Gene phylogenies and protein–protein interactions: possible artifacts resulting from shared protein interaction partners

The study of gene families critically depends on the correct reconstruction of gene genealogies, as for instance in the case of transcription factor genes like Hox genes and Dlx gene families. Proteins belonging to the same family are likely to share some of the same protein interaction partners and may thus face a similar selective environment. This common selective environment can induce co-evolutionary pressures and thus can give rise to correlated rates and patterns of evolution among members of a gene family. In this study, we simulate the evolution of a family of sequences which share a set of interaction partners. Depending on the amount of sequence dedicated to protein–protein interaction and the relative rate parameters of sequence evolution three outcomes are possible: if the fraction of the sequence dedicated to interaction with common co-factors is low and the time since divergence is small, the trees based on sequence information tend to be correct. If the time since gene duplication is long two possible outcomes are observed in our simulations. If the rate of evolution of the interaction partner is small compared to the rate of evolution of the focal protein family, the reconstructed trees tend towards star phylogenies. As the rate of evolution of the interaction partner approaches that of the focal protein family the reconstructed phylogenies tend to be incorrectly resolved. We conclude that the genealogies of gene families can be hard to estimate, in particular if the proteins interact with a conserved set of binding partners, as is likely the case for transcription factors

Excitable Scale Free Networks

When a simple excitable system is continuously stimulated by a Poissonian external source, the response function (mean activity versus stimulus rate) generally shows a linear saturating shape. This is experimentally verified in some classes of sensory neurons, which accordingly present a small dynamic range (defined as the interval of stimulus intensity which can be appropriately coded by the mean activity of the excitable element), usually about one or two decades only. The brain, on the other hand, can handle a significantly broader range of stimulus intensity, and a collective phenomenon involving the interaction among excitable neurons has been suggested to account for the enhancement of the dynamic range. Since the role of the pattern of such interactions is still unclear, here we investigate the performance of a scale-free (SF) network topology in this dynamic range problem. Specifically, we study the transfer function of disordered SF networks of excitable Greenberg-Hastings cellular automata. We observe that the dynamic range is maximum when the coupling among the elements is critical, corroborating a general reasoning recently proposed. Although the maximum dynamic range yielded by general SF networks is slightly worse than that of random networks, for special SF networks which lack loops the enhancement of the dynamic range can be dramatic, reaching nearly five decades. In order to understand the role of loops on the transfer function we propose a simple model in which the density of loops in the network can be gradually increased, and show that this is accompanied by a gradual decrease of dynamic range.Comment: 6 pages, 4 figure

Creation of NOON states by double Fock-state/Bose-Einstein condensates

NOON states (states of the form $|N>_{a}|0>_{b}+|0>_{a}|N>_{b}$ where $a$ and $b$ are single particle states) have been used for predicting violations of hidden-variable theories (Greenberger-Horne-Zeilinger violations) and are valuable in metrology for precision measurements of phase at the Heisenberg limit. We show theoretically how the use of two Fock state/Bose-Einstein condensates as sources in a modified Mach Zender interferometer can lead to the creation of the NOON state in which $a$ and $b$ refer to arms of the interferometer and $N$ is the total number of particles in the two condensates. The modification of the interferometer involves making conditional ``side'' measurements of a few particles near the sources. These measurements put the remaining particles in a superposition of two phase states, which are converted into NOON states by a beam splitter. The result is equivalent to the quantum experiment in which a large molecule passes through two slits. The NOON states are combined in a final beam splitter and show interference. Attempts to detect through which ``slit'' the condensates passed destroys the interference.Comment: 8 pages 5 figure

Novel Collective Effects in Integrated Photonics

Superradiance, the enhanced collective emission of energy from a coherent ensemble of quantum systems, has been typically studied in atomic ensembles. In this work we study theoretically the enhanced emission of energy from coherent ensembles of harmonic oscillators. We show that it should be possible to observe harmonic oscillator superradiance for the first time in waveguide arrays in integrated photonics. Furthermore, we describe how pairwise correlations within the ensemble can be measured with this architecture. These pairwise correlations are an integral part of the phenomenon of superradiance and have never been observed in experiments to date.Comment: 7 pages, 3 figure

Schroedinger cat-like states by conditional measurements on a beam-splitter

A scheme for generating Schr\"{o}dinger cat-like states of a single-mode optical field by means of conditional measurement is proposed. Feeding into a beam splitter a squeezed vacuum and counting the photons in one of the output channels, the conditional states in the other output channel exhibit a number of properties that are very similar to those of superpositions of two coherent states with opposite phases. We present analytical and numerical results for the photon-number and quadrature-component distributions of the conditional states and their Wigner and Husimi functions. Further, we discuss the effect of realistic photocounting on the states.Comment: 6 figures(divided in subfigures) using a4.st

Removal of a single photon by adaptive absorption

We present a method to remove, using only linear optics, exactly one photon from a field-mode. This is achieved by putting the system in contact with an absorbing environment which is under continuous monitoring. A feedback mechanism then decouples the system from the environment as soon as the first photon is absorbed. We propose a possible scheme to implement this process and provide the theoretical tools to describe it

On quantum teleportation with beam-splitter-generated entanglement

Following the lead of Cochrane, Milburn, and Munro [Phys. Rev. A {\bf 62}, 062307 (2000)], we investigate theoretically quantum teleportation by means of the number-sum and phase-difference variables. We study Fock-state entanglement generated by a beam splitter and show that two-mode Fock-state inputs can be entangled by a beam splitter into close approximations of maximally entangled eigenstates of the phase difference and the photon-number sum (Einstein-Podolsky-Rosen -- EPR -- states). Such states could be experimentally feasible with on-demand single-photon sources. We show that the teleportation fidelity can reach near unity when such ``quasi-EPR'' states are used as the quantum channel.Comment: 7 pages (two-column), 7 figures, submitted to Phys. Rev. A. Text unmodified, postscript error correcte

Mean field effects on the scattered atoms in condensate collisions

We consider the collision of two Bose Einstein condensates at supersonic velocities and focus on the halo of scattered atoms. This halo is the most important feature for experiments and is also an excellent testing ground for various theoretical approaches. In particular we find that the typical reduced Bogoliubov description, commonly used, is often not accurate in the region of parameters where experiments are performed. Surprisingly, besides the halo pair creation terms, one should take into account the evolving mean field of the remaining condensate and on-condensate pair creation. We present examples where the difference is clearly seen, and where the reduced description still holds.Comment: 6 pages, 4 figure

Producing the event ready two photon polarization EPR state with linear optics devices

We propose a scheme to produce the maximally two photon polarization entangled state(EPR state) with single photon sources and the linear optics devices. In particular, our scheme requires the photon detectors only to distinguish the vacuum and non-vacuum Fock number states. A sophisticated photon detector distinguishing one or two photon states is unnecessary.Comment: Published in Phys. Rev. A alread