Crystal structure of the autochaperone region from the Shigella flexneri autotransporter IcsA.

The IcsA (intracellular spread gene A) autotransporter from Shigella flexneri is a key virulence factor. We identified a stable fragment comprising residues 591 to 758, which corresponds to the autochaperone region of the IcsA passenger domain. We showed that thermal unfolding of the autochaperone region is reversible and determined its crystal structure at 2.0-Å resolution

Topological Modes in Dual Lattice Models

Lattice gauge theory with gauge group $Z_{P}$ is reconsidered in four dimensions on a simplicial complex $K$. One finds that the dual theory, formulated on the dual block complex $\hat{K}$, contains topological modes which are in correspondence with the cohomology group $H^{2}(\hat{K},Z_{P})$, in addition to the usual dynamical link variables. This is a general phenomenon in all models with single plaquette based actions; the action of the dual theory becomes twisted with a field representing the above cohomology class. A similar observation is made about the dual version of the three dimensional Ising model. The importance of distinct topological sectors is confirmed numerically in the two dimensional Ising model where they are parameterized by $H^{1}(\hat{K},Z_{2})$.Comment: 10 pages, DIAS 94-3

Mixing Effects in the Crystallization of Supercooled Quantum Binary Liquids

By means of Raman spectroscopy of liquid microjets we have investigated the crystallization process of supercooled quantum liquid mixtures composed of parahydrogen (pH$_2$) diluted with small amounts of up to 5\% of either neon or orthodeuterium (oD$_2$), and of oD$_2$ diluted with either Ne or pH$_2$. We show that the introduction of Ne impurities affects the crystallization kinetics in both the pH$_2$-Ne and oD$_2$-Ne mixtures in terms of a significant reduction of the crystal growth rate, similarly to what found in our previous work on supercooled pH$_2$-oD$_2$ liquid mixtures [M. K\"uhnel et {\it al.}, Phys. Rev. B \textbf{89}, 180506(R) (2014)]. Our experimental results, in combination with path-integral simulations of the supercooled liquid mixtures, suggest in particular a correlation between the measured growth rates and the ratio of the effective particle sizes originating from quantum delocalization effects. We further show that the crystalline structure of the mixture is also affected to a large extent by the presence of the Ne impurities, which likely initiate the freezing process through the formation of Ne crystallites.Comment: 19 pages, 7 figures, submitted to J. Chem. Phy

A Closed Contour of Integration in Regge Calculus

The analytic structure of the Regge action on a cone in $d$ dimensions over a boundary of arbitrary topology is determined in simplicial minisuperspace. The minisuperspace is defined by the assignment of a single internal edge length to all 1-simplices emanating from the cone vertex, and a single boundary edge length to all 1-simplices lying on the boundary. The Regge action is analyzed in the space of complex edge lengths, and it is shown that there are three finite branch points in this complex plane. A closed contour of integration encircling the branch points is shown to yield a convergent real wave function. This closed contour can be deformed to a steepest descent contour for all sizes of the bounding universe. In general, the contour yields an oscillating wave function for universes of size greater than a critical value which depends on the topology of the bounding universe. For values less than the critical value the wave function exhibits exponential behaviour. It is shown that the critical value is positive for spherical topology in arbitrary dimensions. In three dimensions we compute the critical value for a boundary universe of arbitrary genus, while in four and five dimensions we study examples of product manifolds and connected sums.Comment: 16 pages, Latex, To appear in Gen. Rel. Gra

Testing nanomaterial toxicity in unicellular eukaryotic algae and fish cell lines.

Nanoecotoxicology as a sub-discipline of ecotoxicology aims to identify and predict effects elicited on ecosystems by nano-sized materials (NM). Two key groups of model organisms in this context are algae and fi sh. In this chapter, we present considerations for testing NM with respect to their impact on unicellular algae and cell lines derived from various organs of fi sh. Based on currently available literature on NM effects in unicellular algae and fi sh cell lines, and our own experience, we provide guidance on test design, including principle test considerations, materials, NM presentation to cells, exposure, bioavailability, and effect assessment. Assessment needs to be based on a meaningful choice of exposure scenario(s) related to the research question. As a fi rst step, one needs to address whether effects of NMs are to be investigated under environmentally relevant or probable conditions, which may include processes such as agglomeration, or whether NM effects from mono-dispersed particles are of interest, which may require special steps to ensure stable NM suspension. Moreover, whether effects on cells are to be studied in the short- or long-term is important with regard to experimental design. Preparation of NM suspensions, which can be done in aqueous media different from the exposure medium, is addressed with regard to energy input, sterility (as required for algae and fi sh cell exposure) and particle purity. Specifi ed for the two model systems, algae and fi sh cell lines, availability and choice of culture media are presented and discussed with regard to impact on NM behavior. Light, temperature, and agitation, which are variables during exposure, are discussed. We further provide guidance on the characterization of the NM in the chosen aqueous exposure media regarding size, zeta potential and electrophoretic mobility. The state of NM in exposure media is decisive for their bioavailability and therefore for potential particle effects. Therefore, we present ways of deriving a mass balance and quantitative/qualitative information on the uptake and distribution of NM in cells. As NM have a high surface-to-volume ratio and possess specifi c physical-chemical properties, which make them prone to interfere with various compounds and certain types of toxicity tests, potential interferences and appropriate controls are introduced. Furthermore, different types of dose metrics, which is still a strongly debated issue in nanotoxicology, are highlighted. We also consider laboratory safety regarding NM handling and disposal

