Libby Miller Senior Thesis Plan (8/24/06):

• ACTION: Work on U-line Database in SLiSE
• Progress Report:
  • DATE:08/28/06 - Unidentified transitions were noted up to the 3800-4000 MHz region. There were a few really high absorption intensity readings which i don't think might be due to interference.... (1874.9, 1904.9, 3839, and 3841.1 MHz). The database was updated and saved.
  • DATE:08/29/06 - The questionable transition lines considered on 08/28 were further inspected with the conclusion that the data in the 3840 MHz - 4370 MHz region were, in fact, obscured by the presence of Radio Frequency Interference. Transitions were then identified up to 4696.5 MHz. Concepts of electromagnetic dipole radiation were reviewed and consideration made in regard to the plausibility of the transitions listed on the SLAIM readout to occur. An astrochemistry lecture on the nature of nitrogen containing molecules within protostellar cores was attended which posited that, with more N species existing in a more compact region, perhaps smaller molecules were transforming into larger ones. Particular insights and comments which piqued my interest included: what the mechanism might be between the high and low-density N2-bearing regions, whether the chemistry for this observation would occur on the surface of a dust grain or in a gas phase, and what might have occurred before the steady-state was reached. After the completion of the lecture, I found and read a copy of the article upon whose results the lecture was based at edpsciences.org.
  • DATE:09/01/06 - Transition lines were inspected and identified from 4696.6 MHz to 5719.12 MHz. There were no data points within the 5740 MHz through 8000 MHz region. The available data then resumes at 8006.08 MHz. There were data breaks at 4840, 5020, 5200, 5530, and 5560 MHz and a considerable amount of RFI between 5050 and 5110 MHz. Approximately 13 possible molecule IDs were made along with notes for things such as high angular momentum values. High intensity Hydrogen recombination lines were often seen coupled with lower intensity Helium recombination lines.
  • DATE:09/06/06 - Transition lines were identified from 8006.08 MHz to 8770.62 MHz. There was moderately heavy RFI from 8110-8140 MHz, 8160-8190 MHz, 8430-8460 MHz, and 8670-8710 MHz. There were data breaks at 8200 MHz, 8400 MHz, 8570 MHz, and 8740 MHz. At 8471 MHz, there was a tight cluster of NH2CHO lines. Commenced to read chapter on recombination lines in Rohlfs and Wilson's Tools of Radio Astronomy.
  • DATE:09/08/06 - Work on the SLiSE program was resumed, beginning at 8770.62 MHz and ending at 10,737.89 MHz. There was RFI from 8780-8810 MHz, 8820-8850 MHz, 8890-8934 MHz, 9120-9160 MHz, 9238-9300 MHz, 9551-9610 MHz, and 9640-9920 MHz. There were data breaks at 8935 MHz, 9304 MHz, 10052 MHz, and 10740 MHz. There were blocks of no available data from 8935 through 9100 MHz, 9304.3 through 9550 MHz, 9750 through 9850 MHz, 10250 through 10300 MHz, and 1520 through 1540 MHz. There was an interesting pattern of four CH3NH2 lines at frequencies 8775.06 MHz, 8777.46 MHz, 8778.26 MHz, and 8779.51 MHz. Continued to read chapter on recombination lines. I was able to at least follow conceptually the sections on hydrogen and helium nebulae, Rydberg atoms, and the interpretation of radio recombination line observations. However, the formulae and derivations in the sections for line intensities under LTE and NLTE conditions will take more time for me to work through and absorb. I printed five articles from the NASA ads/abs website to gain background for the type of research that has been recently done with regard to recombination lines in regions similar to SGRB2N. They are: Dense, Ionized, and Neutral Gas Surrounding Sagittarius A* by Hemant Shukla et al. 2004, Radio Recombination Lines in Galactic HII Regions by Cintia Quireza et al. 2006, Evolution of HII Regions in Hierarchically Structured Molecular Clouds by S.S. Shabala et al. (2006), Radio and Infrared Recombination Studies of the Southern Massive Star Forming Region G333.6-0.2 by Takuya Fujiyoshi et al. (2006), and Magnetic Fields in the Galactic Center by D.A. Roberts 1999. I have gone through the first article and commenced the second.

