Correlated Phenotypic Transitions to Competence in Bacterial Colonies

Genetic competence is a phenotypic state of a bacterial cell in which it is capable of importing DNA, presumably to hasten its exploration of alternate genes in its quest for survival under stress. Recently, it was proposed that this transition is uncorrelated among different cells in the colony. Motivated by several discovered signaling mechanisms which create colony-level responses, we present a model for the influence of quorum-sensing signals on a colony of B. Subtilis cells during the transition to genetic competence. Coupling to the external signal creates an effective inhibitory mechanism, which results in anti-correlation between the cycles of adjacent cells. We show that this scenario is consistent with the specific experimental measurement, which fails to detect some underlying collective signaling mechanisms. Rather, we suggest other parameters that should be used to verify the role of a quorum-sensing signal. We also study the conditions under which phenotypic spatial patterns may emerge

Non-equilibrium mechanics and dynamics of motor activated gels

The mechanics of cells is strongly affected by molecular motors that generate forces in the cellular cytoskeleton. We develop a model for cytoskeletal networks driven out of equilibrium by molecular motors exerting transient contractile stresses. Using this model we show how motor activity can dramatically increase the network's bulk elastic moduli. We also show how motor binding kinetics naturally leads to enhanced low-frequency stress fluctuations that result in non-equilibrium diffusive motion within an elastic network, as seen in recent \emph{in vitro} and \emph{in vivo} experiments.Comment: 21 pages, 8 figure

Topological entropy of realistic quantum Hall wave functions

The entanglement entropy of the incompressible states of a realistic quantum Hall system are studied by direct diagonalization. The subdominant term to the area law, the topological entanglement entropy, which is believed to carry information about topologic order in the ground state, was extracted for filling factors 1/3, 1/5 and 5/2. The results for 1/3 and 1/5 are consistent with the topological entanglement entropy for the Laughlin wave function. The 5/2 state exhibits a topological entanglement entropy consistent with the Moore-Read wave function.Comment: 6 pages, 6 figures; improved computations and graphics; added reference

Exact renormalization-group analysis of first order phase transitions in clock models

We analyze the exact behavior of the renormalization group flow in one-dimensional clock-models which undergo first order phase transitions by the presence of complex interactions. The flow, defined by decimation, is shown to be single-valued and continuous throughout its domain of definition, which contains the transition points. This fact is in disagreement with a recently proposed scenario for first order phase transitions claiming the existence of discontinuities of the renormalization group. The results are in partial agreement with the standard scenario. However in the vicinity of some fixed points of the critical surface the renormalized measure does not correspond to a renormalized Hamiltonian for some choices of renormalization blocks. These pathologies although similar to Griffiths-Pearce pathologies have a different physical origin: the complex character of the interactions. We elucidate the dynamical reason for such a pathological behavior: entire regions of coupling constants blow up under the renormalization group transformation. The flows provide non-perturbative patterns for the renormalization group behavior of electric conductivities in the quantum Hall effect.Comment: 13 pages + 3 ps figures not included, TeX, DFTUZ 91.3

The approach to criticality in sandpiles

A popular theory of self-organized criticality relates the critical behavior of driven dissipative systems to that of systems with conservation. In particular, this theory predicts that the stationary density of the abelian sandpile model should be equal to the threshold density of the corresponding fixed-energy sandpile. This "density conjecture" has been proved for the underlying graph Z. We show (by simulation or by proof) that the density conjecture is false when the underlying graph is any of Z^2, the complete graph K_n, the Cayley tree, the ladder graph, the bracelet graph, or the flower graph. Driven dissipative sandpiles continue to evolve even after a constant fraction of the sand has been lost at the sink. These results cast doubt on the validity of using fixed-energy sandpiles to explore the critical behavior of the abelian sandpile model at stationarity.Comment: 30 pages, 8 figures, long version of arXiv:0912.320

The Anticorrelated Nature of the Primary and Secondary Eclipse Timing Variations for the Kepler Contact Binaries

We report on a study of eclipse timing variations in contact binary systems, using long-cadence lightcurves in the Kepler archive. As a first step, 'observed minus calculated' (O-C) curves were produced for both the primary and secondary eclipses of some 2000 Kepler binaries. We find ~390 short-period binaries with O-C curves that exhibit (i) random-walk like variations or quasi-periodicities, with typical amplitudes of +/- 200-300 seconds, and (ii) anticorrelations between the primary and secondary eclipse timing variations. We present a detailed analysis and results for 32 of these binaries with orbital periods in the range of 0.35 +/- 0.05 days. The anticorrelations observed in their O-C curves cannot be explained by a model involving mass transfer, which among other things requires implausibly high rates of ~0.01 M_sun per year. We show that the anticorrelated behavior, the amplitude of the O-C delays, and the overall random-walk like behavior can be explained by the presence of a starspot that is continuously visible around the orbit and slowly changes its longitude on timescales of weeks to months. The quasi-periods of ~50-200 days observed in the O-C curves suggest values for k, the coefficient of the latitude dependence of the stellar differential rotation, of ~0.003-0.013.Comment: Published in The Astrophysical Journal, 2013, Vol. 774, p.81; 14 pages, 12 figures, and 2 table

Detecting many-body entanglements in noninteracting ultracold atomic fermi gases

We explore the possibility of detecting many-body entanglement using time-of-flight (TOF) momentum correlations in ultracold atomic fermi gases. In analogy to the vacuum correlations responsible for Bekenstein-Hawking black hole entropy, a partitioned atomic gas will exhibit particle-hole correlations responsible for entanglement entropy. The signature of these momentum correlations might be detected by a sensitive TOF type experiment.Comment: 5 pages, 5 figures, fixed axes labels on figs. 3 and 5, added reference

The effect of curvature and topology on membrane hydrodynamics

We study the mobility of extended objects (rods) on a spherical liquid-liquid interface to show how this quantity is modified in a striking manner by both the curvature and the topology of the interface. We present theoretical calculations and experimental measurements of the interfacial fluid velocity field around a moving rod bound to the crowded interface of a water-in-oil droplet. By using different droplet sizes, membrane viscosities, and rod lengths, we show that the viscosity mismatch between the interior and exterior fluids leads to a suppression of the fluid flow on small droplets that cannot be captured by the flat interface predictions.Comment: 4 pages, 3 figure