University of Groningen
Chemical fingerprints of star forming regions and active galaxies
Pérez-Beaupuits, Juan-Pablo
IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to
cite from it. Please check the document version below.
Document Version
Publisher's PDF, also known as Version of record
Publication date:
2010
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Pérez-Beaupuits, J-P. (2010). Chemical fingerprints of star forming regions and active galaxies Groningen:
s.n.
Copyright
Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the
author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).
Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately
and investigate your claim.
Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the
number of authors shown on this cover page is limited to 10 maximum.
Download date: 16-06-2017
Chemical fingerprints of star
forming regions and active
galaxies
Proefschrift
ter verkrijging van het doctoraat in de
Wiskunde en Natuurwetenschappen
aan de Rijksuniversiteit Groningen
op gezag van de
Rector Magnificus, dr. F. Zwarts,
in het openbaar te verdedigen op
vrijdag 8 oktober 2010
om 14.45 uur
door
Juan Pablo Pérez Beaupuits
geboren op 16 mei 1975
te Santiago, Chile
Promotor:
Prof. dr. M. C. Spaans
Beoordelingscommissie:
Prof. dr. W. A. Baan
Prof. dr. K. M. Menten
Prof. dr. K. Wada
ISBN 978-90-367-4544-4
ISBN 978-90-367-4545-1 (electronic version)
The scientist is not a person who gives the right answers,
he is one who asks the right questions.
– Clause Levi-Strauss (French Philosopher, 1908 – 2009)
We have to abandon the idea that schooling is something
restricted to youth. How can it be, in a world where
half the things a man knows at 20 are no longer true at
40 – and half the things he knows at 40 had not been
discovered when he was 20?.
– Arthur C. Clarke (English Writer of science fiction, 1917 – 2008)
The secret of success in life is for a man to be ready for
his opportunity when it comes.
– Benjamin Disraeli (England’s prime minister, 1804 – 1881)
Some men give up their designs when they have almost
reached the goal; while others, on the contrary, obtain
a victory by exerting, at the last moment, more vigorous
efforts than ever before.
– Herodotus (Greek Historian, 484 BC – ca. 425 BC)
A mis padres
Front cover: photography of the Milky Way in the southern hemisphere, taken by
Alexandru Tudorica, merged with a photography of a sunset at the Submillimeter
Array in Mauna Kea, Hawaii, taken by J.P. Pérez-Beaupuits.
Back cover: photography of the Moon taken by Alexandru Tudorica, merged with
a photography of J.P in the shore of the Vulcanoes National park, Hilo, Hawaii,
taken by Raquel Monje.
Digital composition of the cover images designed by J.P. Pérez-Beaupuits.
Printed by: Ipskamp Drukkers B.V., Enschede, the Netherlands.
Copyright ©2010 J.P. Pérez-Beaupuits.
Contents
1 Introduction
1.1 Spectroscopy: a powerful diagnostic tool . .
1.2 Radiative transfer . . . . . . . . . . . . . . . .
1.2.1 Equations of statistical equilibrium . .
1.2.2 The radiation field . . . . . . . . . . . .
1.2.3 The optical depth and source function
1.2.4 Solving the radiative transfer equation
1.3 Astrochemistry . . . . . . . . . . . . . . . . .
1.3.1 Atomic lines . . . . . . . . . . . . . . .
1.3.2 Molecular lines . . . . . . . . . . . . . .
1.4 Active galaxies and active galactic nuclei . .
1.4.1 Seyfert galaxies and Starbursts . . . .
1.4.2 The AGN-starburst connection . . . . .
1.5 Hydrodynamic simulations of an AGN . . . .
1.6 Observatories . . . . . . . . . . . . . . . . . .
1.7 This thesis . . . . . . . . . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
1
3
3
4
5
5
6
6
7
8
9
11
12
14
15
16
2 HNC, HCN and CN in Seyfert galaxies
2.1 Introduction . . . . . . . . . . . . . . . . . . .
2.2 Observations . . . . . . . . . . . . . . . . . .
2.3 Results . . . . . . . . . . . . . . . . . . . . . .
2.3.1 NGC 1068 . . . . . . . . . . . . . . . .
2.3.2 NGC 1365 . . . . . . . . . . . . . . . .
2.3.3 NGC 3079 . . . . . . . . . . . . . . . .
2.3.4 NGC 2623 and NGC 7469 . . . . . . .
2.3.5 Line intensities and ratios . . . . . . .
2.4 Discussion . . . . . . . . . . . . . . . . . . . .
2.4.1 The distribution of dense gas . . . . . .
2.4.2 The HCN/HNC line ratios . . . . . . . .
2.4.3 Excitation conditions of HCN and HNC
2.4.4 The CN/HNC and CN/HCN line ratios .
2.5 Conclusions . . . . . . . . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
19
20
21
22
22
26
26
30
31
33
33
36
39
43
44
.