• ACTION: Become Familiar with Dish and IDL
• Progress Report:
  • DATE:09/11/06 - Was introduced to IDL. Was able to navigate from startup until the point where IDL takes the averages of the scans... and to save the files after that. No data reduced as of yet. I think the trouble therein lies in how to treat the "on" and "off" scans once they're averaged. My understanding is that the "on" scans are collectively averaged, the stack is purged, the "off" scans are collectively averaged, the stack is purged, and then IDL [somehow]subtracts the "off" average from the "on" average.... I thought I remembered from the example that there was not another command to make IDL do this (I also couldn't scroll back up in the terminal to check whether or not this was right. I spent the rest of my time working this out, so only was able to explore the reduction for two more of the scans for AGBT04C_027_01.
  • DATE:09/13/06 - The reduction protocol was revised such that the entire data set for a given observation session would be viewed upon startup rather than just the scans for a particular source. Clarification was made in the nature of taking readout averages that only the "on" scans needed to be read into the IDL program. The sources then (correctly) reduced from the AGBT04C_027_01 observing session were: MWC349, MOL119, MOL136, MOL148, IR23139+59, MOL160, IR00338+63, NGC281, MOL3, IR02541+62, G192_16-03, 3C147, and MOL7. Mistakes that I caught afterwards occurred for MOL138, MOL145, W3_IRS5, and AFGL490. For MOL138, the IDL index table appeared to include data only from scans 12, 13, and 14, so I did the reduction under those parameters. I thought that it was suspicious for there to be an odd number of scans, so I retrieved the entire data set via the sdfits command and wrote down with pencil and paper which scans corresponded to which sources and proceeded from there to reduce the rest of that night's data. For MOL145, there were problems with there being an "incorrect number of arguments", possibly resulting from the fact that the procedure of taking readout averages required that only the "on" scans needed to be read into the IDL program. The sources then (correctly) reduced from the AGBT04C_027_01 observing session were: MWC349, MOL119, MOL136, MOL148, IR23139+59, MOL160, IR00338+63, NGC281, MOL3, IR02541+62, G192_16-03, 3C147, and MOL7. Mistakes that I caught afterwards occurred for MOL138, MOL145, W3_IRS5, and AFGL490. For MOL138, the IDL index table appeared to include data only from scans 12, 13, and 14, so I did the reduction under those parameters. I thought that it was suspicious for there to be an odd number of scans, so I retrieved the entire data set via the sdfits command and wrote down with pencil and paper which scans corresponded to which sources and proceeded from there to reduce the rest of that night's data. For MOL145, there were problems with there being an "incorrect number of arguments", possibly resulting from the fact that the listed scans range from 26-29, skip 30, and then range from 31-36. For MOL148, I initially labeled it as MOL145. For W3_IRS5 and AFGL490, I accidentally included the "off" scans. I currently do not know how to retrieve the misnamed files in order to delete them and replace them with correct reductions... so for now I hope that this wikio note will suffice. All reductions made were saved as .spc files with the format 'sourcename_4C27_ifnumber.spc.'
  • DATE:09/15/06 - Reduced data for the second night of the AGBT04C_027 observation. Will continue on Monday with the third night's data.
  • DATE:09/18/06 - Reduced data for the fourth and fifth nights of the AGBT04C_027 observation. Will reduce night three on Wednesday as well as continue to reduce data for other observations targeted towards massive protostellar regions.
  • DATE:09/20/06 - Reduced data for the third night of AGBT04C_027. (The first reduction of the scans from 9-14 was mislabeled as being for MOL 136. The second reduction was correctly labeled as being for IR18566+04.) Tried to reduce data for AGBT04C_028 and AGBT04C_037, but was not sure how to proceed with identical on and off scan numbers. Tried several approaches, but none were successful. Will inquire about this on Monday.
  • DATE:10/04/06 - Reviewed theory behind stark effect and hyperfine structure in relation to (E) and (Z) isomers of acetaldehyde oxime with assumed Cs and rs coordinates calculated with Kraitchman's equation. Located data for AGBT05C_010 (Search for IS Benzonitrite--tracer of Benzene) on tape-0016. Began an attempt at reduction of the data, but was unable to take second averages for the nod scans (i.e. when the beams were switched). (problem with the data? problem with the program used to take the second averages?) Of note, only one If was taken for many of the scans.
  • DATE:10/06/06 - Problems with taking the second averages of the scans were resolved when Dr. Remijan wrote out/revised a program for this. I was introduced to the process of flagging data by using the protocol: check scan, check polarization (either RR=1 or LL=0), check integration number to see which integrations might have been interfered. Commenced flagging and reduction of data.
  • DATE:10/11/06 - Resumed flagging and reduction of AGBT05C_010 data
  • DATE:10/13/06 - Noted that I had been saving the reduced files to the scratch folder. Saved those files and the subsequent ones via the fileout command to AGBT05C_10_01Red.fits. Resumed flagging and reducing scans for AGBT05C_010.
  • Date:10/16/06 - Flagged and reduced scans for AGBT05C_010.
  • DATE:10/18/06 - Flagged and reduced scans for AGBT05C_010. Developed a track of how I saved the reduced files by creating a table of passband (in MHz), index, scans, procedure (onoff or nod), If, and filename.
  • DATE:10/22/06 - Flagged, reduced, recorded files in table for AGBT05C_010.
  • DATE:10/23/06 - Flagged, reduced, recorded files in table for AGBT05C_010.
  • DATE:10/24/06 - Flagged, reduced, recorded files in table for AGBT05C_010. Of note, there seemed to be exceptional interference (and noise coming from the antenna?) in the higher frequency ranges.
  • DATE:10/25/06 - Finished flagging, reducing, and recording AGBT05C_010 files. Saved and sent the final table of how the files were saved to Dr. Remijan.
  • DATE:11/01/06 - A meeting was set up to talk with Dana Balser on Friday 11/03/06 at 9 AM about the physics of radio recombination lines.

