A practical guide to computer simulations

Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries, random numbers, testing, debugging, data plotting, curve fitting, finite-size scaling, information retrieval, and preparing presentations. Because of the limited space, usually only short introductions to the specific areas are given and references to more extensive literature are cited. All examples of code are in C/C++.Comment: 69 pages, with permission of Wiley-VCH, see http://www.wiley-vch.de (some screenshots with poor quality due to arXiv size restrictions) A comprehensively extended version will appear in spring 2009 as book at Word-Scientific, see http://www.worldscibooks.com/physics/6988.htm

Diagnostics and prognostic evaluation in renal cell tumors: the German S3 guidelines recommendations

The German guidelines on renal cell carcinoma (RCC) have been developed at highest level of evidence based on systematic literature review. In this paper, we are presenting the current recommendations on diagnostics including preoperative imaging and imaging for stage evaluation as well as histopathological classification. The role of tumor biopsy is further discussed. In addition, different prognostic scores and the status of biomarkers in RCC are critically evaluated

Elastic lines on splayed columnar defects studied numerically

We investigate by exact optimization method properties of two- and three-dimensional systems of elastic lines in presence of splayed columnar disorder. The ground state of many lines is separable both in 2d and 3d leading to a random walk -like roughening in 2d and ballistic behavior in 3d. Furthermore, we find that in the case of pure splayed columnar disorder in contrast to point disorder there is no entanglement transition in 3d. Entanglement can be triggered by perturbing the pure splay system with point defects.Comment: 9 pages, 11 figures. Accepted for publication in PR

Das Mittelalter – ein „utopiegeschichtliches Vakuum“?

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.Peer Reviewe

Trans-species transfer of Wolbachia: microinjection of Wolbachia from Litomosoides sigmodontis into Acanthocheilonema viteae

This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.Intracellular bacteria of the genus Wolbachia are found in most filarial nematodes, but are lacking in some species like Acanthocheilonema viteae. Due to their symbiotic nature and their role in the pathology of filarial infections they are considered to be potential targets for intervention against filarial infections in man. Infection of A. viteae (a species which does not naturally carry Wolbachia) with Wolbachia bacteria could allow comparative studies on the effect of the endobacterium on the parasite and on the host's immune systems. As a step towards such studies we microinjected adult female A. viteae with Wolbachia obtained from Litomosoides sigmodontis. The bacteria were isolated from L. sigmodontis by density-gradient centrifugation, microinjected into A. viteae worms and bacterial DNA detected by PCR with Wolbachia specific primers (ftsZ gene). Microinjected worms were cultured in vitro, and 81% survived for 10 days. Implantation of microinjected worms into Meriones unguiculatus, the rodent host of A. viteae resulted in 38% survival. The DNA of the microinjected worms recovered from jirds 8 weeks after implantation contained Wolbachia DNA as shown by PCR, suggesting that Wolbachia of L. sigmodontis can be horizontally transmitted to A. viteae.Peer Reviewe

Superconductor-to-Normal Phase Transition in a Vortex Glass Model: Numerical Evidence for a New Percolation Universality Class

The three-dimensional strongly screened vortex-glass model is studied numerically using methods from combinatorial optimization. We focus on the effect of disorder strength on the ground state and found the existence of a disorder-driven normal-to-superconducting phase transition. The transition turns out to be a geometrical phase transition with percolating vortex loops in the ground state configuration. We determine the critical exponents and provide evidence for a new universality class of correlated percolation.Comment: 11 pages LaTeX using IOPART.cls, 11 eps-figures include

Collective roughening of elastic lines with hard core interaction in a disordered environment

We investigate by exact optimization methods the roughening of two and three-dimensional systems of elastic lines with point disorder and hard-core repulsion with open boundary conditions. In 2d we find logarithmic behavior whereas in 3d simple random walk-like behavior. The line 'forests' become asymptotically completely entangled as the system height is increased at fixed line density due to increasing line wandering

Division of Labor during Biofilm Matrix Production

Organisms as simple as bacteria can engage in complex collective actions, such as group motility and fruiting body formation. Some of these actions involve a division of labor, where phenotypically specialized clonal subpopulations or genetically distinct lineages cooperate with each other by performing complementary tasks. Here, we combine experimental and computational approaches to investigate potential benefits arising from division of labor during biofilm matrix production. We show that both phenotypic and genetic strategies for a division of labor can promote collective biofilm formation in the soil bacterium Bacillus subtilis. In this species, biofilm matrix consists of two major components, exopolysaccharides (EPSs) and TasA. We observed that clonal groups of B. subtilis phenotypically segregate into three subpopulations composed of matrix non-producers, EPS producers, and generalists, which produce both EPSs and TasA. This incomplete phenotypic specialization was outperformed by a genetic division of labor, where two mutants, engineered as specialists, complemented each other by exchanging EPSs and TasA. The relative fitness of the two mutants displayed a negative frequency dependence both in vitro and on plant roots, with strain frequency reaching a stable equilibrium at 30% TasA producers, corresponding exactly to the population composition where group productivity is maximized. Using individual-based modeling, we show that asymmetries in strain ratio can arise due to differences in the relative benefits that matrix compounds generate for the collective and that genetic division of labor can be favored when it breaks metabolic constraints associated with the simultaneous production of two matrix components

Disorder Driven Critical Behavior of Periodic Elastic Media in a Crystal Potential

We study a lattice model of a three-dimensional periodic elastic medium at zero temperature with exact combinatorial optimization methods. A competition between pinning of the elastic medium, representing magnetic flux lines in the mixed phase of a superconductor or charge density waves in a crystal, by randomly distributed impurities and a periodic lattice potential gives rise to a continuous phase transition from a flat phase to a rough phase. We determine the critical exponents of this roughening transition via finite size scaling obtaining $\nu\approx1.3$, $\beta\approx0.05$, $\gamma/\nu\approx2.9$ and find that they are universal with respect to the periodicity of the lattice potential. The small order parameter exponent is reminiscent of the random field Ising critical behavior in 3$d$.Comment: 4 pages, 3 eps-figures include