How mathematical modelling elucidates signalling in Bacillus subtilis

P>Appropriate stimulus perception, signal processing and transduction ensure optimal adaptation of bacteria to environmental challenges. In the Gram-positive model bacterium Bacillus subtilis signalling networks and molecular interactions therein are well-studied, making this species a suitable candidate for the application of mathematical modelling. Here, we review systems biology approaches, focusing on chemotaxis, sporulation, sigma B-dependent general stress response and competence. Processes like chemotaxis and Z-ring assembly depend critically on the subcellular localization of proteins. Environmental response strategies, including sporulation and competence, are characterized by phenotypic heterogeneity in isogenic cultures. The examples of mathematical modelling also include investigations that have demonstrated how operon structure and signalling dynamics are intricately interwoven to establish optimal responses. Our review illustrates that these interdisciplinary approaches offer new insights into the response of B. subtilis to environmental challenges. These case studies reveal modelling as a tool to increase the understanding of complex systems, to help formulating hypotheses and to guide the design of more directed experiments that test predictions

Plastic flow of persistent currents in two dimensional strongly interacting systems

The local persistent current in two dimensional strongly interacting systems is investigated. As the interaction strength is enhanced the current in the sample undergoes a transition from diffusive to ordered flow. The strong interacting flow has the characteristics of a plastic flow through dislocations in the pinned charge density wave which develops in the system at low densities.Comment: 12 pages, 4 figures, accepted for publication in Phys. Rev. B (RC

European Stakeholder Round Table on Citizen and DIY Science and Responsible Research and Innovation

Göbel, C., Agnello, G., Baïz, I., Berditchevskaia, A., Evers, L., García, D., Pritchard, H., Luna, S., Ramanauskaite, E. M., Serrano, F., Boheemen, P. v., Völker, T., Wyszomirski, P., Vohland, K. (2017): European Stakeholder Round Table on Citizen and DIY Science and Responsible Research and Innovation. Doing-it-Together Science Report. URI: http://discovery.ucl.ac.uk/id/eprint/1563626 / The report is the result of an event on 8th November 2016 in Berlin. The round table has been organized by ECSA as part of the Doing-it-Together Science project (DITOs) and realized in the framework of the Berlin Science Week

USTOPIA REQUIREMENTS THOUGHTS ON A USER-FRIENDLY SYSTEM FOR TRANSFORMATION OF PROGRAMS IN ABSTRACTO

Transformational programming is a program development method which is usually applied using 'pen and paper'. Since this requires a lot of clerical work (copying expressions, con- sistent substitution) which is tiresome and prone to error, some form of machine support is desirable. In this paper a number of systems are described that have already been built to this aim. Some of their shortcomings and limitations are identified. Based on experience with program transformation and transformation systems, a long list of features is given that would be useful in an 'utopian' transformation system. This list is presented using an orthogonal division of the problem area. A number of problems with the realisation of some aspects of our 'utopian' system are identified, and some areas for further research are indicated

Thermodynamics of the dissipative two-state system: a Bethe Ansatz study

The thermodynamics of the dissipative two-state system is calculated exactly for all temperatures and level asymmetries for the case of Ohmic dissipation. We exploit the equivalence of the two-state system to the anisotropic Kondo model and extract the thermodynamics of the former by solving the thermodynamic Bethe Ansatz equations of the latter. The universal scaling functions for the specific heat $C_{\alpha}(T)$ and static dielectric susceptibility $\chi_{\alpha}(T)$ are extracted for all dissipation strengths $0<\alpha<1$ for both symmetric and asymmetric two-state systems. The logarithmic corrections to these quantities at high temperatures are found in the Kondo limit $\alpha\to 1^{-}$, whereas for $\alpha< 1$ we find the expected power law temperature dependences with the powers being functions of the dissipative coupling $\alpha$. The low temperature behaviour is always that of a Fermi liquid.Comment: 24 pages, 32 PS figures. Typos corrected, final versio

Dephasing in Disordered Conductors due to Fluctuating Electric Fields

We develop a novel eikonal expansion for the Cooperon to study the effect of space- and time-dependent electric fields on the dephasing rate of disordered conductors. For randomly fluctuating fields with arbitrary covariance we derive a general expression for the dephasing rate which is free of infrared divergencies in reduced dimensions. For time-dependent external fields with finite wavelength and sufficiently small amplitude we show that the dephasing rate is proportional to the square root of the electromagnetic power coupled into the system, in agreement with data by Wang and Lindelof [Phys. Rev. Lett. {\bf{59}}, 1156 (1987)].Comment: 17 Latex-pages, one figure; we now give more technical details and discuss the screening problem more carefully; to appear in Phys. Rev.

