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.     

Study on Inhibitors of Methionine Synthase Ⅷ: Synthesis of 2,5-Diamino-4-oxo-6- (3-butenyl) pyrimidine

Cobalamin-dependent methionine synthase plays a crucial role in folate metabolism and such would appear to be an excellent target for rational antifolate drug design. However, to date, no anticancer agents directed at this enzyme are available, but the enzyme is efficiently and specifically inhibited by N2O and this has proven invaluable for evaluating the biochemical consequence of enzyme inhibition and for mechanistic studies. [1,2] 2,5-Diamino-4-oxo-6-(3-butenyl) pyrimidine, a key intermediate in synthetic inhibitors of methionine synthase, was first synthesized using γbutenyl-β-ketoester and guanidine carbonate (Scheme 1). [3]     

Basins of Attraction of Periodic Oscillations in Suspension Bridges

We consider the dynamics of the lowest order transversal vibration mode of a suspension bridge, for which the hangers are treated as one-sided springs, according to the model of Lazer and McKeena [SIAM Review 58, 1990, 537]. We analyze in particular the multi-stability of periodic attractors and the basin of attraction structure in phase space and its dependence with the model parameters. The parameter values used in numerical simulations have been estimated from a number of bridges built in the United States and in the United Kingdom, thus taking into account realistic, yet sometimes simplified, structural, aerodynamical, and physical considerations.     

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.     

Dynamics of capture and fusion in heavy ion collisions

The effect of entrance channel on decrease of the complete fusion cross sections and on the yield of reaction products are associated with the quasifission which depends on the mass asymmetry and shell structure of colliding nuclei. In reactions of massive projectile and target nuclei, the competition between complete fusion and quasifission appears at the stage of compound nucleus formation, in addition to the increase of the fission probability. It is shown that the yield of quasifission products may be symmetric or asymmetric in dependence on peculiarities of shell structure of reaction fragments. Marima of mass or charge distributions are connected with the peculiarities of shell structure of reaction fragments.     

X-ray damage characterization in BaLiF3,KMgF3 and LiCaAlF6 complex fluorides

Two-inch sized KMgF₃,BaLiF₃ and LiCaAlF₆ (LiCAF) single crystals were grown by the Czochralski method under a CF₄ atmosphere. X-ray irradiation was used to carry out a comparative study of induced optical absorption phenomena and colour centre creation in the ultra-violet and visible spectral regions. The integral of the induced absorption spectra is significantly lower in LiCAF with respect to the other studied materials. It is found that the amplitude of the F-absorption band is suppressed more than a factor of 3 by Mg-doping. For Mg-doped crystals, the optimum doping concentration is about 0.2 mol% of Mg²⁺.     

Infrared facility at the Canadian light source

The Canadian Light Source (CLS) is constructing two beamlines for Infrared Spectroscopy using synchrotron radiation (IRSR). One will supply mid-Infrared (2–25 μ) light to a Fourier Transform Infrared (FTIR) spectrometer and microscope for biological applications. The second will have a high resolution FTIR spectrometer for gas-phase and surface spectroscopy in the far-Infrared (beyond 25 μ). The Infrared beamlines will use dipole bending magnet radiation from a special bend magnet port design which provides a 50 mrad square acceptance. Issues with the first mirror and photon mask design, as well as the beamline layout and features are discussed.