Assessing the impact of non-additive noise on modelling transcriptional regulation with Gaussian processes

In transcriptional regulation, transcription factors (TFs) are often unobservable at mRNA level or may be controlled outside of the system being modelled. Gaussian processes are a promising approach for dealing with these difficulties as a prior distribution can be defined over the latent TF activity profiles and the posterior distribution inferred from the observed expression levels of potential target genes. However previous approaches have been based on the assumption of additive Gaussian noise to maintain analytical tractability. We investigate the influence of a more realistic form of noise on a biologically accurate system based on Michaelis-Menten kinetics

Measurements continuous in time and a posteriori states in quantum

Measurements continuous in time were consistently introduced in quantum mechanics and applications worked out, mainly in quantum optics. In this context a quantum filtering theory has been developed giving the reduced state after the measurement when a certain trajectory of the measured observables is registered (the a posteriori states). In this paper a new derivation of filtering equations is presented, in the cases of counting processes and of measurement processes of diffusive type. It is also shown that the equation for the a posteriori dynamics in the diffusive case can be obtained, by a suitable limit, from that one in the counting case. Moreover, the paper is intended to clarify the meaning of the various concepts involved and to discuss the connections among them. As an illustration of the theory, simple models are worked out.Comment: 31 page. See also related papers at http://www.maths.nott.ac.uk/personal/vpb/research/mes_fou.html and http://www.maths.nott.ac.uk/personal/vpb/research/fil_con.htm

Dynamics of open quantum systems initially entangled with environment: Beyond the Kraus representation

We present a general analysis of the role of initial correlations between the open system and an environment on quantum dynamics of the open system.Comment: 5 revtex pages, no figures, accepted for publication in Phys. Rev.

Magnetoconductance switching in an array of oval quantum dots

Employing oval shaped quantum billiards connected by quantum wires as the building blocks of a linear quantum dot array, we calculate the ballistic magnetoconductance in the linear response regime. Optimizing the geometry of the billiards, we aim at a maximal finite- over zero-field ratio of the magnetoconductance. This switching effect arises from a relative phase change of scattering states in the oval quantum dot through the applied magnetic field, which lifts a suppression of the transmission characteristic for a certain range of geometry parameters. It is shown that a sustainable switching ratio is reached for a very low field strength, which is multiplied by connecting only a second dot to the single one. The impact of disorder is addressed in the form of remote impurity scattering, which poses a temperature dependent lower bound for the switching ratio, showing that this effect should be readily observable in experiments.Comment: 11 pages, 8 figure

Ecological Complexity of Coral Recruitment Processes: Effects of Invertebrate Herbivores on Coral Recruitment and Growth Depends Upon Substratum Properties and Coral Species

Sarah W. Davies, Mikhail V. Matz, Integrative Biology Section, The University of Texas at Austin, Austin, Texas, United States of AmericaSarah W. Davies, Peter D. Vize, Department of Biological Sciences, University of Calgary, Calgary, Alberta, CanadaBackground: The transition from planktonic planula to sessile adult corals occurs at low frequencies and post settlement mortality is extremely high. Herbivores promote settlement by reducing algal competition. This study investigates whether invertebrate herbivory might be modulated by other ecological factors such as substrata variations and coral species identity. Methodology/Principal Findings: The experiment was conducted at the Flower Garden Banks, one of the few Atlantic reefs not experiencing considerable degradation. Tiles of differing texture and orientation were kept in bins surrounded by reef (24 m). Controls contained no herbivores while treatment bins contained urchins (Diadema antillarum) or herbivorous gastropods (Cerithium litteratum). Juvenile corals settling naturally were monitored by photography for 14 months to evaluate the effects of invertebrate herbivory and substratum properties. Herbivory reduced algae cover in urchin treatments. Two genera of brooding coral juveniles were observed, Agaricia and Porites, both of which are common but not dominant on adjacent reef. No broadcast spawning corals were observed on tiles. Overall, juveniles were more abundant in urchin treatments and on vertical, rough textured surfaces. Although more abundant, Agaricia juveniles were smaller in urchin treatments, presumably due to destructive overgrazing. Still, Agaricia growth increased with herbivory and substrata texture-orientation interactions were observed with reduced growth on rough tiles in control treatments and increased growth on vertical tiles in herbivore treatments. In contrast to Agaricia, Porites juveniles were larger on horizontal tiles, irrespective of herbivore treatment. Mortality was affected by substrata orientation with vertical surfaces increasing coral survival. Conclusions/Significance: We further substantiate that invertebrate herbivores play major roles in early settlement processes of corals and highlight the need for deeper understanding of ecological interactions modulating these effects. The absence of broadcast-spawning corals, even on a reef with consistently high coral cover, continues to expose the recruitment failure of these reef-building corals throughout the Caribbean.Natural Sciences and Engineering Research Council of Canada (NSERC) PGS-M to SWD; ACCESS Funding from the University of Calgary to SWD; National Science Foundation grant DEB-1054766 to MVM. Boat time provided by FGBNMS under permit# FGBNMS-2007-006. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School ofIntegrative BiologyEmail: [email protected]

Magnitude of Magnetic Field Dependence of a Possible Selective Spin Filter in ZnSe/Zn_{1-x}Mn_{x}Se Multilayer Heterostructure

Spin-polarized transport through a band-gap-matched ZnSe/Zn_{1-x}Mn_{x} Se/ZnSe/Zn_{1-x}Mn_{x}Se/ZnSe multilayer structure is investigated. The resonant transport is shown to occur at different energies for different spins owing to the split of spin subbands in the paramagnetic layers. It is found that the polarization of current density can be reversed in a certain range of magnetic field, with the peak of polarization moving towards a stronger magnetic field for increasing the width of central ZnSe layer while shifting towards an opposite direction for increasing the width of paramagnetic layer. The reversal is limited in a small-size system. A strong suppression of the spin up component of the current density is present at high magnetic field. It is expected that such a reversal of the polarization could act as a possible mechanism for a selective spin filter device

Dynamical Semigroups for Unbounded Repeated Perturbation of Open System

We consider dynamical semigroups with unbounded Kossakowski-Lindblad-Davies generators which are related to evolution of an open system with a tuned repeated harmonic perturbation. Our main result is the proof of existence of uniquely determined minimal trace-preserving strongly continuous dynamical semigroups on the space of density matrices. The corresponding dual W *-dynamical system is shown to be unital quasi-free and completely positive automorphisms of the CCR-algebra. We also comment on the action of dynamical semigroups on quasi-free states