On the Effects of Resolution on APXS-GUAPX Analytical Results: From Spectrum to Peak Areas to Concentration Estimates by Renato Pardo A Thesis Presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Physics Guelph, Ontario, Canada c Renato Pardo, July, 2015 ABSTRACT On the Effects of Resolution on APXS-GUAPX Analytical Results: From Spectrum to Peak Areas to Concentration Estimates Renato Pardo Advisers: University of Guelph, 2015 Dr. J.L Campbell Dr. R. Gellert The thesis presents an in-depth investigation into the effects of spectral resolution on Alpha Particle X-ray Spectrometer (APXS) measurements processed using the GUAPX fit- ting code. The APXS analytical results contribute to understanding rock and soil types on Mars and the processes by which they formed. However, mission constraints, including in- strumental degradation due to neutron damage and limited temperature control, mean that instrumental resolution cannot always be optimized. A methodology was developed using ratios of relevant analytical results to characterize the relationship between estimated peak areas, concentration estimates, and resolution. A differential effect favouring the heavier element concentration estimates with worsening resolution was observed and the underlying causes identified. The link between relative change in FWHM and concentration estimates was quantified for ten geochemical elements. Lastly, it was found that variations in es- timated concentrations can fall outside precision error over resolution and concentration ranges similar to those seen on Mars. Dedicated to Carmenza de Lara (1927 - 2015) iii Acknowledgements It has been an honour to work alongside some of the brightest minds in the field, and consider them my colleagues and superiors. Sitting alongside them, analyzing, and seeing how they work through various challenges has truly been an enriching and invaluable expe- rience. To further find that these people are some of the kindest souls I have met in my life is truly humbling. Thank you all! To Dr. Campbell and Dr. Gellert I extend my eternal gratitude, for giving me the oppor- tunity to pursue my passion for physics and its application as both an undergraduate and graduate student. This work was done with Dr. Campbell as my direct supervisor. Thus, I can attest the words written by his previous students are not embellished. Dr. Campbell is a man of eternal patience who is personally invested in the success of his students and shows the utmost respect for his colleagues and subordinates. The world of academia would be a better place were we all to follow his example. Special thanks go out to Dustin, my right hand man and a great motivator for developing my passion for physics, and Dr. Perrett for her unwavering desire to help everyone in the research group reach their potential. It has truly been a wonderful 7 and 2 years, respectively. I would not have made it to university or through the past 7 years of academic training were it not for my family. My father’s entrepreneurial and maverick spirit is responsible not only for him being the first member of the Pardo family to attend university, but also for setting the standard for all 6 of his siblings and myself to expand our horizons. Papa, “hasta la victoria siempre.” Equally as important is my mother and her kind, loving, and supportive spirit. The first Master’s graduate in the family and the embodiment of altruism. She has been my rock, my interlocutor, my inspiration, mimimi. Together they have made myriad sacrifices to pave the way for me, and above all they would never accept my gratitude as they felt this was their responsibility. Last but certainly not least; this work was accomplished in great part thanks to Beth, my love and my wife. I would not have made it through the all-nighters that got me here. Whether it was differential equations, formal labs, or reports, she was always there to lend a kind ear, to give the most uplifting hugs, and to surround me with the animals we so love: Sancho, Bernie, Wally, Walter, Gustav, Faith, and whatever else comes into our lives. I am excited for our life together and incredibly thankful we found each other. I am truly blessed for having had crossed paths with all of you. Thank you for believing in me. iv Contents List of Acronyms xi 1 Introduction1 2 Background4 2.1 APXS History....................................4 2.2 The MSL-APXS..................................7 2.2.1 Spectrum Acquisition...........................8 2.3 Resolution & Noise.................................9 2.3.1 Temperature, Radiation, and APXS Resolution............. 12 2.4 GUAPX....................................... 14 2.4.1 Top Hat Filter............................... 16 2.4.2 Characterizing the System......................... 