Inelastic final-state interaction

The final-state interaction in multichannel decay processes is sytematically studied with application to B decay in mind. Since the final-state inteaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like "Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominant inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonethless we are able to obtain some insight in the issue and draw useful conclusions on general fearyres on the strong phases.Comment: The published version. One figure correcte

Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be markedly enhanced by a suitable choice of overlap between the upstream regulatory domains. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons, that regulate each other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX

Robust Trapped-Ion Quantum Logic Gates by Continuous Dynamical Decoupling

We introduce a novel scheme that combines phonon-mediated quantum logic gates in trapped ions with the benefits of continuous dynamical decoupling. We demonstrate theoretically that a strong driving of the qubit decouples it from external magnetic-field noise, enhancing the fidelity of two-qubit quantum gates. Moreover, the scheme does not require ground-state cooling, and is inherently robust to undesired ac-Stark shifts. The underlying mechanism can be extended to a variety of other systems where a strong driving protects the quantum coherence of the qubits without compromising the two-qubit couplings.Comment: Slightly longer than the published versio

Megawatt solar power systems for lunar surface operations

The work presented here shows that a solar power system can provide power on the order of one megawatt to a lunar base with a fairly high specific power. The main drawback to using solar power is still the high mass, and therefore, cost of supplying energy storage through the solar night. The use of cryogenic reactant storage in a fuel cell system, however, greatly reduces the total system mass over conventional energy storage schemes

Sampling rare switching events in biochemical networks

Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because switching events are rapid, yet infrequent. We present a simulation technique that makes it possible to predict the rate and mechanism of flipping of biochemical switches. The method uses a series of interfaces in phase space between the two stable steady states of the switch to generate transition trajectories in a ratchet-like manner. We demonstrate its use by calculating the spontaneous flipping rate of a symmetric model of a genetic switch consisting of two mutually repressing genes. The rate constant can be obtained orders of magnitude more efficiently than using brute-force simulations. For this model switch, we show that the switching mechanism, and consequently the switching rate, depends crucially on whether the binding of one regulatory protein to the DNA excludes the binding of the other one. Our technique could also be used to study rare events and non-equilibrium processes in soft condensed matter systems.Comment: 9 pages, 6 figures, last page contains supplementary informatio

Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

Stability of adhesion clusters under constant force

We solve the stochastic equations for a cluster of parallel bonds with shared constant loading, rebinding and the completely dissociated state as an absorbing boundary. In the small force regime, cluster lifetime grows only logarithmically with bond number for weak rebinding, but exponentially for strong rebinding. Therefore rebinding is essential to ensure physiological lifetimes. The number of bonds decays exponentially with time for most cases, but in the intermediate force regime, a small increase in loading can lead to much faster decay. This effect might be used by cell-matrix adhesions to induce signaling events through cytoskeletal loading.Comment: Revtex, 4 pages, 4 Postscript files include

Calibrating AIS images using the surface as a reference

A method of evaluating the initial assumptions and uncertainties of the physical connection between Airborne Imaging Spectrometer (AIS) image data and laboratory/field spectrometer data was tested. The Tuscon AIS-2 image connects to lab reference spectra by an alignment to the image spectral endmembers through a system gain and offset for each band. Images were calibrated to reflectance so as to transform the image into a measure that is independent of the solar radiant flux. This transformation also makes the image spectra directly comparable to data from lab and field spectrometers. A method was tested for calibrating AIS images using the surface as a reference. The surface heterogeneity is defined by lab/field spectral measurements. It was found that the Tuscon AIS-2 image is consistent with each of the initial hypotheses: (1) that the AIS-2 instrument calibration is nearly linear; (2) the spectral variance is caused by sub-pixel mixtures of spectrally distinct materials and shade, and (3) that sub-pixel mixtures can be treated as linear mixtures of pure endmembers. It was also found that the image can be characterized by relatively few endmembers using the AIS-2 spectra

Investigation of potential diseases associated with Northern Territory mammal declines

There is compelling evidence of broad-scale declines in populations of small terrestrial native mammals in northern Australia, including the Top End of the Northern Territory (NT) over the past 20 years. Causes under consideration include changed fire regimes, introduced fauna (including predators) and disease. To date information on health and disease in northern Australian mammals has been limited. Disease is increasingly recognised as a primary driver of some wildlife population declines and extinctions e.g., Tasmanian devil facial tumour disease, white nose syndrome in bats and chytrid fungus in amphibians. Disease has been identified as a risk factor for extinction in declining and fragmented wildlife populations globally, particularly in situations of increased environmental stressors, changing ecosystems, arrival of new vertebrate threats or climate change. Unless wild populations are studied in detail over long periods of time, the effects of disease are easily overlooked and may be difficult to determine. This study is the largest and most comprehensive study of health and disease in small mammals in northern Australia and is one of a small number of studies worldwide to have approached investigation of wildlife populations in this comprehensive manner