Targets for the MalI repressor at the divergent Escherichia coliK-12malX-malI promoters

Random mutagenesis has been used to identify the target DNA sites for the MalI repressor at the divergent Escherichia coli K-12 malX-malI promoters. The malX promoter is repressed by MalI binding to a DNA site located from position -24 to position -9, upstream of the malX promoter transcript start. The malI promoter is repressed by MalI binding from position +3 to position +18, downstream of the malI transcript start. MalI binding at the malI promoter target is not required for repression of the malX promoter. Similarly, MalI binding at the malX promoter target is not required for repression of the malI. Although the malX and malI promoters are regulated by a single DNA site for cyclic AMP receptor protein, they function independently and each is repressed by MalI binding to a different independent operator site

Shifts and widths of collective excitations in trapped Bose gases by the dielectric formalism

We present predictions for the temperature dependent shifts and damping rates. They are obtained by applying the dielectric formalism to a simple model of a trapped Bose gas. Within the framework of the model we use lowest order perturbation theory to determine the first order correction to the results of Hartree-Fock-Bogoliubov-Popov theory for the complex collective excitation frequencies, and present numerical results for the temperature dependence of the damping rates and the frequency shifts. Good agreement with the experimental values measured at JILA are found for the m=2 mode, while we find disagreements in the shifts for m=0. The latter point to the necessity of a non-perturbative treatment for an explanation of the temperature-dependence of the m=0 shifts.Comment: 10 pages revtex, 3 figures in postscrip

Kernelization and Sparseness: the case of Dominating Set

We prove that for every positive integer $r$ and for every graph class $\mathcal G$ of bounded expansion, the $r$-Dominating Set problem admits a linear kernel on graphs from $\mathcal G$. Moreover, when $\mathcal G$ is only assumed to be nowhere dense, then we give an almost linear kernel on $\mathcal G$ for the classic Dominating Set problem, i.e., for the case $r=1$. These results generalize a line of previous research on finding linear kernels for Dominating Set and $r$-Dominating Set. However, the approach taken in this work, which is based on the theory of sparse graphs, is radically different and conceptually much simpler than the previous approaches. We complement our findings by showing that for the closely related Connected Dominating Set problem, the existence of such kernelization algorithms is unlikely, even though the problem is known to admit a linear kernel on $H$-topological-minor-free graphs. Also, we prove that for any somewhere dense class $\mathcal G$, there is some $r$ for which $r$-Dominating Set is W[$2$]-hard on $\mathcal G$. Thus, our results fall short of proving a sharp dichotomy for the parameterized complexity of $r$-Dominating Set on subgraph-monotone graph classes: we conjecture that the border of tractability lies exactly between nowhere dense and somewhere dense graph classes.Comment: v2: new author, added results for r-Dominating Sets in bounded expansion graph

Energies and damping rates of elementary excitations in spin-1 Bose-Einstein condensed gases

Finite temperature Green's function technique is used to calculate the energies and damping rates of elementary excitations of the homogeneous, dilute, spin-1 Bose gases below the Bose-Einstein condensation temperature both in the density and spin channels. For this purpose the self-consistent dynamical Hartree-Fock model is formulated, which takes into account the direct and exchange processes on equal footing by summing up certain classes of Feynman diagrams. The model is shown to fulfil the Goldstone theorem and to exhibit the hybridization of one-particle and collective excitations correctly. The results are applied to the gases of ^{23}Na and ^{87}Rb atoms.Comment: 26 pages, 21 figures. Added 2 new figures, detailed discussio

Limitations of squeezing due to collisional decoherence in Bose-Einstein condensates

We study the limitations for entanglement due to collisional decoherence in a Bose-Einstein condensate. Specifically we consider relative number squeezing between photons and atoms coupled out from a homogeneous condensate. We study the decay of excited quasiparticle modes due to collisions, in condensates of atoms with one or two internal degrees of freedom. The time evolution of these modes is determined in the linear response approximation to the deviation from equilibrium. We use Heisenberg-Langevin equations to derive equations of motion for the densities and higher correlation functions which determine the squeezing. In this way we can show that decoherence due to quasiparticle interactions imposes an important limit on the degree of number squeezing which may be achieved. Our results are also relevant for the determination of decoherence times in other experiments based on entanglement, e.g. the slowing and stopping of light in condensed atomic gases using dark states.Comment: 16 pages RevTeX, 3 figure

