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$\begin{figure} \par\includegraphics[width=15.4cm,clip]{f01-ms6117.eps}\end{figure}$ Figure 1: IRAM 30 m telescope spectra of CO 4-3, 6-5, 9-8, 10-9, 11-10 and the average CO spectrum from APM 08279+5255, with Gaussian fit profiles superimposed. Velocity scales are relative to a redshift of z=3.911. The velocity resolution for individual spectra is 50 kms^-1. For the average spectrum, the velocity resolution is 22 kms^-1. The individual spectra are plotted on the same scale in flux density ( left axis).
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In the text

$\begin{figure} \par\includegraphics[width=7.7cm,clip]{f02-ms6117.eps}\end{figure}$ Figure 2: Integrated CO(4-3) and CO(9-8) spectra from APM 08279+5255 obtained with the IRAM Interferometer. For both spectra the velocity offsets are given relative to a redshift of z=3.911. Upper panel: CO(4-3) profile above the dust continuum of 1.3 mJy. The channel width is 20 kms^-1with an rms noise of 0.7 mJy. Lower panel: CO(9-8) profile above the dust continuum. The channel width is 20 kms^-1 with an rms noise of 1.7 mJy. The dust continuum is 16.9 mJy.
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In the text

$\begin{figure} \par\includegraphics[angle=-90,width=7.7cm,clip]{f03-ms6117.eps}\end{figure}$ Figure 3: Map of an 8'' field around APM 08279 made with the IRAM Interferometer at 1.4 mm. The signal is the CO(9-8) line integrated over 760 kms^-1, plus the 1.4 mm dust emission at the highest spatial resolution (uniform weighting, beam: $0\hbox{$.\!\!^{\prime\prime}$ }71 \times 0\hbox{$.\!\!^{\prime\prime}$ }64$ ( lower left inset)). Contours start at 3 $\sigma = 1.35$ mJy beam^-1 and increase in steps of 3 $\sigma$ . The peak is 19.4 mJy beam^-1 (43 $\sigma$ ) and the spatially-integrated flux is 33.9 mJy.
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In the text

$\begin{figure} \par\includegraphics[angle=-90,width=7.7cm,clip]{f04-ms6117.eps}\end{figure}$ Figure 4: Size measurement with the IRAM Interferometer: visibility amplitudes of the signal in the receivers' lower sideband at 1.4 mm. The signal is the CO(9-8) line integrated over 760 kms^-1, plus the 1.4 mm dust emission. The plot shows the real part of the visibility amplitude vs. the projected antenna spacing, for u,v-plane data averaged in circular bins 40 m wide, with error bars of $\pm 1\sigma$ . The solid curve is a circular Gaussian fit with half-power width $0\hbox{$.\!\!^{\prime\prime}$ }6\pm 0\hbox{$.\!\!^{\prime\prime}$ }2$ .
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In the text

$\begin{figure} \par\includegraphics[width=8cm,clip]{f05-ms6117.eps}\end{figure}$ Figure 5: HCN(5-4) spectrum from APM 08279+5255 obtained with the IRAM Interferometer. The line profile appears above the dust continuum of 1.3 mJy. The velocity scale is relative to a redshift of z=3.911, the beam is $7\hbox{$.\!\!^{\prime\prime}$ }2 \times 5\hbox{$.\!\!^{\prime\prime}$ }4$ at PA 81 $^\circ$ , and the channel width is 15 MHz (49.84 kms^-1). The rms noise in the spectrum is 0.47 mJy.
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In the text

$\begin{figure} \par\includegraphics[width=15.4cm,clip]{f06-ms6117.eps}\end{figure}$ Figure 6: Single component ( left) and two component ( right) dust models for APM 08279+5255. The continuum fluxes are from Irwin etal. (1998), Lewis etal. (1998, 2002a), Downes etal. (1999), Egami etal. (2000), Papadopoulos etal. (2001), Barvainis & Ivison (2002), Wagg etal. (2005), Beelen etal. (2006) and this work.
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In the text

