Predicting the onset of DNA supercoiling using a non-linear hemitropic elastic rod

Elastic rod models provide a means to interpret single molecule DNA experiments as well as predict DNA behavior under physiological conditions. Here we use an elastic rod model to predict the stability boundary (critical torque vs. applied tension) for single molecule DNA experiments in which the molecule is subjected to applied tension and twist. We discuss the shortcomings of the usual isotropic rod model. We then derive a consistent non-linear material law from the general representation for a hemitropic (chiral) rod. Finally, we present results of a standard bifurcation analysis predicting the stability boundary. We find results from the non-linear hemitropic rod to match the data closely.     

Geometry and electronic structure of a heterometallic cluster Mo<Subscript>2</Subscript>Mg<Subscript>2</Subscript> in different oxidation states of Mo: a DFT study

Reduction of tetranuclear heterometallic complex Mo₂Mg₂ was simulated using the B3LYP and PBE density functional methods. The results of geometry calculations of the initial complex [Mo^VIO₂Mg(MeOH)₂(OMe)₄]₂ and a partially reduced Mo^V complex are in good agreement with experimental data. The reduced Mo^III complex is characterized by a decrease in the binding energy of aqua ligands. Structural rearrangement of the complex with release of a coordination position at the Mo atoms requires small energy expenditure. One can assume that the reduction of the polynuclear complex causes overcrowding of its coordination sphere, which favors formation of dinitrogen complexes. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 441–457, March, 2008.     

Operator‐splitting method for the analysis of cavitation in liquid‐lubricated herringbone grooved journal bearings

This paper presents an operator‐splitting method (OSM) for the solution of the universal Reynolds equation. Jakobsson–Floberg–Olsson (JFO) pressure conditions are used to study cavitation in liquid‐lubricated journal bearings. The shear flow component of the oil film is first solved by a modified upwind finite difference method. The solution of the pressure gradient flow component is computed by the Galerkin finite element method. Present OSM solutions for slider bearings are in good agreement with available analytical and experimental results. OSM is then applied to herringbone grooved journal bearings. The film pressure, cavitation areas, load capacity and attitude angle are obtained with JFO pressure conditions. The calculated load capacities are in agreement with available experimental data. However, a detailed comparison of the present results with those predicted using Reynolds pressure conditions shows some differences. The numerical results showed that the load capacity and the critical mass of the journal (linear stability indicator) are higher and the attitude angle is lower than those predicted by Reynolds pressure conditions for cases of high eccentricities. Copyright © 2004 John Wiley & Sons, Ltd.     

Model based online diagnosis of unbalance and transverse fatigue crack in rotor systems

A model based technique for online identification of malfunctions in rotor systems is discussed. Presence of fault changes the dynamic behavior of the system. This change is taken into account by equivalent loads acting on the undamaged system model. Equivalent loads are fictitious forces and moments acting on the undamaged system model, which generate a dynamic behavior identical to that of the real damaged system. The mathematical representation of equivalent loads is referred to as Fault Model. The work focuses on developing a fault model for a transverse fatigue crack in shaft and testing it through simulated studies. The basic principle of the technique is validated for unbalance identification, through numerical simulations as well as by experiments on a real rotor system.     

Effect of lattice deformation and phase transitions on the electronic spectra of TlGaS<Subscript>2</Subscript>, TlGaSe<Subscript>2</Subscript>, and TlInS<Subscript>2</Subscript> layered semiconductors

The effect of the lattice deformation on the electronic spectra of TlGaS₂, TlGaSe₂, and TlInS₂ layered semiconductor crystals is analyzed. It is shown that changes in the band gap of these semiconductors due to thermal expansion and a change in the composition under hydrostatic or uniaxial pressure can be described within a unified model of the deformation potential. The main feature of this model is the inclusion of deformation potentials with different signs, which is characteristic of other semiconductors with a layered structure. An analysis of the lattice deformation of the studied semiconductors in terms of the proposed model of the deformation potential has revealed that, in the immediate vicinity of the phase transitions, the crystal lattice under pressure undergo an unusual deformation.     

Efficient discretization of pressure‐correction equations on non‐orthogonal grids

An alternative discretization of pressure‐correction equations within pressure‐correction schemes for the solution of the incompressible Navier–Stokes equations is introduced, which improves the convergence and robustness properties of such schemes for non‐orthogonal grids. As against standard approaches, where the non‐orthogonal terms usually are just neglected, the approach allows for a simplification of the pressure‐correction equation to correspond to 5‐point or 7‐point computational molecules in two or three dimensions, respectively, but still incorporates the effects of non‐orthogonality. As a result a wide range (including rather high values) of underrelaxation factors can be used, resulting in an increased overall performance of the underlying pressure‐correction schemes. Within this context, a second issue of the paper is the investigation of the accuracy to which the pressure‐correction equation should be solved in each pressure‐correction iteration. The scheme is investigated for standard test cases and, in order to show its applicability to practical flow problems, for a more complex configuration of a micro heat exchanger. Copyright © 2003 John Wiley & Sons, Ltd.     

Thickness decrease of a grafted polyelectrolyte membrane exposed to shear flow

The effect of the shear flow on the thickness change of a polyelectrolyte membrane grafted onto a glass substrate was directly investigated with a flow cell combined with a confocal laser scanning microscope. The membrane thickness decreased proportionally to an increase in the shear stress of the flow when the shear rate exceeded a critical value of 1 s^?1. The higher the ionic strength was of the fluid, the greater the thinning effect was. The correlation between the critical shear rate and the relaxation of the polymer in the gel membrane was examined. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2808–2815, 2003     

Adsorption of the Cu<Superscript>2+</Superscript> ions from aqueous solutions on the active carbon oxidized with hydrogen peroxide and impregnated with nitrogen-containing compounds

Adsorption of the copper ions from aqueous solutions, benzene, and water on the active carbon obtained by chemical activation from walnut shells was studied. The active carbon was additionally oxidized with hydrogen peroxide and then impregnated with nitrogen-containing compounds. As a result of impregnation with melamine, a secondary porosity is formed within the oxidized active carbon, leading to an increase in the specific surface of the sorbent. A modified carbon surface is heterogeneous, and the carbons themselves exhibit catalytic activity in the oxidation of luminol and decomposition of hydrogen peroxide.