.
.
.
.
.
.
.
.
47
48
49
52
53
53
54
57
59
60
3 Dense molecular gas in NGC 1068
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2 Observations and data reduction . . . . . . . . . . . . . .
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.4.1 Structure of the CND and limitations of the model
3.4.2 Line ratios and starburst contribution . . . . . . .
3.4.3 Modeling the excitation conditions . . . . . . . . .
3.4.4 The physical environment of HCN . . . . . . . . . .
3.4.5 The physical environment of HNC . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
vi
CONTENTS
3.4.6 The physical environment of HCO+ . . . . . . . . . . . . . . . . . 61
3.4.7 The physical environment of CN . . . . . . . . . . . . . . . . . . . 62
3.5 Analysis of the uncertainties . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.5.1 Uncertainties in CN . . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.5.2 Uncertainties in HCO+ . . . . . . . . . . . . . . . . . . . . . . . . 65
3.6 Line intensity and abundance ratios . . . . . . . . . . . . . . . . . . . . 67
3.6.1 HNC/HCN
3.6.2 CN/HCN
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.6.3 HCO+ /HCN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
3.7 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4 The deeply obscured AGN of NGC 4945
75
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.2 Observations and data reduction . . . . . . . . . . . . . . . . . . . . . . 78
4.2.1 SH map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.2.2 SL map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.2.3 Data reduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.3 Analysis and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.3.1 The spectral complex around [Ne V] 14.32 µm . . . . . . . . . . . 82
4.3.2 Estimating the line emission flux
. . . . . . . . . . . . . . . . . . 83
4.3.3 Visual extinction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
4.3.4 The deep silicate absorption around 9.7 µm . . . . . . . . . . . . 89
4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4.4.1 Rotation in the nuclear region . . . . . . . . . . . . . . . . . . . . 95
4.4.2 Excitation temperature of H2 . . . . . . . . . . . . . . . . . . . . . 97
4.4.3 Tracing the starburst ring . . . . . . . . . . . . . . . . . . . . . . 99
4.4.4 Starburst or AGN dominated [Ne V] emission? . . . . . . . . . . . 101
4.5 Final remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.6 Future work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
5 Structure, Chemistry and Dynamics of an AGN torus
107
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.2 Numerical Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.2.1 The X-ray flux
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
5.2.2 Chemical abundances and temperature . . . . . . . . . . . . . . . 114
5.2.3 3-D radiative transfer and line tracing
. . . . . . . . . . . . . . . 116
5.3 Analysis and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5.3.1 CO maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5.3.2 Temperature and density driven by X-rays . . . . . . . . . . . . . 119
5.4 Final remarks and future work . . . . . . . . . . . . . . . . . . . . . . . 123
APPENDIX: Rotational excitation of CO by He
125
6 CHAMP+ observations of warm gas in M17 SW
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2 Observations . . . . . . . . . . . . . . . . . . . . . . . . .
6.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.3.1 Integrated line temperature maps . . . . . . . . . .
6.3.2 The complex internal structure of M17 SW . . . . .
6.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.4.1 Self-absorption in the mid-J 12 CO lines? . . . . . .
6.4.2 Optical depth and excitation temperature (LTE) . .
6.4.3 Ambient condition at selected positions (non-LTE)
6.4.4 Column densities at selected positions . . . . . . .
6.4.5 Volume-filling factors . . . . . . . . . . . . . . . . .
6.4.6 Jeans stability of the clumps . . . . . . . . . . . . .
6.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
127
128
130
131
131
133
136
136
139
142
147
148
149
149
7 Diffuse and dense irradiated gas in M17 SW: [C I], HCN
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
7.2 Observations . . . . . . . . . . . . . . . . . . . . . . . . .
7.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.3.1 The [C I] integrated temperature maps . . . . . . .
7.3.2 The HCN and HCO+ integrated temperature maps
7.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.4.1 The ionization front . . . . . . . . . . . . . . . . . .
7.4.2 The diffuse gas in M17 SW . . . . . . . . . . . . . .
7.4.3 The dense gas in M17 SW . . . . . . . . . . . . . .
7.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . .
and HCO+
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
.
.
.
.
.
.
.
.
.
.
151
152
154
156
156
156
160
160
162
165
171
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
8 Highlights and Outlook
173
8.1 Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
8.2 Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Bibliography
177
Nederlandse samenvatting
189
Summary
195
Acknowledgements
199
viii
CONTENTS