$\begin{figure} \par\includegraphics[width=8.2cm,clip]{f07-ms6117.eps}\end{figure}$ Figure 7: Observed CO fluxes vs. rotational quantum number (CO line SED) for APM 08279+5255, obtained with the IRAM 30 m telescope (filled squares) and the IRAM Interferometer (open triangles) (D99; this paper). Errors include the calibration uncertainties. The fluxes for the 1-0 and 2-1 lines are from Papadopoulos etal. (2001, filled triangles), and Riechers etal. (2006, circle at J=1). The single-component LVG model fluxes are shown for ( $n(\mbox{H$_2$ })$ , $\mbox{$T_{\rm kin}$ }$ ) combinations as follows: solid line: (10^4.4 cm^-3, 125 K); dashed line: (10^4.2 cm^-3, 220 K); dotted line: (10^5.4 cm^-3, 40 K); dashed-dotted line: (10^4.0 cm^-3, 350 K). The inset shows a zoom, for the observed and model-predicted fluxes of the 1-0 and 2-1 lines. The two CO(1-0) data points are shown with a small offset in the rotational quantum number for legibility reasons.
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In the text

$\begin{figure} \par\includegraphics[width=7.8cm,clip]{f08-ms6117.eps}\end{figure}$ Figure 8: $\chi ^2$ distribution for a single component LVG model fit to the observed line luminosity ratios (greyscale and grey contours, contours: $\chi ^2=2$ , 4, 8, 10 and 20). The CO abundance per velocity gradient for the LVG models is [CO]/ $\mbox{$({\rm d}v/{\rm d}r)$ }= 1\times 10^{-5}~{\rm pc}~(\mbox{\thinspace km\thinspace s$^{-1}$ })^{-1}$ . Black lines show gas to dust mass ratios of 60, 150 and 500 calculated from the LVG H₂ mass for a dust mass of $M_{\rm dust}=7.5\times 10^8~m^{-1}$ $M_{\odot }$ (single component dust fit, see Sect. 3.1). For the calculation of the LVG H₂ mass we have used a turbulence line width of ${\rm d}v_{\rm turb}=100~\mbox{\thinspace km\thinspace s$^{-1}$ }$ and a velocity gradient of $\mbox{$({\rm d}v/{\rm d}r)$ }=5~\mbox{\thinspace km\thinspace s$^{-1}$ }~{\rm pc}^{-1}$ (see also Sect. 4.2).
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In the text

$\begin{figure} \par\includegraphics[width=8.2cm,clip]{f09-ms6117.eps}\end{figure}$ Figure 9: 2-component model for the CO lines. The dotted line represents the "cold'', dense gas, the dashed line the "warm'' gas and the solid line the sum of both components. Model parameters are listed in Table 3.
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In the text

$\begin{figure} \par\includegraphics[width=16.4cm,clip]{f10-ms6117.eps}\end{figure}$ Figure 10: Left: HCN line SED as a function of the IR radiation temperature for a H₂ density of 10⁵ cm^-3, a kinetic temperature of 65 K and an delution factor for the IR radiation field of 10% for each model. All SEDs are normalized to the HCN(1-0) flux density for the pure collisional excitation model ( $T_{\rm IR}=0$ K). The plot exemplifies the large effect of IR pumping on the HCN excitation for dust temperatures above $\sim$ 100 K. Middle: HCN excitation in APM 08279+5255 for gas parameters as derived from the single component dust/CO model (n(H₂) = 10^4.2 cm^-3, $T_{\rm IR}=\mbox{$T_{\rm kin}$ }=220$ K and r₀=790 pc) as a function of the IR filling factor. For IR $_{\rm ff}=10$ % or above the IR pumping boosts the HCN excitation such that the HCN(5-4) flux density is in agreement with the observations. Right: HCN excitation model for the two-component dust/CO model for APM 08279+5255. The dashed line represents the "warm'' gas with and IR illumination factor of unity, the dotted lines the "cold'', dense gas with pure collisional excitation (IR $_{\rm ff}=0$ ) and with an IR illumination of 0.25%. The solid line the sum of both IR illuminated components. The IR radiation temperature for both components is 220 K.
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In the text

