal cations complexes formation in the subphase and at the monolayer surface can be an instrument for optimization, the conditions to form metal-containing LB film with regulated structure and properties.
Colloids and Surfaces A Physicochemical and Engineering Aspects 02/2002; · 2.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Magnetic, structural and electronic properties of Langmuir–Blodgett films with incorporated Gd3+ ions has been detected using a scanning DC SQUID microscope, scanning electron microscope and X-ray diffraction. The magnetic images of 28 and 50 layer thick films at 77 K have been obtained after in-plane and out-of-plane pre-magnetization in a field of 1.4 T at 300 K. Randomly placed “magnetic volcanos” with a remanent magnetic moment of the order of 10−13 A m2 was observed. A decay of the remanent magnetization with a characteristic time of about 120 h was observed. It is suggested that the magnetic order is relatively long ranged, and that topological defects (vortices) lead to the observed out-of-plane field lines, and are responsible for the magnetic volcanos. Finally, it is hypothesized that a similar topology of field lines is responsible for superconductivity as observed in ceramic high-TC superconductors.
Journal of Magnetism and Magnetic Materials 09/2001; · 2.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This paper presents a quantum description of L-alanine in aqueous solution predicting the Raman and Raman optical activity (ROA) spectra. We have investigated theoretically the chiral sensitive spectroscopic method of ROA as a probe for secondary structural features. We have utilized the Becke 3LYP/6-31G* description to determine the geometries and Hessians [Theoretical and Computational Genome Research, Plenum Press, New York, 1997, p. 225; J. Phys. Chem. B 102 (1998) 5899; Chem. Phys. 225 (2000) 165], and have calculated the Becke 3LYP/6-31G* level electric dipole–electric dipole polarizability derivatives. The electric dipole–magnetic dipole polarizability derivatives and electric dipole–electric quadrupole polarizability derivatives further required to obtain the ROA spectra have also been calculated. The Raman scattering and ROA spectral simulations for the various structures are compared with the experimentally measured spectra and previously reported spectral simulations. The combination of Raman and ROA spectroscopy is shown to be as sensitive to secondary structural changes as its sister combination of vibrational absorption and vibrational circular dichroism and thus offers a complementary source of information when investigating the secondary structural and chiral features of biomolecules.
[Show abstract][Hide abstract] ABSTRACT: 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 Structure Function and Bioinformatics 11/2000; 41(1):17-20. · 2.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This work is focused on the preparation and characterization of gadolinium-containing stearic acid (SA) Langmuir–Blodgett (LB) films. SA monolayer behavior on the gadolinium-containing aqueous subphase has been analyzed by thermodynamic measurements. The compression isotherm shape changed substantially under varying anion type at the constant rare-earth cation content and pH in aqueous subphase. Those changes were ascribed to different monolayer surface charging under gadolinium binding. Small angle X-ray diffraction was used to study the structure of formed multilayer rare-earth-containing LB films. Considerable structural defects in multilayer LB films were found when gadolinium chloride solution was exploited as aqueous subphase for LB film formation, caused presumably by electrostatic interactions under charged monolayer deposition. The use of monodentate complexions like acetic acid residue was proposed to form bulk phase low-charged complexes with trivalent cations. The electroneutral ligand exchange reactions of such complexes with fatty acid Langmuir monolayer results in the formation of quasi-neutral trivalent cation complexes bound to the monolayer surface. This approach allowed effective neutralization of the monolayer surface under gadolinium binding and formation of condensed monolayer below the triple-point temperature. The compression and subsequent deposition of such monolayers resulted in the formation of highly ordered LB films with high content of adsorbed gadolinium cations arranged in two-dimensional (2-D) monatomic layers.
Colloids and Surfaces A Physicochemical and Engineering Aspects 06/2000; 166(1):33-43. · 2.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially beta-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves hold promises for a wide range of biotechnological applications, such as protein synthesis, protein aggregation, etc., and may have implications for biological systems as well.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2000; 61(4 Pt B):4310-4. · 2.33 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The present invention relates to calculation of the structure and/or the structural, biological, chemical or physical features of chemical substances from their constituents, such as the features of proteins from their amino acid sequence. In a first aspect of the invention prediction is obtained by using a system comprising a plurality of prediction means, which method comprises using a plurality of different individual prediction means, such as at least (16), thereby providing an individual prediction of the set of features for each of the individual prediction means and predicting the set of features on the basis of combining the individual predictions. According to the invention the combining being performed in such a manner that the combined prediction is more accurate on a test set than substantially any of the predictions of the individual prediction means.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: We describe the preparation and characterization of rare-earth-containing stearic acid Langmuir–Blodgett (LB) films. Stearic acid monolayer behavior on the rare-earth-containing aqueous subphase has been analyzed by thermodynamic measurements. The monolayer compression isotherm shape changed substantially by varying the anion type at the constant rare-earth cation content and pH in aqueous subphase. The conditions necessary to form highly integrated mono- and multilayered rare-earth-containing LB films were investigated. The deposited mono- and multilayer gadolinium (Gd)-containing LB films were studied by scanning tunneling microscopy (STM) and electron paramagnetic resonance (EPR) techniques. The temperature dependence of EPR signal in Gd-containing LB films indicates the magnetic ordering with a characteristic temperature of transition to complete disordered paramagnetic state of about 500 K, significantly higher than Curie temperature in bulk metal Gd. Low-field hysteresis of microwave absorption was observed in these films and pointed out to the existence of remanence magnetism in created material.