• ACTION: Update the SLiSE database with new GBT data
• Progress Report:
  • DATE:

• ACTION: Reduce acetone data from GBT - (write paper)
• Progress Report:
  • DATE:09/27/06 - Commenced CH3CHO project for the molecule in the vt = 0 vibrational state. Agreement between the SLiSE spreadsheet frequencies and the line list printout for frequencies was immediately noted for 1849.67, 8243.5, 9110.21, 10720.61, 41212.17, and 45897.34 MHz. The spreadsheet itself was incomplete, so I entered values into the SLiSE program for values within the range of those on the line list one by one and found agreement for the frequencies 10648.42, 10649.58, 19262.14, and 19265.14 MHz and updated the spreadsheet accordingly. There was much RFI present between 4068.41 and 4677.89 MHz, 8556.07 and 8908.32 MHz, and 13923.74 and 15416.22 MHz which made agreement between the line list and the plots produced from the SLiSE program difficult to ascertain. There were large spans of no data produced between 2067.33 and 3712.72 MHz and 5777.88 and 7984.94 MHz. Ended at 25008.62 MHz and will continue on Friday at 25043 MHz.
  • *DATE:09/29/06 - Resumed CH3CHO project. Attended astrochemistry meeting on new capabilities for species identification in Microwave, IR, and UV regions by Rick Suenram and Brooks Pate.

• ACTION: Determine electron temperature from H+ and 4He+ recombination lines in SGRB2N
• Progress Report:
  • DATE:11/03/06 - Meeting with Dana Balser concerning fundamentals of radio recombination line theory
  • DATE:11/06/06 - Commenced research on radio recombination theory with the appendix section of Dr. Balser's thesis
  • DATE:11/08/06 - Resumed research on recombination line theory
  • DATE:11/10/06 - Research on recombination line theory at UVA library
  • DATE:11/13/06 - Research on recombination line theory at UVA library
  • DATE:11/16/06 - Commenced spreadsheet for electron temperatures based on parameters of the SGRB2N data. Searched for pairs of H+ and 4He+ recombination lines with the SLiSE program. The 4He+ lines that I used were located at frequencies generally not more than 3 MHz greater than the H+ rest frequency. In addition to searching for the H+ and 4He+ pairs and obtaining electron temperature values from their parameters, I have and will be (out of necessity) updating the spreadsheet for the SGRB2N survey as I find more H+ and 4He+ recombination line pairs. So far (from 4380 - 8872 MHz), no potential C+ lines were noted. If present, maybe this is due to blending with the He+ lines by Stark Effect broadening at lower frequencies.... (?) The line to free-free continuum intensity ratio vs. frequency plot in the M.A. Gordon book Radio Recombination Lines seems to indicate that the observed intensity is expected to be decreased for frequencies in the range less than 10 GHz. Maybe C+ is too heavy to be located in the galactic center? At any rate, it does seem overall that the line profiles for 4He+ become more defined as frequency increases. Will continue to search for and calculate electron temperature of recombination line pairs. The plot that I have created for frequency vs. electron temperature so far does not appear to show any particular well-defined trend. The electron temperature values from the function I created for the spreadsheet read as typically on the order of 3E5 K, but I believe that this value is too large. I used the assumptions for a homogeneous sphere at LTE.
  • DATE:11/17/06 - Considered non-LTE effects (namely stimulated emission and pressure broadening from electron impacts). Also reviewed relaionship between frequency and velocity with regard to line width.
  • DATE:12/04/06 - Looked for potential places where Carbon lines might be in SGR B2N. Found theoretical frequencies and began to compare with frequencies in Orion.
  • DATE:01/07/07 - 01/08/07- Compared line intensities between SGR B2N and Orion in effort to determine whether Carbon lines were not seen in SGR B2N because either a.) Carbon was absent or b.) Carbon was present but had lines blended with those of neighboring Helium. Generally, the Hydrogen/Helium pairs for SGR B2N had lower intensities than those for Orion. The interpretation taken was that there may well be Helium/Carbon line blending for the data being used but that, for the purpose of this thesis project, the contribution is small enough that taking the Hydrogen and Helium line intensity ratios still yields a useful approximation of electron temperature.
  • DATE:01/22/07 - Reviewed fine points of parameters necessary for calculating electron temperature based on line intensity. Once these values are obtained, the goal will be to use them to calculate line emission measures as well as electron density values. Today, I was introduced to NRAO staff with regard to my upcoming task to transfer raw data from the Green Bank to Charlottesville headquarters and to generate from them stfits files for the NRAO's archives.
  • DATE:01/25/07 - Reorganized and revised electron temperature spreadsheet in Open Office for the purpose of calculating electron temperature from a given ratio of line intensities. The formula used was: (Temperature of electron in Kelvins) = [7103.3 * ((frequency of H+ line in GHz)^(1.1))*((continuum temperature / line temperature of H+) * ((FWHM line width of H+)^(-1)) * (1 + n(4He+)/n(H+)). The ionic abundance ratio was taken from the product of 4He+ line temperature and FWHM line width divided by the product of the H+ line temperature and FWHM line width. 7103.3 is the constant value used by Quireza, Rood, et al in their paper The Electron Temperature Gradient in the Galactic Disk from August 2006.
  • DATE:01/26/07 - Inserted temperature and FWHM values of 12 different H+ and 4He+ pairs into my spreadsheet for the frequency range 4875 MHz through 42952 MHz in order to generate a zeroth order plot of frequency vs. electron temperature. From the lines inspected, it appears that an average value is around 7E3 or 8E3 K and that values of electron temperature might decrease as passband frequency increases.