$\begin{figure} \par\includegraphics[width=8.4cm,clip]{f11-ms6117.eps}\end{figure}$ Figure 11: Radial dependence of $L^\prime _{\rm CO}$ calculated using the differential triple-image lens model from Egami etal. (2000, their Fig. 9) for a filled, face-on disk (top) and a disk seen at an inclination of $70^\circ$ with an area filling factor for the CO emission of $f_{\rm A}=0.5$ (bottom). Curves are shown for selected LVG models. For the cold component $r_{\rm min}$ has been set based on the radius of the warm component to 50 and 100 pc for the face-on and inclined case respectively. For all other models we used $r_{\rm min}=1$ pc. The horizontal lines show the total, observed CO(1-0) line luminosity (Riechers etal. 2006, solid line) and the contributions to $L^\prime _{\rm CO}$ from the cold (dashed line) and the warm (dotted line) gas components derived in Sect. 3.2.3. The relevant intersections between these curves are marked by the arrows for the four models. Resulting source radii and effective magnifications are given in the plot.
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In the text

$\begin{figure} \par\includegraphics[width=8.24cm,clip]{f12-ms6117.ps}\end{figure}$ Figure 12: Schematic diagram of our 2-component model for the CO, HCN, and mm-FIR dust emission from APM 08279+5255. There are two constraints on the geometry: 1) the large CO and HCN linewidths of 480 kms^-1 imply the molecular rings are being viewed at high inclination. 2) Our line of sight to the black hole must intersect the BAL outflow cone, as in the model by Elvis (2000), so that UV broad absorption lines are seen against the UV continuum and UV emission lines of the accretion disk. In the molecular rings, the HCN and high-J CO lines mainly come from the "cold'', dense component at >100 pc (outer disk), and some of the mid-J CO emission comes from the "warm'', lower-density component at 50-100 pc (inner disk). The NIR radiation (Egami etal. 2000; Soifer etal. 2004) comes from the 1500 K-dust sublimation radius at $\sim$ 1 pc. The absorbers responsible for the X-ray BALs are located at radii of <0.1 pc from the black hole (Chartas etal. 2002; Hasinger etal. 2002).
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In the text

$\begin{figure} \par\includegraphics[width=8.2cm,clip]{f13-ms6117.eps}\end{figure}$ Figure 13: Black hole, molecular, stellar and dynamical mass in the central region of APM 08279 as a function of assumed inclination of the molecular disk. Radii as a function of the inclination have been calculated from Eq. (13) for the cold, dense gas (r₀=995 pc, $r_{\rm min}=1$ pc) using a filling factor of unity. The stellar mass has been calculated using a scalelength of the stellar bulge of 5 and 10 kpc and assuming the $M_{\rm BH}-\sigma\!_*$ relation were to hold. Variations of the stellar bulge contribution with inclination are only due to changes of the size of the region considered. The corresponding radii are given at the top axis of the plot. The inclination for which the total mass (gas + stellar + BH) matches the dynamical mass are given for both bulge geometries together with the corresponding numbers for the true CO radius, effective magnification of the molecular gas, and the CO rotation velocity.
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In the text

$\begin{figure} \par\includegraphics[width=8.2cm,clip]{f14-ms6117.eps}\end{figure}$ Figure 14: Comparison of the CO line SEDs of selected local and high-z galaxies. The SEDs are shown for APM 08279 (this paper, Fig. 7), BR1202-0725 (z=4.7, Carilli etal. 2002; Riechers etal. 2006), J1148+5251 (z=6.4, open squares, Bertoldi etal. 2003; Walter etal. 2003) the high-excitation component in the center of M82 (Weiß etal. 2005b), NGC 253 center (Güsten etal. 2006) SMM 16359 (z=2.5, Weiß etal. 2005a) and the Galactic Center (solid circles, Fixsen etal. 1999). The CO line SEDs are normalized by their CO(1-0) flux density.
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In the text

$\begin{figure} \par\includegraphics[width=15.4cm,clip]{f06-ms6117.eps}\end{figure}$	Figure 6: Single component ( left) and two component ( right) dust models for APM 08279+5255. The continuum fluxes are from Irwin etal. (1998), Lewis etal. (1998, 2002a), Downes etal. (1999), Egami etal. (2000), Papadopoulos etal. (2001), Barvainis & Ivison (2002), Wagg etal. (2005), Beelen etal. (2006) and this work.
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$\begin{figure} \par\includegraphics[width=8.2cm,clip]{f09-ms6117.eps}\end{figure}$	Figure 9: 2-component model for the CO lines. The dotted line represents the "cold'', dense gas, the dashed line the "warm'' gas and the solid line the sum of both components. Model parameters are listed in Table 3.
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