Gas emissions and active tectonics within the submerged section of the North Anatolian Fault zone in the Sea of Marmara

The submerged section of the North Anatolian fault within the Marmara Sea was investigated using acoustic techniques and submersible dives. Most gas emissions in the water column were found near the surface expression of known active faults. Gas emissions are unevenly distributed. The linear fault segment crossing the Central High and forming a seismic gap – as it has not ruptured since 1766, based on historical seismicity, exhibits relatively less gas emissions than the adjacent segments. In the eastern Sea of Marmara, active gas emissions are also found above a buried transtensional fault zone, which displayed micro-seismic activity after the 1999 events. Remarkably, this zone of gas emission extends westward all along the southern edge of Cinarcik basin, well beyond the zone where 1999 aftershocks were observed. The long term monitoring of gas seeps could hence be highly valuable for the understanding of the evolution of the fluid-fault coupling processes during the earthquake cycle within the Marmara Sea

Acceleration of lead ions in the CERN PS booster and the CERN PS

The new CERN Heavy Ion Accelerating Facility also requires besides a new Linac substantial modifications of existing accelerators. They are imposed by the low speed and the low intensity of the ion beam and, crucially at low energy, by the short lifetime of the partially stripped ions due to charge exchange with the atoms of the residual gas. The upgraded vacuum system hits the limits of a non-bakeable machine and consequently the acceleration had to be sped up by all means. In the Booster this led to injection and RF capture on a fast-rising magnet cycle and a new digital RF beam control system. Beam current transformers had to be replaced by new, heavily shielded ones. Other modifications include a new staircase magnet to distribute ions over the four Booster rings, lengthening of septa and kicker pulses, plus new, bakeable extraction septa and an energy stabilizing RF loop on the flat top in the CPS, and a stripper in the transfer line to the SPS

A simple and efficient GIS tool for volume calculations of submarine landslides

A numeric tool is presented for calculating volumes of topographic voids such as slump scars of landslides, canyons or craters (negative/concave morphology), or alternatively, bumps and hills (positive/convex morphology) by means of digital elevation models embedded within a geographical information system (GIS). In this study, it has been used to calculate landslide volumes. The basic idea is that a (singular) event (landslide, meteorite impact, volcanic eruption) has disturbed an intact surface such that it is still possible to distinguish between the former (undisturbed) landscape and the disturbance (crater, slide scar, debris avalanche). In such cases, it is possible to reconstruct the paleo-surface and to calculate the volume difference between both surfaces, thereby approximating the volume gain or loss caused by the event. I tested the approach using synthetically generated land surfaces that were created on the basis of Shuttle Radar Topography Mission data. Also, I show the application to two real cases, (1) the calculation of the volume of the Masaya Slide, a submarine landslide on the Pacific continental slope of Nicaragua, and (2) the calculation of the void of a segment of the Fish River Canyon, Namibia. The tool is provided as a script file for the free GIS GRASS. It performs with little effort, and offers a range of interpolation parameters. Testing with different sets of interpolation parameters results in a small range of uncertainty. This tool should prove useful in surface studies not exclusively on earth

Conversion of the PS complex as LHC proton pre-injector

CERNs Large Hadron Collider (LHC) [1][2] will be supplied with protons from the injector chain Linac2-PS Booster (PSB)-PS-SPS (Fig. 1). The required transverse beam brilliance (intensity/emittance) is almost twice that of current PS beams and the LHC bunch spacing of 25 ns must be impressed on the beam before its transfer to the SPS. The scheme involves new RF harmonics in the PSB and the PS, an increase of the PSB energy, and two-batch filling of the PS. After a successful test of the main ingredients, a project for converting the PS complex was launched in 1994. Major additions are (i) h=1 RF systems in the PSB, (ii) upgrading of the PSB main magnet supply from 1 to 1.4 GeV operation, (iii) new magnets, septa, power supplies, kicker pulsers for the PSB-PS beam transfer, (iv) 40 and 80 MHz systems in the PS, (v) beam profile measurement devices with improved resolution. A significant part of the effort is being provided by TRIUMF under the Canada-CERN co-operation agreement on the LHC