Exact and Approximate Stochastic Simulation of Intracellular Calcium Dynamics

In simulations of chemical systems, the main task is to find an exact or approximate solution of the chemical master equation (CME) that satisfies certain constraints with respect to computation time and accuracy. While Brownian motion simulations of single molecules are often too time consuming to represent the mesoscopic level, the classical Gillespie algorithm is a stochastically exact algorithm that provides satisfying results in the representation of calcium microdomains. Gillespie's algorithm can be approximated via the tau-leap method and the chemical Langevin equation (CLE). Both methods lead to a substantial acceleration in computation time and a relatively small decrease in accuracy. Elimination of the noise terms leads to the classical, deterministic reaction rate equations (RRE). For complex multiscale systems, hybrid simulations are increasingly proposed to combine the advantages of stochastic and deterministic algorithms. An often used exemplary cell type in this context are striated muscle cells (e.g., cardiac and skeletal muscle cells). The properties of these cells are well described and they express many common calcium-dependent signaling pathways. The purpose of the present paper is to provide an overview of the aforementioned simulation approaches and their mutual relationships in the spectrum ranging from stochastic to deterministic algorithms

One-dimensional dynamics of the d-electrons in α′\alpha'-NaV2_{2}O5_{5}

We have studied the electronic properties of the ladder compound $\alpha'$-NaV$_{2}$O$_{5}$, adopting a joint experimental and theoretical approach. The momentum-dependent loss function was measured using electron energy-loss spectroscopy in transmission. The optical conductivity derived from the loss function by a Kramers-Kronig analysis agrees well with our results from LSDA+U band-structure calculations upon application of an antiferromagnetic alignment of the V~3$d_{xy}$ spins along the legs and an on-site Coulomb interaction U of between 2 and 3 eV. The decomposition of the calculated optical conductivity into contributions from transitions between selected energy regions of the DOS reveals the origin of the observed anisotropy of the optical conductivity. In addition, we have investigated the plasmon excitations related to transitions between the vanadium states within an effective 16 site vanadium cluster model. Good agreement between the theoretical and experimental loss function was obtained using the hopping parameters derived from the tight binding fit to the band-structure and moderate Coulomb interactions between the electrons within the ab plane.Comment: 23 pages, 8 figures; submitted to PR

Enhancement of Anisotropy due to Fluctuations in Quasi-One-Dimensional Antiferromagnets

It is shown that the observed anisotropy of magnetization at high magnetic fields in RbMnBr3 , a quasi-one-dimensional antiferromagnet on a distorted stacked triangular lattice, is due to quantum and thermal fluctuations. These fluctuations are taken into account in the framework of linear spin-wave theory in the region of strong magnetic fields. In this region the divergent one-dimensional integrals are cut off by magnetic field and the bare easy-plane anisotropy. Logarithmical dependence on the cutoff leads to the "enhancement" of the anisotropy in magnetization. Comparison between magnetization data and our theory with parameters obtained from neutron scattering experiments has been done.Comment: 15 pages + 5 postscript figures available upon request, RevTex

Charge order and low frequency spin dynamics in lanthanum cuprates revealed by Nuclear Magnetic Resonance

We report detailed 17O, 139La, and 63Cu Nuclear Magnetic Resonance (NMR) and Nuclear Quadrupole Resonance (NQR) measurements in a stripe ordered La1.875Ba0.125CuO4 single crystal and in oriented powder samples of La1.8-xEu0.2SrxCuO4. We observe a partial wipeout of the 17O NMR intensity and a simultaneous drop of the 17O electric field gradient (EFG) at low temperatures where the spin stripe order sets in. In contrast, the 63Cu intensity is completely wiped out at the same temperature. The drop of the 17O quadrupole frequency is compatible with a charge stripe order. The 17O spin lattice relaxation rate shows a peak similar to that of the 139La, which is of magnetic origin. This peak is doping dependent and is maximal at x ~ 1/8.Comment: submitted to European Physical Journal Special Topic

Rate-equation calculations of the current flow through two-site molecular device and DNA-based junction

Here we present the calculations of incoherent current flowing through the two-site molecular device as well as the DNA-based junction within the rate-equation approach. Few interesting phenomena are discussed in detail. Structural asymmetry of two-site molecule results in rectification effect, which can be neutralized by asymmetric voltage drop at the molecule-metal contacts due to coupling asymmetry. The results received for poly(dG)-poly(dC) DNA molecule reveal the coupling- and temperature-independent saturation effect of the current at high voltages, where for short chains we establish the inverse square distance dependence. Besides, we document the shift of the conductance peak in the direction to higher voltages due to the temperature decrease.Comment: 12 pages, 6 figure

All electron and pseudopotential study of the spin polarization of the V (001) surface: LDA versus GGA

The spin-polarization at the V(001) surface has been studied by using different local (LSDA) and semilocal (GGA) approximations to the exchange-correlation potential of DFT within two ab initio methods: the all-electron TB-LMTO-ASA and the pseudopotential LCAO code SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms). A comparative analysis is performed first for the bulk and then for a N-layer V(001) film (7 < N < 15). The LSDA approximation leads to a non magnetic V(001) surface with both theoretical models in agreement (disagreement) with magneto-optical Kerr (electron-capture spectroscopy) experiments. The GGA within the pseudopotential method needs thicker slabs than the LSDA to yield zero moment at the central layer, giving a high surface magnetization (1.70 Bohr magnetons), in contrast with the non magnetic solution obtained by means of the all-electron code.Comment: 12 pages, 1 figure. Latex gzipped tar fil