Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

Yeast glycolysis is considered the prototype of dissipative biochemical oscillators. In cellular conditions, under sinusoidal source of glucose, the activity of glycolytic enzymes can display either periodic, quasiperiodic or chaotic behavior. In order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the non-linear statistical tool of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic speed functions of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. In agreement with experimental conditions, the studied time series corresponded to a quasi-periodic route to chaos. The results of the analysis are three-fold: first, in addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. Second, the dynamical structure exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis.Comment: Biologically improve

Detection of CO+ in the nucleus of M82

We present the detection of the reactive ion CO+ towards the prototypical starburst galaxy M82. This is the first secure detection of this short-lived ion in an external galaxy. Values of [CO+]/[HCO+]>0.04 are measured across the inner 650pc of the nuclear disk of M82. Such high values of the [CO+]/[HCO+] ratio had only been previously measured towards the atomic peak in the reflection nebula NGC7023. This detection corroborates that the molecular gas reservoir in the M82 disk is heavily affected by the UV radiation from the recently formed stars. Comparing the column densities measured in M82 with those found in prototypical Galactic photon-dominated regions (PDRs), we need \~20 clouds along the line of sight to explain our observations. We have completed our model of the molecular gas chemistry in the M82 nucleus. Our PDR chemical model successfully explains the [CO+]/[HCO+] ratios measured in the M~82 nucleus but fails by one order of magnitude to explain the large measured CO+ column densities (~1--4x10^{13} cm^{-2}). We explore possible routes to reconcile the chemical model and the observations.Comment: 12 pages, 2 figure

Molecular line probes of activity in galaxies

The use of specific tracers of the dense molecular gas phase can help to explore the feedback of activity on the interstellar medium (ISM) in galaxies. This information is a key to any quantitative assessment of the efficiency of the star formation process in galaxies. We present the results of a survey devoted to probe the feedback of activity through the study of the excitation and chemistry of the dense molecular gas in a sample of local universe starbursts and active galactic nuclei (AGNs). Our sample includes also 17 luminous and ultraluminous infrared galaxies (LIRGs and ULIRGs). From the analysis of the LIRGs/ULIRGs subsample, published in Gracia-Carpio et al.(2007) we find the first clear observational evidence that the star formation efficiency of the dense gas, measured by the L_FIR/L_HCN ratio, is significantly higher in LIRGs and ULIRGs than in normal galaxies. Mounting evidence of overabundant HCN in active environments would even reinforce the reported trend, pointing to a significant turn upward in the Kennicutt-Schmidt law around L_FIR=10^11 L_sun. This result has major implications for the use of HCN as a tracer of the dense gas in local and high-redshift luminous infrared galaxies.Comment: 4 pages, 2 figures, contributed paper to Far-Infrared Workshop 07 (FIR 2007

The IC1396N proto-cluster at a scale of 250 AU

We investigate the mm-morphology of IC1396N with unprecedented spatial resolution to analyze its dust and molecular gas properties, and draw comparisons with objects of similar mass. We have carried out sensitive observations in the most extended configurations of the IRAM Plateau de Bure interferometer, to map the thermal dust emission at 3.3 and 1.3mm, and the emission from the $J$=13$_k\to12_k$ hyperfine transitions of methyl cyanide (CH$_3$CN). We unveil the existence of a sub-cluster of hot cores in IC1396N, distributed in a direction perpendicular to the emanating outflow. The cores are embedded in a common envelope of extended and diffuse dust emission. We find striking differences in the dust properties of the cores ($\beta\simeq$ 0) and the surrounding envelope ($\beta\simeq$ 1), very likely testifying to differences in the formation and processing of dust material. The CH$_3$CN emission peaks towards the most massive hot core and is marginally extended in the outflow direction

ISO observations toward the reflection nebula NGC 7023: A nonequilibrium ortho- to para-H2 ratio

We have observed the S(0), S(1), S(2), S(3), S(4) and S(5) rotational lines of molecular hydrogen (H2) towards the peak of the photodissociation region (PDR) associated with the reflection nebula NGC 7023. The observed H2 line ratios show that they arise in warm gas with kinetic temperatures ~300 - 700 K. However, the data cannot be fitted by an ortho- to para- (OTP) ratio of 3. An OTP ratio in the range ~1.5 - 2 is necessary to explain our observations. This is the first detection of a non-equilibrium OTP ratio measured from the H2 pure-rotational lines in a PDR. The existence of a dynamical PDR is discussed as the most likely explanation for this low OTP ratio.Comment: 4 pages, 3 figure

Structure and electronic properties of molybdenum monoatomic wires encapsulated in carbon nanotubes

Monoatomic chains of molybdenum encapsulated in single walled carbon nanotubes of different chiralities are investigated using density functional theory. We determine the optimal size of the carbon nanotube for encapsulating a single atomic wire, as well as the most stable atomic arrangement adopted by the wire. We also study the transport properties in the ballistic regime by computing the transmission coefficients and tracing them back to electronic conduction channels of the wire and the host. We predict that carbon nanotubes of appropriate radii encapsulating a Mo wire have metallic behavior, even if both the nanotube and the wire are insulators. Therefore, encapsulating Mo wires in CNT is a way to create conductive quasi one-dimensional hybrid nanostructures.Comment: 8 pages, 10 figure

Impact of dimerization and stretching on the transport properties of molybdenum atomic wires

We study the electrical and transport properties of monoatomic Mo wires with different structural characteristics. We consider first periodic wires with inter-atomic distances ranging between the dimerized wire to that formed by equidistant atoms. We find that the dimerized case has a gap in the electronic structure which makes it insulating, as opposed to the equidistant or near-equidistant cases which are metallic. We also simulate two conducting one-dimensional Mo electrodes separated by a scattering region which contains a number of dimers between 1 and 6. The $I-V$ characteristics strongly depend on the number of dimers and vary from ohmic to tunneling, with the presence of different gaps. We also find that stretched chains are ferromagnetic.Comment: 8 pages, 7 figure