Landau damping in trapped Bose-condensed gases

We study Landau damping in dilute Bose-Einstein condensed gases in both spherical and prolate ellipsoidal harmonic traps. We solve the Bogoliubov equations for the mode spectrum in both of these cases, and calculate the damping by summing over transitions between excited quasiparticle states. The results for the spherical case are compared to those obtained in the Hartree-Fock approximation, where the excitations take on a single-particle character, and excellent agreement between the two approaches is found. We have also taken the semiclassical limit of the Hartree-Fock approximation and obtain a novel expression for the Landau damping rate involving the time dependent self-diffusion function of the thermal cloud. As a final approach, we study the decay of a condensate mode by making use of dynamical simulations in which both the condensate and thermal cloud are evolved explicitly as a function of time. A detailed comparison of all these methods over a wide range of sample sizes and trap geometries is presented.Comment: 18 pages, 13 figures, submitted to the New Journal of Physics focus issue on Quantum Gase

Quadrupole collective modes in trapped finite-temperature Bose-Einstein condensates

Finite temperature simulations are used to study quadrupole excitations of a trapped Bose-Einstein condensate. We focus specifically on the m=0 mode, where a long-standing theoretical problem has been to account for an anomalous variation of the mode frequency with temperature. We explain this behavior in terms of the excitation of two separate modes, corresponding to coupled motion of the condensate and thermal cloud. The relative amplitudes of the modes depends sensitively on the temperature and on the frequency of the harmonic drive used to excite them. Good agreement with experiment is found for appropriate drive frequencies.Comment: 4 pages, 3 figure

Equilibrium and dynamical properties of two dimensional self-gravitating systems

A system of N classical particles in a 2D periodic cell interacting via long-range attractive potential is studied. For low energy density $U$ a collapsed phase is identified, while in the high energy limit the particles are homogeneously distributed. A phase transition from the collapsed to the homogeneous state occurs at critical energy U_c. A theoretical analysis within the canonical ensemble identifies such a transition as first order. But microcanonical simulations reveal a negative specific heat regime near $U_c$. The dynamical behaviour of the system is affected by this transition : below U_c anomalous diffusion is observed, while for U > U_c the motion of the particles is almost ballistic. In the collapsed phase, finite $N$-effects act like a noise source of variance O(1/N), that restores normal diffusion on a time scale diverging with N. As a consequence, the asymptotic diffusion coefficient will also diverge algebraically with N and superdiffusion will be observable at any time in the limit N \to \infty. A Lyapunov analysis reveals that for U > U_c the maximal exponent \lambda decreases proportionally to N^{-1/3} and vanishes in the mean-field limit. For sufficiently small energy, in spite of a clear non ergodicity of the system, a common scaling law \lambda \propto U^{1/2} is observed for any initial conditions.Comment: 17 pages, Revtex - 15 PS Figs - Subimitted to Physical Review E - Two column version with included figures : less paper waste

The transverse breathing mode of an elongated Bose-Einstein condensate

We study experimentally the transverse monopole mode of an elongated rubidium condensate. Due to the scaling invariance of the non-linear Schr\"odinger (Gross-Pitaevski) equation, the oscillation is monochromatic and sinusoidal at short times, even under strong excitation. For ultra-low temperatures, the quality factor $Q=\omega_0/\gamma_0$ can exceed 2000, where $\omega_0$ and $\gamma_0$ are the mode angular frequency and damping rate. This value is much larger than any previously reported for other eigenmodes of a condensate. We also present the temperature variation of $\omega_0$ and $\gamma_0$.Comment: 4 pages, 4 figures, submitted to PR

Finite temperature theory of the trapped two dimensional Bose gas

We present a Hartree-Fock-Bogoliubov (HFB) theoretical treatment of the two-dimensional trapped Bose gas and indicate how semiclassical approximations to this and other formalisms have lead to confusion. We numerically obtain results for the fully quantum mechanical HFB theory within the Popov approximation and show that the presence of the trap stabilizes the condensate against long wavelength fluctuations. These results are used to show where phase fluctuations lead to the formation of a quasicondensate.Comment: 4 pages, 3 figure