Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

▪ Abstract This review surveys the observed properties of interstellar dust grains: the wavelength-dependent extinction of starlight, including absorption features, from UV to infrared; optical lum...

https://www.ifa.hawaii.edu/users/reipurth/reviews/draine.pdf

Interstellar dust grains

IR emission spectra are calculated for dust heated by starlight, for mixtures of amorphous silicate and graphitic grains, including varying amounts of PAH particles. The models are constrained to reproduce the average Milky Way extinction curve. The calculations include the effects of single-photon heating. Updated IR absorption properties for the PAHs are presented that are consistent with observed emission spectra, including those newly obtained by Spitzer. We find a size distribution for the PAHs giving emission band ratios consistent with the observed spectra of the Milky Way and other galaxies. Emission spectra are presented for a wide range of starlight intensities. We calculate how the efficiency of emission into different IR bands depends on PAH size; the strong 7.7 μm emission feature is produced mainly by PAH particles containing Umin. We present graphical procedures using Spitzer IRAC and MIPS photometry to estimate the parameters qPAH, Umin, and γ, the fraction fPDR of the dust luminosity coming from photodissociation regions with U > 100, and the total dust mass Mdust.

https://iopscience.iop.org/article/10.1086/511055/pdf

Infrared Emission from Interstellar Dust. IV. The Silicate-Graphite-PAH Model in the Post-Spitzer Era

Large polycyclic aromatic hydrocarbon (PAH) molecules carry the infrared (IR) emission features that dominate the spectra of most galactic and extragalactic sources. This review surveys the observed mid-IR characteristics of these emission features and summarizes laboratory and theoretical studies of the spectral characteristics of PAHs and the derived intrinsic properties of emitting interstellar PAHs. Dedicated experimental studies have provided critical input for detailed astronomical models that probe the origin and evolution of interstellar PAHs and their role in the universe. The physics and chemistry of PAHs are discussed, emphasizing the contribution of these species to the photoelectric heating and the ionization balance of the interstellar gas and to the formation of small hydrocarbon radicals and carbon chains. Together, these studies demonstrate that PAHs are abundant, ubiquitous, and a dominant force in the interstellar medium of galaxies.

Interstellar Polycyclic Aromatic Hydrocarbon Molecules

We present a quantitative model for the infrared emission from dust in the diffuse interstellar medium. The model consists of a mixture of amorphous silicate grains and carbonaceous grains, each with a wide size distribution ranging from molecules containing tens of atoms to large grains 1 μm in diameter. We assume that the carbonaceous grains have properties like polycyclic aromatic hydrocarbons (PAHs) at very small sizes and graphitic properties for radii a 50 A. On the basis of recent laboratory studies and guided by astronomical observations, we propose astronomical absorption cross sections for use in modeling neutral and ionized PAHs from the far-ultraviolet to the far-infrared. We also propose modifications to the far-infrared emissivity of astronomical silicate. We calculate energy distribution functions for small grains undergoing temperature spikes caused by stochastic absorption of starlight photons using realistic heat capacities and optical properties. Using a grain-size distribution consistent with the observed interstellar extinction, we are able to reproduce the near-IR to submillimeter emission spectrum of the diffuse interstellar medium, including the PAH emission features at 3.3, 6.2, 7.7, 8.6, and 11.3 μm. The model is compared with the observed emission at high Galactic latitudes as well as in the Galactic plane, as measured by the COBE/DIRBE, COBE/FIRAS, IRTS/MIRS, and IRTS/NIRS instruments. The model has 60 × 10-6 of C (relative to H) locked up in PAHs, with 45 × 10-6 of C in a component peaking at ~6 A (NC ≈ 100 carbon atoms) to account for the PAH emission features and with 15 × 10-6 of C in a component peaking at ~50 A to account for the 60 μm flux. The total infrared emission is in excellent agreement with COBE/DIRBE observations at high Galactic latitudes, just as the albedo for our grain model is in accord with observations of the diffuse Galactic light. The aromatic absorption features at 3.3 and 6.2 μm predicted by our dust model are consistent with observations. We calculate infrared emission spectra for our dust model heated by a range of starlight intensities, from 0.3 to 104 times the local interstellar radiation field, and we tabulate the intensities integrated over the SIRTF/IRAC and MIPS bands. We also provide dust opacities tabulated from the extreme-ultraviolet to submillimeter wavelengths.

https://iopscience.iop.org/article/10.1086/323147/pdf

Infrared Emission from Interstellar Dust. II. The Diffuse Interstellar Medium

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Formaldehyde production in diffuse interstellar clouds

