Direct inscription and evaluation of fiber Bragg gratings in carbon-coated optical sensor glass fibers for harsh environment oil and gas applications.

In this research work, we show the successful inscription of fiber Bragg gratings into carbon-coated pure silica as well as germanium-doped glass fibers by applying the pulsed laser point-by-point manufacturing technique. First, the parameters used for the Ti:sapphire femtosecond laser process are demonstrated. Without removing the polymeric carbon coating, destruction-free formation of highly reflective Bragg gratings is performed with selected types of hermetically enclosed fibers. We demonstrate the advantage of the carbon coating by long-term exposure to a pure hydrogen atmosphere at an elevated temperature. Such harsh conditions exist in the oil and gas industry, which means there is high application potential for technologically advanced optical sensors. Compared to the also examined standard glass fibers with a distinct signal attenuation, carbon-coated fibers show no significant degradation. Finally, we analyze the mechanical stability of the processed fibers via standardized tensile tests. No substantial decrease in strength occurs among the sensor-integrated samples.

Multiple off-axis fiber Bragg gratings for 3D shape sensing.

Point-by-point femtosecond laser processed fiber Bragg gratings are arranged around the edge of a standard single-mode optical fiber core. The relative amplitudes of at least three such fiber Bragg gratings are utilized to detect the central position of the mode field within the fiber core and calculate the local curvature of the fiber. An analytical approximation is given, and an experimental validation is performed.

Cladding waveguide gratings in standard single-mode fiber for 3D shape sensing.

Femtosecond laser pulses were used for the direct point-by-point inscription of waveguides into the cladding of standard single-mode fibers. Homogeneous S-shaped waveguides have been processed as a bundle of overlapping lines without damaging the surrounding material. Within these structures, FBGs have been successfully inscribed and characterized. A sensor device to measure the bending direction of a fiber was created by two perpendicular inscribed cladding waveguides with FBG. Finally, a complete 3D shape sensor consisting of several bending sensor planes, capable of detecting bending radii even below 2.5 cm is demonstrated.

Point-by-point inscription of phase-shifted fiber Bragg gratings with electro-optic amplitude modulated femtosecond laser pulses.

Femtosecond laser pulses were used for the direct point-by-point inscription of phase-shifted fiber Bragg gratings (FBGs) in a single fabrication step without postprocessing. An electro-optic amplitude modulator is used in the setup to generate a defined delay between two identical laser pulse trains for the grating inscription. The grating structure with a central phase shift is formed by focusing the modulated laser pulses into the core of a fiber, while the fiber is translated with a constant velocity. The induced phase shift leads to a narrow transmission band with a bandwidth considerably below 10 pm within the stop band of the FBG. The inscribed FBGs show a birefringence of 3.9×10(-5) whereas their temperature and strain sensitivities are 10.4 pm/K and 1.4 pm/µstrain, respectively. The fabrication process is fast and offers a high grade of flexibility for the control of all grating parameters.

Information theory based approaches to cellular signaling.

BACKGROUND: Cells interact with their environment and they have to react adequately to internal and external changes such changes in nutrient composition, physical properties like temperature or osmolarity and other stresses. More specifically, they must be able to evaluate whether the external change is significant or just in the range of noise. Based on multiple external parameters they have to compute an optimal response. Cellular signaling pathways are considered as the major means of information perception and transmission in cells. SCOPE OF REVIEW: Here, we review different attempts to quantify information processing on the level of individual cells. We refer to Shannon entropy, mutual information, and informal measures of signaling pathway cross-talk and specificity. MAJOR CONCLUSIONS: Information theory in systems biology has been successfully applied to identification of optimal pathway structures, mutual information and entropy as system response in sensitivity analysis, and quantification of input and output information. GENERAL SIGNIFICANCE: While the study of information transmission within the framework of information theory in technical systems is an advanced field with high impact in engineering and telecommunication, its application to biological objects and processes is still restricted to specific fields such as neuroscience, structural and molecular biology. However, in systems biology dealing with a holistic understanding of biochemical systems and cellular signaling only recently a number of examples for the application of information theory have emerged. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Signal integration in budding yeast.