• ACTION: Reduce ammonia data from GBT - (write paper)
• Progress Report:
  • DATE:

• 28 Aug 2006 - Libby Start (10-2)
• 30 Aug 2006 - Libby Work (10-1)
• 01 Sep 2006 - Libby Work (10-1)
• 06 Sep 2006 - Libby Work (10-1)
• 08 Sep 2006 - Libby Work (10-1)
• 11 Sep 2006 - Libby Work (10:30-1)
• 13 Sep 2006 - Libby Work (11-1)
• 15 Sep 2006 - Libby Work (11:30-1:30)
• 18 Sep 2006 - Libby Work (11-2)
• 19 Sep 2006 - Libby Work (5-7)
• 7 Sep 2006 - 9 Sep 2006 - Tony to Green Bank
• 21 Sep 2006 - 24 Sep 2006 - Tony and Libby to Green Bank for Snyder Lectures
• 27 Sep 2006 - Libby Work (10-1:30)
• 29 Sep 2006 - Libby Work (10-1:30)
• 04 Oct 2006 - Libby Work (11:30-2:00)
• 06 Oct 2006 - Libby Work (11:00-2:30)
• 11 Oct 2006 - Libby Work (2:30-4:10)
• 13 Oct 2006 - Libby Work (1:30-4:30)
• 16 Oct 2006 - Libby Work (2:30-4:30)
• 18 Oct 2006 - Libby Work (3:50-7:00
• 22 Oct 2006 - Libby Work (5:00-7:00)
• 23 Oct 2006 - Libby Work (3:40-7:00)
• 24 Oct 2006 - Libby Work (11:00-12:30)
• 25 Oct 2006 - Libby Work (3:30-7:30)
• 01 Nov 2006 - Libby Work (1:00-3:30)
• 03 Nov 2006 - Meeting with Dana Balser about radio recombination lines (9:00-10:00), astrochemistry meeting (4:00-5:00)
• 06 Nov 2006 - Researched radio recombination line theory (1:00-3:00)
• 08 Nov 2006 - Researched radio recombination line theory (1:15-3:00)
• 10 Nov 2006 - Researched radio recombination line theory at UVA library (2:00-4:00)
• 13 Nov 2006 - Researched radio recombination line theory at UVA library (1:00-3:00)
• 16 Nov 2006 - Commenced spreadsheet for electron temperatures (9:00-11:00 p.m.)
• 17 Nov 2006 - Considerations of non-LTE effects
• 20 Nov 2006 - Libby Work (7:30-8:30)
• 04 Dec 2006 - Libby Work (12:30 - 2:00)
• 10 Dec 2006 - Left Charlottesville for UVa's winter recess
• 07 Jan 2007 - Returned to Charlottesville for spring semester classes
• 08 Jan 2007 - Libby Work (5:00-6:00)
• 22 Jan 2007 - Libby Work (10:00-12:30)
• 25 Jan 2007 - Libby Work (4:00-5:00)
• 26 Jan 2007 - Libby Work (5:00-6:30)