SIMMUNE, a tool for simulating and analyzing immune system behavior

We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents (cells, molecules) on a microscopial (i.e. agent-agent interaction) scale by defining cellular stimulus-response mechanisms. Since the behavior of the agents in SIMMUNE can be very flexibly configured, its application is not limited to immune system simulations. We outline the principles of SIMMUNE's multiscale analysis of emergent structure within the simulated immune system that allow the identification of immunological contexts using minimal a priori assumptions about the higher level organization of the immune system.Comment: 23 pages, 10 figure

Supersaturated dispersions of rod-like viruses with added attraction

The kinetics of isotropic-nematic (I-N) and nematic-isotropic (N-I) phase transitions in dispersions of rod-like {\it fd}-viruses are studied. Concentration quenches were applied using pressure jumps in combination with polarization microscopy, birefringence and turbidity measurements. The full biphasic region could be accessed, resulting in the construction of a first experimental analogue of the bifurcation diagram. The N-I spinodal points for dispersions of rods with varying concentrations of depletion agents (dextran) were obtained from orientation quenches, using cessation of shear flow in combination with small angle light scattering. We found that the location of the N-I spinodal point is independent of the attraction, which was confirmed by theoretical calculations. Surprisingly, the experiments showed that also the absolute induction time, the critical nucleus and the growth rate are insensitive of the attraction, when the concentration is scaled to the distance to the phase boundaries.Comment: 13 pages, 14 figures. accepted in Phsical Review

Forward-backward asymmetry of photoemission in C60_{60} excited by few-cycle laser pulses

We theoretically analyze angle-resolved photo-electron spectra (ARPES) generated by the interaction of C$_{60}$ with intense, short laser pulses. In particular, we focus on the impact of the carrier-envelope phase (CEP) onto the angular distribution. The electronic dynamics is described by time-dependent density functional theory, and the ionic background of \csixty is approximated by a particularly designed jellium model. Our results show a clear dependence of the angular distributions onto the CEP for very short pulses covering only very few laser cycles, which disappears for longer pulses. For the specific laser parameters used in a recent experiments, a very good agreement is obtained. Furthermore, the asymmetry is found to depend on the energy of the emitted photoelectrons. The strong influence of the angular asymmetry of electron emission onto the CEP and pulse duration suggests to use this sensitivity as a means to analyze the structure of few-cycle laser pulses.Comment: 8 pages, 6 figure

Longitudinal spin Seebeck coefficient: heat flux vs. temperature difference method

The determination of the longitudinal spin Seebeck effect (LSSE) coefficient is currently plagued by a large uncertainty due to the poor reproducibility of the experimental conditions used in its measurement. In this work we present a detailed analysis of two different methods used for the determination of the LSSE coefficient. We have performed LSSE experiments in different laboratories, by using different setups and employing both the temperature difference method and the heat flux method. We found that the lack of reproducibility can be mainly attributed to the thermal contact resistance between the sample and the thermal baths which generate the temperature gradient. Due to the variation of the thermal resistance, we found that the scaling of the LSSE voltage to the heat flux through the sample rather than to the temperature difference across the sample greatly reduces the uncertainty. The characteristics of a single YIG/Pt LSSE device obtained with two different setups was $(1.143\pm0.007)\cdot 10^{-7}$ Vm/W and $(1.101\pm0.015)\cdot 10^{-7}$ Vm/W with the heat flux method and $(2.313\pm0.017)\cdot 10^{-7}$ V/K and $(4.956\pm0.005)\cdot 10^{-7}$ V/K with the temperature difference method. This shows that systematic errors can be considerably reduced with the heat flux method.Comment: PDFLaTeX, 10 pages, 6 figure

Pauli blockade of the electron spin flip in bulk GaAs

By means of time-resolved optical orientation under strong optical pumping, the k-dependence of the electron spin-flip time (t_sf) in undoped GaAs is experimentally determined. t_sf monotonically decreases by more than one order of magnitude when the electron kinetic energy varies from 2 to 30 meV. At the high excitation densities and low temperatures of the reported experiments the main spin-flip mechanism of the conduction band electrons is the Bir-Aronov-Pikus. By means of Monte-Carlo simulations we evidence that phase-space filling effects result in the blocking of the spin flip, yielding an increase of t_sf with excitation density. These effects obtain values of t_sf up to 30 ns at k=0, the longest reported spin-relaxation time in undoped GaAs in the absence of a magnetic field.Comment: new author added, major changes in section IV (phenomenological model), minor changes throughout the entire manuscrip

Hole spin relaxation in intrinsic and pp-type bulk GaAs

We investigate hole spin relaxation in intrinsic and $p$-type bulk GaAs from a fully microscopic kinetic spin Bloch equation approach. In contrast to the previous study on hole spin dynamics, we explicitly include the intraband coherence and the nonpolar hole-optical-phonon interaction, both of which are demonstrated to be of great importance to the hole spin relaxation. The relative contributions of the D'yakonov-Perel' and Elliott-Yafet mechanisms on hole spin relaxation are also analyzed. In our calculation, the screening constant, playing an important role in the hole spin relaxation, is treated with the random phase approximation. In intrinsic GaAs, our result shows good agreement with the experiment data at room temperature, where the hole spin relaxation is demonstrated to be dominated by the Elliott-Yafet mechanism. We also find that the hole spin relaxation strongly depends on the temperature and predict a valley in the density dependence of the hole spin relaxation time at low temperature due to the hole-electron scattering. In $p$-type GaAs, we predict a peak in the spin relaxation time against the hole density at low temperature, which originates from the distinct behaviors of the screening in the degenerate and nondegenerate regimes. The competition between the screening and the momentum exchange during scattering events can also lead to a valley in the density dependence of the hole spin relaxation time in the low density regime. At high temperature, the effect of the screening is suppressed due to the small screening constant. Moreover, we predict a nonmonotonic dependence of the hole spin relaxation time on temperature associated with the screening together with the hole-phonon scattering. Finally, we find that the D'yakonov-Perel' mechanism can markedly contribute to the .... (omitted due to the limit of space)Comment: 11 pages, 7 figures, Phys. Rev. B, in pres