Modeling the geometry of the endoplasmic reticulum network

Conference ProceedingFirst International Conference, AlCoB 2014, held in July 2014 in Tarragona, Spain.We have studied the network geometry of the endoplasmic reticulum by means of graph theoretical and integer programming models. The purpose is to represent this structure as close as possible by a class of finite, undirected and connected graphs the nodes of which have to be either of degree three or at most of degree three. We determine plane graphs of minimal total edge length satisfying degree and angle constraints, and we show that the optimal graphs are close to the ER network geometry. Basically, two procedures are formulated to solve the optimization problem: a binary linear program, that iteratively constructs an optimal solution, and a linear program, that iteratively exploits additional cutting planes from different families to accelerate the solution process. All formulations have been implemented and tested on a series of real-life and randomly generated cases. The cutting plane approach turns out to be particularly efficient for the real-life testcases, since it outperforms the pure integer programming approach by a factor of at least 10. © 2014 Springer International Publishing

Fronts dynamics in the presence of spatio-temporal structured noises

Front dynamics modeled by a reaction-diffusion equation are studied under the influence of spatio-temporal structured noises. An effective deterministic model is analytical derived where the noise parameters, intensity, correlation time and correlation length appear explicitely. The different effects of these parameters are discussed for the Ginzburg-Landau and Schl\"ogl models. We obtain an analytical expression for the front velocity as a function of the noise parameters. Numerical simulations results are in a good agreement with the theoretical predictions.Comment: 11 pages, 6 figures; REVTEX; to be published in Phys.Rev.E, july 200

Elastic fluctuations as observed in a confocal slice

Recent confocal experiments on colloidal solids motivate a fuller study of the projection of three-dimensional fluctuations onto a two-dimensional confocal slice. We show that the effective theory of a projected crystal displays several exceptional features, such as non-standard exponents in the dispersion relations. We provide analytic expressions for the effective two-dimensional elastic properties which allow one to work back from sliced experimental observations to three-dimensional elastic constants.Comment: 5 pages, 2 figure

Refractive index determination of SiO2 layer in the UV/Vis/NIR range: spectrophotometric reverse engineering on single and bi-layer designs

In this paper we use spectrophotometric measurements and a Clustering Global Optimization procedure to determine the complex refractive index of SiO2 layer from 250 nm to 1250 nm. A special commercial optical module allows the reflection and transmission measurements to be made under exactly the same illumination and measurement conditions. We compare the index determination results obtained from two different single layer SiO2 samples, with high and low index glass substrates, respectively. We then determine the refractive index of SiO2 for a bi-layer design in which the first deposited layer is Ta2O5. The corresponding solutions are discussed and we show that the real part of the complex refractive index obtained for a bi-layer is slightly different to that found for a single layer investigation. When SiO2 is included inside a thin film stack, we propose the use of an index determination method in which a bi-layer is used for the real part of the complex refractive index, and single layer determination is used for the imaginary part of the refractive index in the UV range

Fluctuating "Pulled" Fronts: the Origin and the Effects of a Finite Particle Cutoff

Recently it has been shown that when an equation that allows so-called pulled fronts in the mean-field limit is modelled with a stochastic model with a finite number $N$ of particles per correlation volume, the convergence to the speed $v^*$ for $N \to \infty$ is extremely slow -- going only as $\ln^{-2}N$. In this paper, we study the front propagation in a simple stochastic lattice model. A detailed analysis of the microscopic picture of the front dynamics shows that for the description of the far tip of the front, one has to abandon the idea of a uniformly translating front solution. The lattice and finite particle effects lead to a ``stop-and-go'' type dynamics at the far tip of the front, while the average front behind it ``crosses over'' to a uniformly translating solution. In this formulation, the effect of stochasticity on the asymptotic front speed is coded in the probability distribution of the times required for the advancement of the ``foremost bin''. We derive expressions of these probability distributions by matching the solution of the far tip with the uniformly translating solution behind. This matching includes various correlation effects in a mean-field type approximation. Our results for the probability distributions compare well to the results of stochastic numerical simulations. This approach also allows us to deal with much smaller values of $N$ than it is required to have the $\ln^{-2}N$ asymptotics to be valid.Comment: 26 pages, 11 figures, to appear in Phys. rev.

Major flaws in conflict prevention policies towards Africa : the conceptual deficits of international actors’ approaches and how to overcome them

Current thinking on African conflicts suffers from misinterpretations oversimplification, lack of focus, lack of conceptual clarity, state-centrism and lack of vision). The paper analyses a variety of the dominant explanations of major international actors and donors, showing how these frequently do not distinguish with sufficient clarity between the ‘root causes’ of a conflict, its aggravating factors and its triggers. Specifically, a correct assessment of conflict prolonging (or sustaining) factors is of vital importance in Africa’s lingering confrontations. Broader approaches (e.g. “structural stability”) offer a better analytical framework than familiar one-dimensional explanations. Moreover, for explaining and dealing with violent conflicts a shift of attention from the nation-state towards the local and sub-regional level is needed.Aktuelle Analysen afrikanischer Gewaltkonflikte sind häufig voller Fehlinterpretationen (Mangel an Differenzierung, Genauigkeit und konzeptioneller Klarheit, Staatszentriertheit, fehlende mittelfristige Zielvorstellungen). Breitere Ansätze (z. B. das Modell der Strukturellen Stabilität) könnten die Grundlage für bessere Analyseraster und Politiken sein als eindimensionale Erklärungen. häufig differenzieren Erklärungsansätze nicht mit ausreichender Klarheit zwischen Ursachen, verschärfenden und auslösenden Faktoren. Insbesondere die richtige Einordnung konfliktverlängernder Faktoren ist in den jahrzehntelangen gewaltsamen Auseinandersetzungen in Afrika von zentraler Bedeutung. Das Diskussionspapier stellt die große Variationsbreite dominanter Erklärungsmuster der wichtigsten internationalen Geber und Akteure gegenüber und fordert einen Perspektivenwechsel zum Einbezug der lokalen und der subregionalen Ebene für die Erklärung und Bearbeitung gewaltsamer Konflikte