Enzyme localization can drastically affect signal amplification in signal transduction pathways

Push-pull networks are ubiquitous in signal transduction pathways in both prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals via the mechanism of zero-order ultrasensitivity. In a push-pull network, two antagonistic enzymes control the activity of a protein by covalent modification. These enzymes are often uniformly distributed in the cytoplasm. They can, however, also be colocalized in space, for instance, near the pole of the cell. Moreover, it is increasingly recognized that these enzymes can also be spatially separated, leading to gradients of the active form of the messenger protein. Here, we investigate the consequences of the spatial distributions of the enzymes for the amplification properties of push-pull networks. Our calculations reveal that enzyme localization by itself can have a dramatic effect on the gain. The gain is maximized when the two enzymes are either uniformly distributed or colocalized in one region in the cell. Depending on the diffusion constants, however, the sharpness of the response can be strongly reduced when the enzymes are spatially separated. We discuss how our predictions could be tested experimentally.Comment: PLoS Comp Biol, in press. 32 pages including 6 figures and supporting informatio

The switching dynamics of the bacterial flagellar motor

Many swimming bacteria are propelled by flagellar motors that stochastically switch between the clockwise and counterclockwise rotation direction. While the switching dynamics are one of the most important characteristics of flagellar motors, the mechanisms that control switching are poorly understood. We present a statistical-mechanical model of the flagellar rotary motor, which consists of a number of stator proteins that drive the rotation of a ring of rotor proteins, which in turn drives the rotation of a flagellar filament. At the heart of our model is the assumption that the rotor protein complex can exist in two conformational states corresponding to the two respective rotation directions, and that switching between these states depends on interactions with the stator proteins. This naturally couples the switching dynamics to the rotation dynamics, making the switch sensitive to torque and speed. Another key element of our model is that after a switching event, it takes time for the load to build up, due to polymorphic transitions of the filament. Our model predicts that this slow relaxation dynamics of the filament, in combination with the load dependence of the switching frequency, leads to a characteristic switching time, in agreement with recent observations.Comment: 7 pages, 6 figures, RevTeX

Chaotic Scattering with Resonance Enhancement

The passage of light or of electrons through a disordered medium is modified in the presence of resonances. We describe a simple model for this problem, and present first results.Comment: 13 pages, 2 figures, REVTEX. To appear in Nucl. Phys. A (1996

The Balance of Dark and Luminous Mass in Rotating Galaxies

A fine balance between dark and baryonic mass is observed in spiral galaxies. As the contribution of the baryons to the total rotation velocity increases, the contribution of the dark matter decreases by a compensating amount. This poses a fine-tuning problem for \LCDM galaxy formation models, and may point to new physics for dark matter particles or even a modification of gravity.Comment: 4 pages RevTeX. Phys. Rev. Letters, in pres

The scale-free character of the cluster mass function and the universality of the stellar IMF

Our recent determination of a Salpeter slope for the IMF in the field of 30 Doradus (Selman and Melnick 2005) appears to be in conflict with simple probabilistic counting arguments advanced in the past to support observational claims of a steeper IMF in the LMC field. In this paper we re-examine these arguments and show by explicit construction that, contrary to these claims, the field IMF is expected to be exactly the same as the stellar IMF of the clusters out of which the field was presumably formed. We show that the current data on the mass distribution of clusters themselves is in excellent agreement with our model, and is consistent with a single spectrum {\it by number of stars} of the type $n^\beta$ with beta between -1.8 and -2.2 down to the smallest clusters without any preferred mass scale for cluster formation. We also use the random sampling model to estimate the statistics of the maximal mass star in clusters, and confirm the discrepancy with observations found by Weidner and Kroupa (2006). We argue that rather than signaling the violation of the random sampling model these observations reflect the gravitationally unstable nature of systems with one very large mass star. We stress the importance of the random sampling model as a \emph{null hypothesis} whose violation would signal the presence of interesting physics.Comment: 9 pages emulateap