Triangulations and Severi varieties

We consider the problem of constructing triangulations of projective planes over Hurwitz algebras with minimal numbers of vertices. We observe that the numbers of faces of each dimension must be equal to the dimensions of certain representations of the automorphism groups of the corresponding Severi varieties. We construct a complex involving these representations, which should be considered as a geometric version of the (putative) triangulations

Crumpled triangulations and critical points in 4D simplicial quantum gravity

This is an expanded and revised version of our geometrical analysis of the strong coupling phase of 4D simplicial quantum gravity. The main differences with respect to the former version is a full discussion of singular triangulations with singular vertices connected by a subsingular edge. In particular we provide analytical arguments which characterize the entropical properties of triangulations with a singular edge connecting two singular vertices. The analytical estimate of the location of the critical coupling at k_2\simeq 1.3093 is presented in more details. Finally we also provide a model for pseudo-criticality at finite N_4(S^4).Comment: 44 page

Formation of phase lags at the cyclotron energies in the pulse profiles of magnetized, accreting neutron stars

Context: Accretion-powered X-ray pulsars show highly energy-dependent and complex pulse-profile morphologies. Significant deviations from the average pulse profile can appear, in particular close to the cyclotron line energies. These deviations can be described as energy-dependent phase lags, that is, as energy-dependent shifts of main features in the pulse profile. Aims: Using a numerical study we explore the effect of cyclotron resonant scattering on observable, energy-resolved pulse profiles. Methods: We generated the observable emission as a function of spin phase, using Monte Carlo simulations for cyclotron resonant scattering and a numerical ray-tracing routine accounting for general relativistic light-bending effects on the intrinsic emission from the accretion columns. Results: We find strong changes in the pulse profile coincident with the cyclotron line energies. Features in the pulse profile vary strongly with respect to the average pulse profile with the observing geometry and shift and smear out in energy additionally when assuming a non-static plasma. Conclusions: We demonstrate how phase lags at the cyclotron energies arise as a consequence of the effects of angular redistribution of X-rays by cyclotron resonance scattering in a strong magnetic field combined with relativistic effects. We also show that phase lags are strongly dependent on the accretion geometry. These intrinsic effects will in principle allow us to constrain a system's accretion geometry.Comment: 4 pages, 4 figures; updated reference lis

Feature Lines for Illustrating Medical Surface Models: Mathematical Background and Survey

This paper provides a tutorial and survey for a specific kind of illustrative visualization technique: feature lines. We examine different feature line methods. For this, we provide the differential geometry behind these concepts and adapt this mathematical field to the discrete differential geometry. All discrete differential geometry terms are explained for triangulated surface meshes. These utilities serve as basis for the feature line methods. We provide the reader with all knowledge to re-implement every feature line method. Furthermore, we summarize the methods and suggest a guideline for which kind of surface which feature line algorithm is best suited. Our work is motivated by, but not restricted to, medical and biological surface models.Comment: 33 page

Phase transitions and configuration space topology

Equilibrium phase transitions may be defined as nonanalytic points of thermodynamic functions, e.g., of the canonical free energy. Given a certain physical system, it is of interest to understand which properties of the system account for the presence of a phase transition, and an understanding of these properties may lead to a deeper understanding of the physical phenomenon. One possible approach of this issue, reviewed and discussed in the present paper, is the study of topology changes in configuration space which, remarkably, are found to be related to equilibrium phase transitions in classical statistical mechanical systems. For the study of configuration space topology, one considers the subsets M_v, consisting of all points from configuration space with a potential energy per particle equal to or less than a given v. For finite systems, topology changes of M_v are intimately related to nonanalytic points of the microcanonical entropy (which, as a surprise to many, do exist). In the thermodynamic limit, a more complex relation between nonanalytic points of thermodynamic functions (i.e., phase transitions) and topology changes is observed. For some class of short-range systems, a topology change of the M_v at v=v_t was proved to be necessary for a phase transition to take place at a potential energy v_t. In contrast, phase transitions in systems with long-range interactions or in systems with non-confining potentials need not be accompanied by such a topology change. Instead, for such systems the nonanalytic point in a thermodynamic function is found to have some maximization procedure at its origin. These results may foster insight into the mechanisms which lead to the occurrence of a phase transition, and thus may help to explore the origin of this physical phenomenon.Comment: 22 pages, 6 figure