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Stars form in a cold, dense, molecular phase of the interstellar medium (ISM) that appears to be organized into coherent, localized volumes or clouds. The star formation history of the universe, the evolution of galaxies, and the formation of planets in stellar environments are all coupled to the formation of these clouds, the collapse of unstable regions within them to stars, and the clouds' final dissipation. The physics of these regions is complex, and descriptions of cloud structure and evolution remain incomplete and require continued exploration. Here we review the current status of observations and theory of molecular clouds, focusing on key advances in the field since Protostars and Planets V.

The first detections of molecules in the ISM date from the 1930s, with the discovery of CH and CN within the diffuse interstellar bands (Swings and Rosenfeld 1937, McKellar 1940) and later the microwave lines of OH (Weinreb et al. 1963), NH3 (Cheung et al. 1968), water vapor (Cheung et al. 1969) and H2CO (Snyder et al. 1969). Progress accelerated in the 1970s with the first measurements of molecular hydrogen (Carruthers 1970) and the 12CO J = 1-0 line at 2.6mm (Wilson et al. 1970) and the continued development of millimeter wave instrumentation and facilities.

The first maps of CO emission in nearby star forming regions and along the Galactic Plane revealed the unexpectedly large spatial extent of giant molecular clouds (GMCs, Kutner et al. 1977, Lada 1976, Blair et al. 1978, Blitz and Thaddeus 1980), and their substantial contribution to the mass budget of the ISM (Scoville 1975, Gordon and Burton 1976, Burton and Gordon 1978, Sanders et al. 1984). Panoramic imaging of 12CO emission in the Milky Way from both the Northern and Southern Hemispheres enabled the first complete view of the molecular gas distribution in the Galaxy (Dame et al. 1987, Dame et al. 2001) and the compilation of GMC properties (Solomon et al. 1987, Scoville et al. 1987). Higher angular resolution observations of optically thin tracers of molecular gas in nearby clouds revealed a complex network of filaments (Bally et al. 1987, Heyer et al. 1987), and high density tracers such as NH3, CS, and HCN revealed the dense regions of active star formation (Myers 1983, Snell et al. 1984). Since this early work, large, millimeter filled aperture (IRAM 30m, NRO 45m), interferometric (BIMA, OVRO, Plateau de Bure) and submillimeter (CSO, JCMT) facilities have provided improved sensitivity and the ability to measure higher excitation conditions. Observations to date have identified ~ 200 distinct interstellar molecules (van Dishoeck and Blake 1998, Müller et al. 2005), and the last 40 years of observations using these molecules have determined a set of cloud properties on which our limited understanding of cloud physics is based.

Theoretically, the presence of molecular hydrogen in the ISM was predicted long before the development of large scale CO surveys (e.g., Spitzer 1949). In the absence of metals, formation of H2 by gas phase reactions catalyzed by electrons and protons is extremely slow, but dust grains catalyze the reaction and speed it up by orders of magnitude. As a result, H2 formation is governed by the density of dust grains, gas density, and the ability of hydrogen atoms to stick to dust grains and recombine (van de Hulst 1948, McCrea and McNally 1960, Gould and Salpeter 1963, Hollenbach and Salpeter 1971). The ISM exhibits a sharp transition in molecular fraction from low to high densities, typically at 1-100 cm-3 (or Sigma ~ 1-100 Modot pc-2), dependent mostly on the UV radiation field and metallicity (van Dishoeck and Black 1986, Pelupessy et al. 2006, Glover and Mac Low 2007a, Dobbs et al. 2008, Krumholz et al. 2008, Krumholz et al. 2009a, Gnedin et al. 2009). This dramatic increase in H2 fraction represents a change to the regime where H2 becomes self shielding. Many processes have been invoked to explain how atomic gas reaches the densities (gtapprox 100 cm-3) required to become predominantly molecular (see Section 3). Several mechanisms likely to govern ISM structure became apparent in the 1960s: cloud-cloud collisions (Oort 1954, Field and Saslaw 1965), gravitational instabilities (e.g., Goldreich and Lynden-Bell 1965a), thermal instabilities (Field 1965), and magnetic instabilities (Parker 1966, Mouschovias 1974). At about the same time, Roberts (1969) showed that the gas response to a stellar spiral arm produces a strong spiral shock, likely observed as dust lanes and associated with molecular gas. Somewhat more recently, the idea of cloud formation from turbulent flows in the ISM has emerged (Ballesteros-Paredes et al. 1999), as well as colliding flows from stellar feedback processes (Koyama and Inutsuka 2000).

The nature of GMCs, their lifetime, and whether they are virialized, remains unclear. Early models of cloud-cloud collisions required very long-lasting clouds (100 Myr) in order to build up more massive GMCs (Kwan 1979). Since then, lifetimes have generally been revised downwards. Several observationally derived estimates, including up to the present date, have placed cloud lifetimes at around 20-30 Myr (Bash et al. 1977, Blitz and Shu 1980, Fukui et al. 1999, Kawamura et al. 2009, Miura et al. 2012), although there have been longer estimates for molecule rich galaxies (Tomisaka 1986, Koda et al. 2009) and shorter estimates for smaller, nearby clouds (Elmegreen 2000, Hartmann et al. 2001).

In the 1980s and 1990s, GMCs were generally thought to be supported against gravitational collapse, and in virial equilibrium. Magnetic fields were generally favored as a means of support (Shu et al. 1987). Turbulence would dissipate unless replenished, whilst rotational support was found to be insufficient (e.g., Silk 1980). More recently these conclusions have been challenged by new observations, which have revised estimates of magnetic field strengths downwards, and new simulations and theoretical models that suggest that clouds may in fact be turbulence-supported, or that they may be entirely transient objects that are not supported against collapse at all. These questions are all under active discussion, as we review below.

In Section 2, we describe the main new observational results, and corresponding theoretical interpretations. These include the extension of the Schmidt-Kennicutt relation to other tracers, notably H2, as well as to much smaller scales, e.g., those of individual clouds. Section 2 also examines the latest results on GMC properties, both within the Milky Way and in external galaxies. Compared to the data that were available at the time of PPV, CO surveys offer much higher resolution and sensitivity within the Milky Way, and are able to better cover a wider range of environments beyond it. In Section 3, we discuss GMC formation, providing a summary of the main background and theory, whilst reporting the main advances in numerical simulations since PPV. We also discuss progress on calculating the conversion of atomic to molecular gas, and CO chemistry. Section 4 describes the various scenarios for the evolution of GMCs, including the revival of globally collapsing clouds as a viable theoretical model, and examines the role of different forms of stellar feedback as internal and external sources of cloud motions. Then in Section 5 we relate the star forming properties in GMCs to these different scenarios. Finally in Section 6 we look forward to what we can expect between now and PPVII.

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