Sprouting side chain conformations in X-PLOR simulations of peptides

A scheme for sprouting peptide side chains using X-PLOR is introduced using an example from the collagen system to show how reasonable starting structures for minimization studies may be created. © 1993 John Wiley & Sons, Inc.     

Effect of oxygen exposure on the magnetic properties of ultrathin Co/Ge(1 1 1) films

Influences of oxygen exposure on the magnetic properties of Co/Ge(1 1 1) ultrathin films have been investigated by surface magneto-optic Kerr effect technique. As the oxygen exposure increases on Co/Ge(1 1 1) films, their magnetic properties could be modified. As an example for 15 ML Co/Ge(1 1 1) films, the coercivity increases from 730 to 920 Oe and the remanence Kerr intensity is reduced for 500 Langmuir (L) of oxygen exposure. Corresponding compositions analyzed by Auger electron spectroscopy measurement shows that the amount of oxygen on the surface layers increases with increasing the oxygen exposure time. Oxygen distributes on the topmost layers of the film. The adsorbed oxygen influences the electronic density of states of Co and results in the changes of the magnetic properties. Besides, the appearance of O/Co/Ge interface could modify the stress anisotropy, and as a result the coercivity of ultrathin Co/Ge(1 1 1) film is enhanced.     

Fatty acid binding site of mitochondrial uncoupling protein UCP2 as probed by EPR spectroscopy of spin-labeled fatty acids

Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled fatty acids was used to investigate their interaction withEscherichia coli-expressed human mitochondrial uncoupling protein UCP2 refolded from inclusion bodies in nonaethylene glycol monododecyl ether (C₁₂E₉) micelles. 5-DOXYL-stearic acid and 4-PROXYL-palmitic acid bound to UCP2 exhibited additional clearly separated h_+1I, h_?1I “immobile” peaks in the low- and high-field region, respectively, separated by 42 and 44 Gauss, and extensively reduced h_+1M, h_?1M “mobile” peaks, separated by about 30 G, whereas with 7-DOXYL-stearic acid the I and M peaks were smoothed together into one wide peak. Competition of 4-PROXYL-palmitic acid with added palmitic acid, arachidonic acid, and all-cis-8,11,14-eicosatrienoic acid and of 7-DOXYL-stearic acid with arachidonic acid was indicated by the disappearance of the h_+1I, h_?1I “immobile” peaks, whereas redistribution in micelles without protein was indicated by the rising of the h_+1M, h_?1M “mobile” peaks. In conclusion, a competition of palmitic, arachidonic, and eicosatrienoic acid within a putative fatty acid binding site was observed for mitochondrial uncoupling protein UCP2. This finding together with the observation of EPR spectra of highly immobilized probes exclusively in the presence of the recombinant UCP2 suggest the existence of a fatty acid binding site on UCP2 which is a prerequisite of the fatty acid cycling mechanism as previously postulated for UCP1.     

Letters to the Editor

The Mathematical Intelligencer encourages comments about the material in this issue. Letters to the editor should be sent to either of the editors-in-chief, Chandler Davis or Marjorie Senechal.     

A novel specimen for investigating the mechanical behavior of elastomers under multiaxial loading conditions

In this paper we describe the design and manufacture of an axial-torsion test specimen, and provide relationships needed when conducting stress-strain characterization experiments with the specimen. The specimen is a short hollow cylinder of rubber bonded between two steel mounting rings, in which simultaneous axial and shear strains are produced via independently controlled axial and twist displacements. We present calculations for the strain-displacement and stress-load relationships, and strain energy density. These relationships have been established and validated via a combination of analytical and experimental techniques, and finite element analysis. We have investigated the extent and effects of strain and stress field non-uniformity in the test specimen. The specimen design is sufficiently simple that a closed-form expression for the strain-displacement relationship has been successfully developed.     

A dynamic finite volume scheme for large-eddy simulation on unstructured grids

In recent years there has been considerable progress in the application of large-eddy simulation (LES) to increasingly complex flow configurations. Nevertheless a lot of fundamental problems still need to be solved in order to apply LES in a reliable way to real engineering problems, where typically finite-volume codes on unstructured meshes are used. A self-adaptive discretisation scheme, in the context of an unstructured finite-volume flow solver, is investigated in the case of isotropic turbulence at infinite Reynolds number. The Smagorinsky and dynamic Smagorinsky sub-grid scale models are considered. A discrete interpolation filter is used for the dynamic model. It is one of the first applications of a filter based on the approach presented by Marsden et al. In this work, an original procedure to impose the filter shape through a specific selection process of the basic filters is also proposed. Satisfactory results are obtained using the self-adaptive scheme for implicit LES. When the scheme is coupled with the sub-grid scale models, the numerical dissipation is shown to be dominant over the sub-grid scale component. Nevertheless the effect of the sub-grid scale models appears to be important and beneficial, improving in particular the energy spectra. A test on fully developed channel flow at Re_τ = 395 is also performed, comparing the non-limited scheme with the self-adaptive scheme for implicit LES. Once again the introduction of the limiter proves to be beneficial.     

How many black holes fit on the head of a pin?

The Bekenstein–Hawking entropy of certain black holes can be computed microscopically in string theory by mapping the elusive problem of counting microstates of a strongly gravitating black hole to the tractable problem of counting microstates of a weakly coupled D-brane system, which has no event horizon, and indeed comfortably fits on the head of a pin. We show here that, contrary to widely held beliefs, the entropy of spherically symmetric black holes can easily be dwarfed by that of stationary multi-black-hole “molecules” of the same total charge and energy. Thus, the corresponding pin-sized D-brane systems do not even approximately count the microstates of a single black hole, but rather those of a zoo of entropically dominant multicentered configurations. Fourth Award in the 2007 Essay Competition of the Gravity Research Foundation.     

On the Zero-Energy-Limit Solution for the Modified Gross–Pitaevskii Equation

The modified Gross–Pitaevskii equation was derived and solved to obtain the 1D solution in the zero-energy limit. This stationary solution could account for the dominated contributions due to the kinetic effect as well as the chemical potential in inhomogeneous Bose gases.