Self-consistent models of triaxial galaxies in MOND gravity

The Bekenstein-Milgrom gravity theory with a modified Poisson equation is tested here for the existence of triaxial equilibrium solutions. Using the non-negative least square method, we show that self-consistent triaxial galaxies exist for baryonic models with a mild density cusp $\rho \sim {\Sigma \over r}$. Self-consistency is achieved for a wide range of central concentrations, $\Sigma \sim 10-1000\mathrm{M_{\odot}pc^{-2}}$, representing low-to-high surface brightness galaxies. Our results demonstrate for the first time that the orbit superposition technique is fruitful for constructing galaxy models beyond Newtonian gravity, and triaxial cuspy galaxies might exist without the help of Cold dark Matter.Comment: 19 pages, 1 table, 7 figures, Accepted for publication in Ap

Effect of resonances on the transport properties of two-dimensional disordered systems

We study both analytically and numerically how the electronic structure and the transport properties of a two-dimensional disordered system are modified in the presence of resonances. The energy dependence of the density of states and the localization length at different resonance energies and strengths of coupling between resonances and random states are determined. The results show, that at energy equals to the resonance energy there is an enhancement in the density of states. In contrast, the localization length remains unaffected from the presence of the resonances and is similar to the one of the standard Anderson model. Finally, we calculate the diffusion constant as a function of energy and we reveal interesting analogies with experimental results on light scattering in the presence of Mie resonances.Comment: 4 pages, 4 figures, accepted in Phys. Rev. B (2000

The properties of the Galactic bar implied by gas kinematics in the inner Milky Way

Longitude-velocity (l-V) diagrams of H I and CO gas in the inner Milky Way have long been known to be inconsistent with circular motion in an axisymmetric potential. Several lines of evidence suggest that the Galaxy is barred, and gas flow in a barred potential could be consistent with the observed ``forbidden'' velocities and other features in the data. We compare the H I observations to l-V diagrams synthesized from 2-D fluid dynamical simulations of gas flows in a family of barred potentials. The gas flow pattern is very sensitive to the parameters of the assumed potential, which allows us to discriminate among models. We present a model that reproduces the outer contour of the H I l-V diagram reasonably well; this model has a strong bar with a semimajor axis of 3.6 kpc, an axis ratio of approximately 3:1, an inner Lindblad resonance (ILR), and a pattern speed of 42 km/s/kpc, and matches the data best when viewed from 34\deg to the bar major axis. The behavior of the models, combined with the constraint that the shocks in the Milky Way bar should resemble those in external barred galaxies, leads us to conclude that wide ranges of parameter space are incompatible with the observations. In particular we suggest that the bar must be fairly strong, must have an ILR, and cannot be too end-on, with the bar major axis at 35\deg +/- 5\deg to the line of sight. The H I data exhibit larger forbidden velocities over a wider longitude range than are seen in molecular gas; this important difference is the reason our favored model differs so significantly from other recently proposed models.Comment: 23 pages, 14 figures, 1 table, uses emulateapj and psfig, 640 kb. Submitted to Ap

Comment on Viscous Stability of Relativistic Keplerian Accretion Disks

Recently Ghosh (1998) reported a new regime of instability in Keplerian accretion disks which is caused by relativistic effects. This instability appears in the gas pressure dominated region when all relativistic corrections to the disk structure equations are taken into account. We show that he uses the stability criterion in completely wrong way leading to inappropriate conclusions. We perform a standard stability analysis to show that no unstable region can be found when the relativistic disk is gas pressure dominated.Comment: 9 pages, 4 figures, uses aasms4.sty, submitted for ApJ Letter

Coherent Backscattering of Light by Cold Atoms

Light propagating in an optically thick sample experiences multiple scattering. It is now known that interferences alter this propagation, leading to an enhanced backscattering, a manifestation of weak localization of light in such diffuse samples. This phenomenon has been extensively studied with classical scatterers. In this letter we report the first experimental evidence for coherent backscattering of light in a laser-cooled gas of Rubidium atoms.Comment: 4 pages REVTEX, 1 page color image GIF, accepted for publication in Phys. Rev. Let