Estimation and reduction of the uncertainties in chemical models: Application to hot core chemistry

It is not common to consider the role of uncertainties in the rate coefficients used in interstellar gas-phase chemical models. In this paper, we report a new method to determine both the uncertainties in calculated molecular abundances and their sensitivities to underlying uncertainties in the kinetic data utilized. The method is used in hot core models to determine if previous analyses of the age and the applicable cosmic-ray ionization rate are valid. We conclude that for young hot cores ($\le 10^4$ yr), the modeling uncertainties related to rate coefficients are reasonable so that comparisons with observations make sense. On the contrary, the modeling of older hot cores is characterized by strong uncertainties for some of the important species. In both cases, it is crucial to take into account these uncertainties to draw conclusions from the comparison of observations with chemical models.Comment: Accepted for publication in A&

Molecular basis of FIR-mediated c-myc transcriptional control

The far upstream element (FUSE) regulatory system promotes a peak in the concentration of c-Myc during cell cycle. First, the FBP transcriptional activator binds to the FUSE DNA element upstream of the c-myc promoter. Then, FBP recruits its specific repressor (FIR), which acts as an on/off transcriptional switch. Here we describe the molecular basis of FIR recruitment, showing that the tandem RNA recognition motifs of FIR provide a platform for independent FUSE DNA and FBP protein binding and explaining the structural basis of the reversibility of the FBP-FIR interaction. We also show that the physical coupling between FBP and FIR is modulated by a flexible linker positioned sequentially to the recruiting element. Our data explain how the FUSE system precisely regulates c-myc transcription and suggest that a small change in FBP-FIR affinity leads to a substantial effect on c-Myc concentration.MRC Grant-in-aid U11757455

Phase diffusion as a model for coherent suppression of tunneling in the presence of noise

We study the stabilization of coherent suppression of tunneling in a driven double-well system subject to random periodic $\delta-$function ``kicks''. We model dissipation due to this stochastic process as a phase diffusion process for an effective two-level system and derive a corresponding set of Bloch equations with phase damping terms that agree with the periodically kicked system at discrete times. We demonstrate that the ability of noise to localize the system on either side of the double-well potenital arises from overdamping of the phase of oscillation and not from any cooperative effect between the noise and the driving field. The model is investigated with a square wave drive, which has qualitatively similar features to the widely studied cosinusoidal drive, but has the additional advantage of allowing one to derive exact analytic expressions.Comment: 17 pages, 4 figures, submitted to Phys. Rev.

Effects of a Protein Preload on Gastric Emptying, Glycemia, and Gut Hormones After a Carbohydrate Meal in Diet-Controlled Type 2 Diabetes

OBJECTIVE: We evaluated whether a whey preload could slow gastric emptying, stimulate incretin hormones, and attenuate postprandial glycemia in type 2 diabetes. RESEARCH DESIGN AND METHODS: Eight type 2 diabetic patients ingested 350 ml beef soup 30 min before a potato meal; 55 g whey was added to either the soup (whey preload) or potato (whey in meal) or no whey was given. RESULTS: Gastric emptying was slowest after the whey preload (P < 0.0005). The incremental area under the blood glucose curve was less after the whey preload and whey in meal than after no whey (P < 0.005). Plasma glucose-dependent insulinotropic polypeptide, insulin, and cholecystokinin concentrations were higher on both whey days than after no whey, whereas glucagon-like peptide 1 was greatest after the whey preload (P < 0.05). CONCLUSIONS: Whey protein consumed before a carbohydrate meal can stimulate insulin and incretin hormone secretion and slow gastric emptying, leading to marked reduction in postprandial glycemia in type 2 diabetes.Jing Ma, Julie E. Stevens, Kimberly Cukier, Anne F. Maddox, Judith M. Wishart, Karen L. Jones, Peter M. Clifton, Michael Horowitz, and Christopher K. Rayne

Electron energy loss and induced photon emission in photonic crystals

The interaction of a fast electron with a photonic crystal is investigated by solving the Maxwell equations exactly for the external field provided by the electron in the presence of the crystal. The energy loss is obtained from the retarding force exerted on the electron by the induced electric field. The features of the energy loss spectra are shown to be related to the photonic band structure of the crystal. Two different regimes are discussed: for small lattice constants $a$ relative to the wavelength of the associated electron excitations $\lambda$, an effective medium theory can be used to describe the material; however, for $a\sim\lambda$ the photonic band structure plays an important role. Special attention is paid to the frequency gap regions in the latter case.Comment: 12 pages, 7 figure

Chaos or Noise - Difficulties of a Distinction

In experiments, the dynamical behavior of systems is reflected in time series. Due to the finiteness of the observational data set it is not possible to reconstruct the invariant measure up to arbitrary fine resolution and arbitrary high embedding dimension. These restrictions limit our ability to distinguish between signals generated by different systems, such as regular, chaotic or stochastic ones, when analyzed from a time series point of view. We propose to classify the signal behavior, without referring to any specific model, as stochastic or deterministic on a certain scale of the resolution $\epsilon$, according to the dependence of the $(\epsilon,\tau)$-entropy, $h(\epsilon, \tau)$, and of the finite size Lyapunov exponent, $\lambda(\epsilon)$, on $\epsilon$.Comment: 24 pages RevTeX, 9 eps figures included, two references added, minor corrections, one section has been split in two (submitted to PRE

Understanding Uncertainties in Model-Based Predictions of Aedes aegypti Population Dynamics

Dengue is one of the most important insect-vectored human viral diseases. The principal vector is Aedes aegypti, a mosquito that lives in close association with humans. Currently, there is no effective vaccine available and the only means for limiting dengue outbreaks is vector control. To help design vector control strategies, spatial models of Ae. aegypti population dynamics have been developed. However, the usefulness of such models depends on the reliability of their predictions, which can be affected by different sources of uncertainty including uncertainty in the model parameter estimation, uncertainty in the model structure, measurement errors in the data fed into the model, individual variability, and stochasticity in the environment. This study quantifies uncertainties in the mosquito population dynamics predicted by Skeeter Buster, a spatial model of Ae. aegypti, for the city of Iquitos, Peru. The uncertainty quantification should enable us to better understand the reliability of model predictions, improve Skeeter Buster and other similar models by targeting those parameters with high uncertainty contributions for further empirical research, and thereby decrease uncertainty in model predictions

Photoabsorption and photoion spectroscopy of atomic uranium in the region of 6p and 5d excitations

The photoabsorption process in atomic uranium has been investigated experimentally and theoretically in the 15–150-eV region. Using the dual laser plasma technique, the 6p photoabsorption spectrum has been recorded while for the first time the 5d region has been remeasured photoelectrically using both photoabsorption and photoion spectroscopy. Interpretation of the photoabsorption spectra is supported by Hartree-Fock calculations which take into account spin-flip decay and the interaction of many discrete states with many continua. The 6p spectrum is entirely dominated by spin-orbit split 6p⃗6d transitions. The 5d-subshell photoabsorption is shown to consist predominantly of discrete 5d⃗5f excitations; here the electrostatic and spin-orbit interactions are comparable in strength