Feedback control architecture & the bacterial chemotaxis network

Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to ‘reset’ (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a ‘cascade control’ feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance

Theoretical confirmation of Feynman's hypothesis on the creation of circular vortices in Bose-Einstein condensates: III

In two preceding papers (Infeld and Senatorski 2003 J. Phys.: Condens. Matter 15 5865, and Senatorski and Infeld 2004 J. Phys.: Condens. Matter 16 6589) the authors confirmed Feynman's hypothesis on how circular vortices can be created from oppositely polarized pairs of linear vortices (first paper), and then gave examples of the creation of several different circular vortices from one linear pair (second paper). Here in part III, we give two classes of examples of how the vortices can interact. The first confirms the intuition that the reconnection processes which join two interacting vortex lines into one, practically do not occur. The second shows that new circular vortices can also be created from pairs of oppositely polarized coaxial circular vortices. This seems to contradict the results for such pairs given in Koplik and Levine 1996 Phys. Rev. Lett. 76 4745.Comment: 10 pages, 7 figure

Relativistic phase space: dimensional recurrences

We derive recurrence relations between phase space expressions in different dimensions by confining some of the coordinates to tori or spheres of radius $R$ and taking the limit as $R \to \infty$. These relations take the form of mass integrals, associated with extraneous momenta (relative to the lower dimension), and produce the result in the higher dimension.Comment: 13 pages, Latex, to appear in J Phys

Violation of the equivalence principle from light scalar fields: from Dark Matter candidates to scalarized black holes

Tensor-scalar theory is a wide class of alternative theory of gravitation that can be motivated by higher dimensional theories, by models of dark matter or dark ernergy. In the general case, the scalar field will couple non-universally to matter producing a violation of the equivalence principle. In this communication, we review a microscopic model of scalar/matter coupling and its observable consequences in terms of universality of free fall, of frequencies comparison and of redshifts tests. We then focus on two models: (i) a model of ultralight scalar dark matter and (ii) a model of scalarized black hole in our Galactic Center. For both these models, we present constraints using recent measurements: atomic clocks comparisons, universality of free fall measurements, measurement of the relativistic redshift with the short period star S0-2 orbiting the supermassive black hole in our Galactic Center.Comment: 8 pages, 1 figure, contribution to the 2019 Gravitation session of the 54th Rencontres de Morion

Kinematic dynamo action in a sphere. I. Effects of differential rotation and meridional circulation on solutions with axial dipole symmetry

A sphere containing electrically conducting fluid can generate a magnetic field by dynamo action, provided the flow is sufficiently complicated and vigorous. The dynamo mechanism is thought to sustain magnetic fields in planets and stars. The kinematic dynamo problem tests steady flows for magnetic instability, but rather few dynamos have been found so far because of severe numerical difficulties. Dynamo action might, therefore, be quite unusual, at least for large-scale steady flows. We address this question by testing a two-parameter class of flows for dynamo generation of magnetic fields containing an axial dipole. The class of flows includes two completely different types of known dynamos, one dominated by differential rotation (D) and one with none. We find that 36% of the flows in seven distinct zones in parameter space act as dynamos, while the remaining 64% either fail to generate this type of magnetic field or generate fields that are too small in scale to be resolved by our numerical method. The two previously known dynamo types lie in the same zone, and it is therefore possible to change the flow continuously from one to the other without losing dynamo action. Differential rotation is found to promote large-scale axisymmetric toroidal magnetic fields, while meridional circulation (M) promotes large-scale axisymmetric poloidal fields concentrated at high latitudes near the axis. Magnetic fields resembling that of the Earth are generated by D > 0, corresponding to westward flow at the surface, and M of either sign but not zero. Very few oscillatory solutions are found

Impact of an improved neutrino energy estimate on outflows in neutron star merger simulations

Binary neutron star mergers are promising sources of gravitational waves for ground-based detectors such as Advanced LIGO. Neutron-rich material ejected by these mergers may also be the main source of r-process elements in the Universe, while radioactive decays in the ejecta can power bright electromagnetic post-merger signals. Neutrino-matter interactions play a critical role in the evolution of the composition of the ejected material, which significantly impacts the outcome of nucleosynthesis and the properties of the associated electromagnetic signal. In this work, we present a simulation of a binary neutron star merger using an improved method for estimating the average neutrino energies in our energy-integrated neutrino transport scheme. These energy estimates are obtained by evolving the neutrino number density in addition to the neutrino energy and flux densities. We show that significant changes are observed in the composition of the polar ejecta when comparing our new results with earlier simulations in which the neutrino spectrum was assumed to be the same everywhere in optically thin regions. In particular, we find that material ejected in the polar regions is less neutron rich than previously estimated. Our new estimates of the composition of the polar ejecta make it more likely that the color and timescale of the electromagnetic signal depend on the orientation of the binary with respect to an observer's line-of-sight. These results also indicate that important observable properties of neutron star mergers are sensitive to the neutrino energy spectrum, and may need to be studied through simulations including a more accurate, energy-dependent neutrino transport scheme.Comment: 19p, 17 figures, Accepted by Phys.Rev.

Effects of Flight on Gene Expression and Aging in the Honey Bee Brain and Flight Muscle

Honey bees move through a series of in-hive tasks (e.g., “nursing”) to outside tasks (e.g., “foraging”) that are coincident with physiological changes and higher levels of metabolic activity. Social context can cause worker bees to speed up or slow down this process, and foragers may revert back to their earlier in-hive tasks accompanied by reversion to earlier physiological states. To investigate the effects of flight, behavioral state and age on gene expression, we used whole-genome microarrays and real-time PCR. Brain tissue and flight muscle exhibited different patterns of expression during behavioral transitions, with expression patterns in the brain reflecting both age and behavior, and expression patterns in flight muscle being primarily determined by age. Our data suggest that the transition from behaviors requiring little to no flight (nursing) to those requiring prolonged flight bouts (foraging), rather than the amount of previous flight per se, has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. Combined with our real-time PCR data, these data suggest an epigenetic control and energy balance role in honey bee functional senescence

Effective Dielectric Constants of Photonic Crystal of Aligned Anisotropic Cylinders: Application to the Optical Response of Periodic Array of Carbon Nanotubes

We calculate the static dielectric tensor of a periodic system of aligned anisotropic dielectric cylinders. Exact analytical formulas for the effective dielectric constants for the E- and H- eigenmodes are obtained for arbitrary 2D Bravais lattice and arbitrary cross-section of anisotropic cylinders. It is shown that depending on the symmetry of the unit cell photonic crystal of anisotropic cylinders behaves in the low-frequency limit like uniaxial or biaxial natural crystal. The developed theory of homogenization of anisotropic cylinders is applied for calculations of the dielectric properties of photonic crystals of carbon nanotubes