Notes from meeting with Ted on 31 October

I met with Ted today. My PhD committee meeting is next Wednesday.

Context:
over the last week, my priority has been to get h13cn column density measurements for IRAS 16293, which has meant compiling data from a few different sources. I found the Herschel CHESS HIFI spectral scans of this source in the Herschel Science Archive, "reduced" them lightly (really this only involved downloading, converting to CLASS format, doing simple baselining and single-component Gaussian fitting to the h13cn lines, and extracting integrated fluxes in K km /s units). I also fetched low-J line fluxes (single-dish) from the Caux+11 paper, which had IRAM-30m and JCMT data for J=1-0, 3-2 and 4-3.

In the pursuit of getting a source size measurement for the h13cn emission, I tracked down the ALMA science verification data for this source - turns out they had an already-reduced h13cn 8–7 datacube sitting and ready to analyze on their server, and it even has a whole CASA tutorial attached to it. Screenshot of the moment-0 map of the h13cn line is shown below, where the beam is a filled white ellipse, and "component A" is in the bottom-left while "component B" is in the top-right.

I started the meeting by discussing with Ted whether the inclusion of all this extra data (lots of Herschel, this ALMA dataset, and the Caux fluxes so far) justifies turning this h13cn analysis of IRAS 16293 into its own separate (small) paper. He says "unless there is additional info (another interferometric h13cn map of this source at a different line, or some other substantial additional data) I don't agree." Basically the idea right now (from my point of view) is to stick the details of the abundance measurement in the appendix of the Nitrogen accounting paper. Maybe multiple appendices for multiple sources.

We discussed how I'd get the CO column density. A few ideas, including "look it up in a Jørgensen paper" were thrown around, but Ted settled on this:
(New task for me.)
Since I have all the Herschel HIFI spectral data in-hand already, I can (almost trivially) replicate the exact analysis that Plume+2012 does towards Orion KL, for CO. I'd have to track down the C17O and C18O lines in the spectrum but since the analysis is already completely described in Plume+12, I wouldn't be easily misguided. If the CO isotopg. lines are comparable in strength to the HCN isotopg. lines, then we should be in great shape.

I also need to track down the hc15n lines at IRAS 16293 in order to confirm (or debunk) the "optically thin" assumption that goes into using h13cn lines for column density analysis. This would be in the HIFI data somewhere - hopefully they're not too weak. This table should help me estimate the expected line strengths -  it looks like I'd expect the hc15n lines to be (12c/13c) x (15n/14n) = ~0.18 times as strong as the h13cn lines, assuming "local ISM" isotopic ratios.

Another thing: I mentioned that I felt like the Kama+2013 paper (CHESS molecular line identification towards the intermediate-mass young star OMC-2 FIR4) probably didn't identify ALL the h13cn lines that were probably present in the data - I suspect that 1-2 more could be identified and extracted by someone dedicated enough. He suggested that I email Mikhail Kama about it. I said I could probably just download the Herschel data myself

Pretty much we want to do the h13cn column density + abundance measurement for ANY source that has (a) Herschel data with h13cn lines in it and (b) a reasonable source size measurement or estimation. This partially rules out Orion S since its hot-core source size is v. unconstrained.

How to load Herschel FITS files into CLASS

I think I need to load some Herschel / HIFI data into CLASS. I retrieved it today (October 2016) from the Herschel Science Archive.

I'm using this as a starting point
http://iram-institute.org/medias/uploads/class-herschel-fits.pdf

and will update this post if I learn anything.

Update #1:

I'm finding this page super critical:
http://herschel.esac.esa.int/twiki/bin/view/Public/ExportingDataProducts

and especially the "CLASS" block, which contains the following code snippet:

file out MyHIFISpectra.hifi mul
    fits read MyHIFISpectra.fits
#
# Now you have a CLASS file named MyHIFISpectra.hifi (you can use whatever you want as an 
# extension) you can access like you always do in CLASS:
#
    file in MyHIFISpectra.hifi
    find
    get first
    set unit f i
    device image white
    plot

Notes from Jean-luc Doumont's presentation at UMich, 10 October 2016: "Creating Effective Presentation Slides"

Today I attended Jean-luc Doumont's session on "Creating Effective Presentation Slides". Some notes I took in response to follow-up questions:

1. Do you have any Keynote templates for this style of presentation?
A: No, but others may have made them, and if not, I won't stop you from doing so yourself!