We have obtained infrared spectra of amorphous forsterite, Mg2SiO4, prepared in the presence of gaseous methane and find that hydrocarbon groups such as CH2 and CH3 can be incorporated in the silicate lattice. These chemical groups have little effect on the 10 μm silicate Si–O stretching band but introduce a 3.4 μm band similar, but not identical, to that seen in pure carbonaceous deposits including hydrogenated amorphous carbon. Absorption in this band is enhanced in the 2958 and 2873 cm-1 (3.38 and 3.48 μm) transitions of the CH3 asymmetric and symmetric stretching vibrations, respectively. Additional absorption features identified with Si(CH3)1, 2, 3 and Si(CH2)Si groups have also been observed, and a band corresponding to the Si-phenyl stretch has been detected. We discuss the possibility that hydrocarbon-silicate grains may be a component of interstellar matter, particularly in the winds from asymptotic giant branch stars with mixed carbon-silicate chemistry.

A 3.4 Micron Band in Magnesium Silicates: Preparation of Hydrocarbon-Silicate Condensates

It is shown that interstellar extinction between 1 and 10 μm−1 can be obtained from a grain mixture containing Fe3O4, SiO, MgO, and glassy carbon. MgO produces the 220 nm extinction bump and eliminates the need for graphite as a component of interstellar dust.

A fit to the interstellar extinction curve without graphite

A number of vibronic progressions based on low-energy vibrational modes of a large molecule have been found in the diffuse interstellar band (DIB) spectrum of HD 183143. Four active vibrational modes have been identified with energies at 5.18 cm–1, 21.41 cm–1, 31.55 cm–1, and 34.02 cm–1. The mode at 34.02 cm–1 was previously recognized by Herbig. Four bands are associated with this molecule, with origins at 6862.61 A, 6843.64 A, 6203.14 A, and 5545.11 A (14589.1 cm–1, 14608.08 cm–1, 16116.41 cm–1, and 18028.9 cm–1, respectively). The progressions are harmonic and combination bands are observed involving all modes. The appearance of harmonic, rather than anharmonic, terms in these vibronic progressions is consistent with torsional motion of pendant rings, suggesting that the carrier is a "floppy" molecule. Some constraints on the type and size of the molecule producing these bands are discussed.

Vibronic progressions in several diffuse interstellar bands

Complex Organic Molecules (COMs), such as propylene (CH3CHCH2) and the isomers of C2H4O2 are detected in cold molecular clouds (such as TMC-1) with high fractional abundances (Marcelino et al., Astrophys. J., 2007, 665, L127). The formation mechanism for these species is the subject of intense speculation, as is the possibility of the formation of simple amino acids such as glycine (NH2CH2COOH). At typical dark cloud densities, normal interstellar gas-phase chemistries are inefficient, whilst surface chemistry is at best ill defined and does not easily reproduce the abundance ratios observed in the gas phase. Whatever mechanism(s) is/are operating, it/they must be both efficient at converting a significant fraction of the available carbon budget into COMs, and capable of efficiently returning the COMs to the gas phase. In our previous studies we proposed a complementary, alternative mechanism, in which medium- and large-sized molecules are formed by three-body gas kinetic reactions in the warm high density gas phase. This environment exists, for a very short period of time, after the total sublimation of grain ice mantles in transient co-desorption events. In order to drive the process, rapid and efficient mantle sublimation is required and we have proposed that ice mantle ‘explosions’ can be driven by the catastrophic recombination of trapped hydrogen atoms, and other radicals, in the ice. Repeated cycles of freeze-out and explosion can thus lead to a cumulative molecular enrichment of the interstellar medium. Using existing studies we based our chemical network on simple radical addition, subject to enthalpy and valency restrictions. In this work we have extended the chemistry to include the formation pathways of glycine and other large molecular species that are detected in molecular clouds. We find that the mechanism is capable of explaining the observed molecular abundances and complexity in these sources. We find that the proposed mechanism is easily capable of explaining the large abundances of all three isomers of C2H4O2 that are observationally inferred for star-forming regions. However, the model currently does not provide an obvious explanation for the predominance of methyl formate, suggesting that some refinement to our (very simplistic) chemistry is necessary. The model also predicts the production of glycine at a (lower) abundance level, that is consistent with its marginal detection in astrophysical sources.

Walter W. Duley

Papers

Formaldehyde production in diffuse interstellar clouds

A 3.4 Micron Band in Magnesium Silicates: Preparation of Hydrocarbon-Silicate Condensates

A fit to the interstellar extinction curve without graphite

Vibronic progressions in several diffuse interstellar bands

The formation of glycine and other complex organic molecules in exploding ice mantles