18 2.4.3 The Yield Equation............................ 20 2.5 Calibration..................................... 24 3 Precursory Work 26 3.1 Accuracy of AGV-2 Concentration Estimates.................. 27 4 Laboratory 33 4.1 FEU-APXS Configurations............................ 33 4.1.1 Sample Spectra Acquired Under Different Configurations........ 34 4.2 Dataset....................................... 36 4.2.1 Data Selection............................... 37 5 Photopeak Areas (Background Removal and Deconvolution) 39 5.1 Count Rates & Source Decay Correction..................... 39 5.2 Count Rate Ratio (RCPS) ............................. 40 5.3 Results........................................ 40 5.3.1 Predominantly PIXE............................ 41 5.3.2 Predominantly XRF............................ 47 5.4 Discussion...................................... 50 6 From Peak Area to Concentration (Matrix Effects & The Closure Rule) 56 6.1 GUAPX Concentration Ratio R[C] ....................... 56 6.2 Results........................................ 56 6.2.1 Predominantly PIXE............................ 58 6.2.2 PIXE & XRF................................ 62 v 6.2.3 Predominantly XRF............................ 66 6.3 Discussion...................................... 70 6.3.1 Mapping Count Rates to Concentrations................. 72 6.3.2 Matrix Corrections and the Closure Rule................. 72 6.3.3 Mg Correction............................... 73 7 Concentration and Resolution 76 7.1 FWHM Ratio (RFWHM) .............................. 76 7.2 Results........................................ 77 7.2.1 Primarily PIXE............................... 78 7.2.2 PIXE & XRF................................ 81 7.2.3 Predominantly XRF............................ 83 7.3 Discussion...................................... 85 7.3.1 Negative Correlation............................ 87 7.3.2 Positive Correlation............................ 88 7.3.3 Precision Error & Estimate Variation................... 88 7.4 Conclusion...................................... 90 8 Conclusions 92 8.1 Future Work.................................... 94 A Campaign GRMs 99 vi List of Tables 3.1 Number of spectra summed for tranches A - F with average temperature and summed spectrum FWHM............................. 27 3.2 GUAPX settings used for AGV-2 spectrum fitting................ 28 4.1 Summary of different APXS configurations from May 2009 - August 2014... 34 4.2 GUAPX settings used for spectrum fitting in each configuration........ 36 5.1 Percent mean elemental composition for the different igneous GRMs utilized for instrumental calibration [51].......................... 51 7.1 Summary of results for the entire GRM suite and the subset that falls within the Martian concentration range (denoted MR).................. 85 A.1 Distribution of certified geochemical reference materials among sample groups in the 2012 campaign................................ 99 A.2 Distribution of certified geochemical reference materials among sample groups in the 2013 campaign................................ 100 vii List of Figures 2.1 X-ray spectra acquired from Allende meteorite using the ALPHA-X [14]....6 2.2 X-ray spectra acquired from Allende meteorite using the Pathfinder APXS [10].6 2.3 X-ray spectra acquired from basalt reference materials BCR-1 and BCR-2 using MER and MSL APXS instruments respectively [5].............7 2.4 Schematic cross-section of the MSL-APXS [5]...................8 2.5 Schematic of the MSL-APXS Sensor Head [15]..................9 2.6 Convolution of a top-hat digital filter function with a experimental spectrum. Adapted from [36].................................. 17 3.1 GUAPX estimated Na concentration at various resolutions for AGV-2..... 28 3.2 GUAPX estimated Mg concentration at various resolutions for AGV-2..... 29 3.3 GUAPX estimated Al concentration at various resolutions for AGV-2..... 29 3.4 GUAPX estimated Si concentration at various resolutions for AGV-2..... 29 3.5 GUAPX estimated K concentration at various resolutions for AGV-2...... 30 3.6 GUAPX estimated Ca concentration at various resolutions for AGV-2..... 30 3.7 GUAPX estimated Ti concentration at various resolutions for AGV-2..... 30 3.8 GUAPX estimated Mn concentration at various resolutions for AGV-2..... 31 3.9 GUAPX estimated Fe concentration at various resolutions for AGV-2..... 31 3.10 GUAPX estimated Zn concentration at various resolutions for AGV-2..... 31 4.1 GSP-2 Spectrum taken in 2010 for the instrumental calibration (FWHM at 5.9 keV = 168 eV).................................. 35 4.2 GSP-2 Spectrum taken in 2012 (FWHM at 5.9 keV = 198 eV)......... 35 4.3 GSP-2 Spectrum taken in 2013 (FWHM at 5.9 keV = 164 eV)......... 35 5.1 Na count rate ratios vs.