2. Are there any online videos of yourself that you would recommend?
A: Yes, these:
http://principiae.be/X0302.php
most prominently:

https://www.youtube.com/watch?v=meBXuTIPJQk&feature=youtu.be

and:

https://www.youtube.com/watch?v=VK74BIaxkYE&feature=youtu.be

Notes on Cosmic Abundances

adsabs.harvard.edu/abs/2012A%26A...539A.143N

Tables of Isotopic Ratios from Wilson '99

The following table, which contains basic isotopic ratios for important elements in different contexts, appears in the following article:

"Isotopes in the interstellar medium and circumstellar envelopes", T L Wilson, 1999

Also of interest:

 

At this very moment, I am unaware of a better reference for these general values.

Abundances of HCN from Shimajiri + 2015

Ok, so one thing I'm working on today is compiling numbers on the molecular column density & fractional abundance of HCN towards the intermediate-mass protostar OMC-2 FIR 4. It's the subject of a lot of study - it's a very bright prominent infrared-revealed protostar in the Orion region, and is the prototype intermediate mass protostar that the CHESS Herschel program selected.

Here's the paper I'm working with:
http://adsabs.harvard.edu/abs/2015ApJS..221...31S
Spectral-line Survey at Millimeter and Submillimeter Wavelengths toward an Outflow-shocked Region, OMC 2-FIR 4

Observations:

Nobeyama 45m and Atacama submillimeter telescope experiment (ASTE)
82–106GHz and 335–355GHz

This means they can see the H13CN and HC15N J=1–0 and 4–3 transitions, from which they make rotation diagrams.

Here's the rotation diagrams for H13CN and HC15N towards this source.

 

The difference between Tables 10 and 11:
Table 10 assumes FIR 4 is 19'' in size. Table 11 assumes that the emission filling factor is 1, with a beam of 15'' to 19.7''.

Table 10 gives the following numbers. N_mol is given in cm^-2. X_mol is given relative to H₂, as estimated via 1.1mm dust continuum measurements under two different temperature assumptions.

H¹³CN

N_mol = 6.4 x 10¹³

X_mol = 1.4 – 6.4 x 10^-10

HC¹⁵N

N_mol = 2.9 x 10¹²

X_mol = 0.6 – 2.9 x 10^-11

Table 11 gives the following numbers

H¹³CN

N_mol = 3.4 x 10¹³

X_mol = 7.6 – 34 x 10^-11

HC¹⁵N

N_mol = 1.5 x 10¹²

X_mol = 0.3 – 1.5 x 10^-11

If I use averaged ISM isotopic ratios to scale these X values to what is expected for HCN, they look like this:

Table 10

H¹³CN - SCALED to HCN

N_mol = 4.4 x 10¹⁵

X_mol = 9.7 – 44 x 10^-9

HC¹⁵N - SCALED to HCN

N_mol = 1.1 x 10¹⁵

X_mol = 2.3 – 11 x 10^-9

Table 11 gives the following numbers

H¹³CN - SCALED to HCN

N_mol = 2.3 x 10¹⁵

X_mol = 5.2 – 23 x 10^-9

HC¹⁵N - SCALED to HCN

N_mol = 5.8 x 10¹⁴

X_mol = 1.2 – 5.8 x 10^-9

Ideas on "what makes an excellent spectral survey plot"

I'm working on an observational project that includes millimeter radio data, spanning a 3.6 GHz spectral window. There are lots of lines (identified and not) in the region, and (as part of a general summary document) I'd like to show the whole spectrum, with the so-far-identified lines clearly labeled. What's the best way to do this - to show the wide-band spectrum clearly?

I'm looking through recent literature (haphazardly looking at papers that cite the following reference: "Weeds: a CLASS extension for the analysis of millimeter and sub-millimeter spectral surveys") to look for inspiration.

Below will appear some screenshots showing approaches I like or don't.