A complex signalling network governs the response of Saccharomyces cerevisiae to an array of environmental stimuli and stresses. In the present article, we provide an overview of the main signalling system and discuss the mechanisms by which yeast integrates and separates signals from these sources. We apply our classification scheme to a simple semi-quantitative model of the HOG (high-osmolarity glycerol)/FG (filamentous growth)/PH (pheromone) MAPK (mitogen-activated protein kinase) signalling network by perturbing its signal integration mechanisms under combinatorial stimuli of osmotic stress, starvation and pheromone exposure in silico. Our findings include that the Hog1 MAPK might act as a timer for filamentous differentiation, not allowing morphological differentiation before osmo-adaptation is sufficiently completed. We also see that a mutually exclusive decision-making between pheromone and osmo-response might not be taken on the MAPK level and transcriptional regulation of MAPK targets. We conclude that signal integration mechanisms in a wider network including the cell cycle have to be taken into account for which our framework might provide focal points of study.

Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway.

Cellular signalling networks integrate environmental stimuli with the information on cellular status. These networks must be robust against stochastic fluctuations in stimuli as well as in the amounts of signalling components. Here, we challenge the yeast HOG signal-transduction pathway with systematic perturbations in components' expression levels under various external conditions in search for nodes of fragility. We observe a substantially higher frequency of fragile nodes in this signal-transduction pathway than that has been observed for other cellular processes. These fragilities disperse without any clear pattern over biochemical functions or location in pathway topology and they are largely independent of pathway activation by external stimuli. However, the strongest toxicities are caused by pathway hyperactivation. In silico analysis highlights the impact of model structure on in silico robustness, and suggests complex formation and scaffolding as important contributors to the observed fragility patterns. Thus, in vivo robustness data can be used to discriminate and improve mathematical models.

G1 and G2 arrests in response to osmotic shock are robust properties of the budding yeast cell cycle.

Boolean modeling has been successfully applied to the budding yeast cell cycle to demonstrate that both its structure and its timing are robustly designed. However, from these studies few conclusions can be drawn how robust the cell cycle arrest upon osmotic stress and pheromone exposure might be. We therefore implement a compact Boolean model of the S. cerevisiae cell cycle including its interfaces with the High Osmolarity Glycerol (HOG) and the pheromone pathways. We show that all initial states of our model robustly converge to a cyclic attractor in the absence of stress inputs whereas pheromone exposure and osmotic stress lead to convergence to singleton states which correspond to G1 and G2 arrest in silico. A comparison with random Boolean networks reveals, that cell cycle arrest under osmotic stress is a highly robust property of the yeast cell cycle. We implemented our model using the novel frontend booleannetGUI to the python software booleannet.

Spontaneous synchronization of coupled circadian oscillators.

In mammals, the circadian pacemaker, which controls daily rhythms, is located in the suprachiasmatic nucleus (SCN). Circadian oscillations are generated in individual SCN neurons by a molecular regulatory network. Cells oscillate with periods ranging from 20 to 28 h, but at the tissue level, SCN neurons display significant synchrony, suggesting a robust intercellular coupling in which neurotransmitters are assumed to play a crucial role. We present a dynamical model for the coupling of a population of circadian oscillators in the SCN. The cellular oscillator, a three-variable model, describes the core negative feedback loop of the circadian clock. The coupling mechanism is incorporated through the global level of neurotransmitter concentration. Global coupling is efficient to synchronize a population of 10,000 cells. Synchronized cells can be entrained by a 24-h light-dark cycle. Simulations of the interaction between two populations representing two regions of the SCN show that the driven population can be phase-leading. Experimentally testable predictions are: 1), phases of individual cells are governed by their intrinsic periods; and 2), efficient synchronization is achieved when the average neurotransmitter concentration would dampen individual oscillators. However, due to the global neurotransmitter oscillation, cells are effectively synchronized.