Materials Science and Engineering C 12/1999; · 2.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We have applied a dc SQUID based microscope to study surface
magnetization of a Ho single crystal at 77 K in parallel (up to 0.4
kA/m) and perpendicular (up to 0.1 kA/m) magnetic fields. Magnetization
curves and the topographic maps of the magnetic field distribution near
the polished surface (0001) of the crystals have been recorded with a
spatial resolution better than 50 μm. Qualitative evidence for
ferromagnetic ordering at the (0001) surface have been found
IEEE Transactions on Applied Superconductivity 07/1999; · 1.32 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this paper we present a method for manipulating nanometer-sized particles on surfaces using a commercial atomic force microscope (AFM). A PC-mouse-based `click and move' manipulation scheme was implemented without the need for additional software or hardware development. The success of the scheme depends mostly on the choice of tip and cantilever which should be able to operate in both the contact mode and vibrating cantilever mode. Four different tip/cantilever combinations were tested and suitable types were found among those commercially available. The necessary properties are defined. The technique enables the fabrication of various kinds of two-dimensional structures of nanoparticles but may have relevance also to other areas of nanoscience, e.g. biotechnology. We developed the technique in order to study the magnetization of single nanoparticles using a very sensitive Hall micromagnetometer. The AFM is used as a tool to select and position a specific particle in the active region of the magnetometer.
[Show abstract][Hide abstract] ABSTRACT: Supercooling of crystalline bismuth inclusions in aluminium crystals has been observed and studied with different techniques: X-ray diffraction, in situ Rutherford backscattering/channelling spectrometry and transmission electron microscopy. The results of the measurements with different experimental methods (and on different samples) agree remarkably well. The inclusions melt at temperatures at or below the bismuth bulk melting point, and the solid/liquid phase transition exhibits a hysteresis of 100-150 K. Average inclusion sizes ranged from a few nm to some tens of nm. The X-ray diffraction melting data are discussed in relation to different existing models for the melting temperature of an inclusion as a function of its size. From this an approximate size distribution for the inclusions is derived.
Journal of Physics D Applied Physics 12/1998; 28(3):539. · 2.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A single crystal of a rare-earth random-site alloy, Ho0.5Er0.5, has been studied with X-ray diffraction. We have used the technique of resonance-enhanced scattering at the Ho and Er LIII absorption edges to study element-specific effects in the temperature dependence of the magnetic structure below the Neel temperature. In the highest-temperature phase, a c-axis modulated structure in which the Ho and Er moments take different tilt angles from the basal plane, measurements at the two edges show identical satellite positions. The lowest temperature phase, a conical spiral which locks to a structure with wavevector 9/40c* below 20 K, is accompanied by a basal-plane lattice modulation that is related to the magnetic structure. The modulation changes the symmetry of the crystal lattice; as a consequence we suggest that the magnetic structure locks to one with equidistant spin-slip discommensurations. In addition, we find an unusual energy and polarization dependence in the satellite intensity in this phase that is not seen at higher temperatures. We present arguments to demonstrate that the unusual behaviour is not accounted for by multiple-scattering events.
[Show abstract][Hide abstract] ABSTRACT: The magnetic properties of Au/Ni/Si(100) films with Ni thicknesses of 8–200 Å are studied at T=77 K using a scanning magnetic microscope with a thin-film high-temperature dc SQUID. It is found that the Ni films, with
an area of 0.6×0.6 mm, which are thicker than 26 Å have a single-domain structure with the magnetic moment oriented in the
plane of the film and a saturation magnetization close to 0.17 MA/m. For films less than 26 Å thick, the magnetization of
the film is found to drop sharply.
Physics of the Solid State 01/1998; 40(9):1530-1533. · 0.78 Impact Factor