Dendritic Actin Filament Nucleation Causes Traveling Waves and Patches

The polymerization of actin via branching at a cell membrane containing nucleation-promoting factors is simulated using a stochastic-growth methodology. The polymerized-actin distribution displays three types of behavior: a) traveling waves, b) moving patches, and c) random fluctuations. Increasing actin concentration causes a transition from patches to waves. The waves and patches move by a treadmilling mechanism which does not require myosin II. The effects of downregulation of key proteins on actin wave behavior are evaluated.Comment: 10 pages, 4 figure

Time-dependent hydrogen ionisation in the solar chromosphere. I: Methods and first results

An approximate method for solving the rate equations for the hydrogen populations was extended and implemented in the three-dimensional radiation (magneto-)hydrodynamics code CO5BOLD. The method is based on a model atom with six energy levels and fixed radiative rates. It has been tested extensively in one-dimensional simulations. The extended method has been used to create a three-dimensional model that extends from the upper convection zone to the chromosphere. The ionisation degree of hydrogen in our time-dependent simulation is comparable to the corresponding equilibrium value up to 500 km above optical depth unity. Above this height, the non-equilibrium ionisation degree is fairly constant over time and space, and tends to be at a value set by hot propagating shock waves. The hydrogen level populations and electron density are much more constant than the corresponding values for statistical equilibrium, too. In contrast, the equilibrium ionisation degree varies by more than 20 orders of magnitude between hot, shocked regions and cool, non-shocked regions. The simulation shows for the first time in 3D that the chromospheric hydrogen ionisation degree and electron density cannot be calculated in equilibrium. Our simulation can provide realistic values of those quantities for detailed radiative transfer computations.Comment: 8 pages, 7 figure

The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

A method for generating angular forces around $\sigma$-bonded transition metal ions is generalized to treat $\pi$-bonded configurations. The theoretical approach is based on an analysis of a ligand-field Hamiltonian based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which however requires very little increased in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are $\sigma$- or $\pi$-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%. The resulting force field is used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when $\pi$-bonded ligands are present.Comment: Latex source, 9 postscript figure

Convergence of density-matrix expansions for nuclear interactions

We extend density-matrix expansions in nuclei to higher orders in derivatives of densities and test their convergence properties. The expansions allow for converting the interaction energies characteristic to finite- and short-range nuclear effective forces into quasi-local density functionals. We also propose a new type of expansion that has excellent convergence properties when benchmarked against the binding energies obtained for the Gogny interaction.Comment: 4 pages, 3 figure

Order-N Density-Matrix Electronic-Structure Method for General Potentials

A new order-N method for calculating the electronic structure of general (non-tight-binding) potentials is presented. The method uses a combination of the ``purification''-based approaches used by Li, Nunes and Vanderbilt, and Daw, and a representation of the density matrix based on ``travelling basis orbitals''. The method is applied to several one-dimensional examples, including the free electron gas, the ``Morse'' bound-state potential, a discontinuous potential that mimics an interface, and an oscillatory potential that mimics a semiconductor. The method is found to contain Friedel oscillations, quantization of charge in bound states, and band gap formation. Quantitatively accurate agreement with exact results is found in most cases. Possible advantages with regard to treating electron-electron interactions and arbitrary boundary conditions are discussed.Comment: 13 pages, REVTEX, 7 postscript figures (not quite perfect

Morphology and Dynamics of the Low Solar Chromosphere

The Interferometric Bidimensional Spectrometer (IBIS) installed at the Dunn Solar Telescope of the NSO/SP is used to investigate the morphology and dynamics of the lower chromosphere and the virtually non-magnetic fluctosphere below. The study addresses in particular the structure of magnetic elements that extend into these layers. We choose different quiet Sun regions in and outside coronal holes. In inter-network regions with no significant magnetic flux contributions above the detection limit of IBIS, we find intensity structures with the characteristics of a shock wave pattern. The magnetic flux elements in the network are long lived and seem to resemble the spatially extended counterparts to the underlying photospheric magnetic elements. We suggest a modification to common methods to derive the line-of-sight magnetic field strength and explain some of the difficulties in deriving the magnetic field vector from observations of the fluctosphere.Comment: accepted by ApJ, 16 pages, 8 figure

Twisted flux tube emergence from the convection zone to the corona

3D numerical simulations of a horizontal magnetic flux tube emergence with different twist are carried out in a computational domain spanning the upper layers of the convection zone to the lower corona. We use the Oslo Staggered Code to solve the full MHD equations with non-grey and non-LTE radiative transfer and thermal conduction along the magnetic field lines. The emergence of the magnetic flux tube input at the bottom boundary into a weakly magnetized atmosphere is presented. The photospheric and chromospheric response is described with magnetograms, synthetic images and velocity field distributions. The emergence of a magnetic flux tube into such an atmosphere results in varied atmospheric responses. In the photosphere the granular size increases when the flux tube approaches from below. In the convective overshoot region some 200km above the photosphere adiabatic expansion produces cooling, darker regions with the structure of granulation cells. We also find collapsed granulation in the boundaries of the rising flux tube. Once the flux tube has crossed the photosphere, bright points related with concentrated magnetic field, vorticity, high vertical velocities and heating by compressed material are found at heights up to 500km above the photosphere. At greater heights in the magnetized chromosphere, the rising flux tube produces a cool, magnetized bubble that tends to expel the usual chromospheric oscillations. In addition the rising flux tube dramatically increases the chromospheric scale height, pushing the transition region and corona aside such that the chromosphere extends up to 6Mm above the photosphere. The emergence of magnetic flux tubes through the photosphere to the lower corona is a relatively slow process, taking of order 1 hour.Comment: 53 pages,79 figures, Submitted to Ap