Course Twiki for Advanced Physics Lab, PHY 4821L

Introduction:

This course is likely the last laboratory course you will take as an undergraduate at FIU. The course is intended to complement and extend what you've learned in the intro and modern physics labs to prepare you for graduate studies in physics or employment in industry or government. In contrast to prior lab coursework in this class, you are expected to work much more independently in both the preparation of your experiments and the analysis of your results. The lab instructor while always willing and available to help will not provide you with a detailed set of instructions to perform the experiment or do the analysis. The primary goal and emphasis of the course is the production of research quality work; the final product being a paper suitable, in both content and formatting, for submission to a physics journal.

The course is organized around the production of publication-quality research papers on a variety of physics experiments that emphasize different aspects of data taking and analysis. Each student, working in small two-person teams, is presented with a series of experiments (listed below) over the 16 week semester. You are encouraged to collaborate closely with your lab partner, other members of the class, or even your lab instructor; however, you are responsible for your own research papers. PLEASE DO NOT TURN IN THE SAME PAPER as your lab partner. Research papers should be written to the standards of a typical modern physics journal. This includes conforming to the specific set of style and formatting requirements that are adhered to strictly. You can choose from among the various styles of publications in use today. The particular type-setting or word processing application used is up to you so you may choose whatever you are familiar with. For example, latex or tex provide the "best looking" or professional papers as these are applications are typesetting applications specifically designed for this purpose. Latex, relies on the use of "coded" keywords to draw symbols and equations after a compilation from "scripts" into pdf or postscript. This process is what creates the pdf document so learning how to script and compile latex code is a little more work than those WYSIWG applications like MS Word. On the other hand, MS Word or Openoffice's are perfectly suitable for writing papers and can be made to produce excellent results. In fact, most journals today provide templates in word alongside latex/tex. As a guide for what is expected of you in this class feel free to pull down one of the journals located above cabinets along the walls of our lab room. Likewise, you can download pdfs of recent physics papers I've linked for you that are of recent interest, attached below in the "Attachment box". Finally, I've provided you with word templates as well as a stand-alone latex template, for those of you who've used latex before also in the attachment are below. Recently, I've begun to use http://overleaf.com and have attached a latex template that I created within overleaf for your convenience. Overleaf is an online latex-based system that should make it both easy to do the compilation and collaboration on latex documents. This is what people do these days when collaborating on documents. FIU doesn't, at this time, have a overlead account so feel free to create your own and download the items in the zip file below into your overleaf shell. Good luck.

Please note that this is a three-credit UPPER-LEVEL class and you will be expected to put in the corresponding amount of effort.

Course Textbook and Recommended Reference Material

In this course, none of the textbooks below are specifically required but you are strongly encouraged to purchase at least a copy of Bevington and Robinson. The book by Lyons parallels the recommended text but focuses more on counting experiments. The book by Melissinos is a classic which focuses on several important experiments and excellent discussions on statistical distributions at the end.

1. "Data Reduction and Error Analysis for the Physical Sciences 3rd Edition" (ISBN: 0072472278) by Philp R. Bevington and D. Keith Robinson. This is a classic and every experimentalist should have a copy of their own. This is the only book I would highly recommend you purchase for this class. You can find the latest edition on Amazon for about 45 dollars. Older editions are also available but I do not recommend those. Get the latest or 3rd edition.
2. "Statistics for Nuclear and Particle Physicists" (ISBN: 0521379342) by Louis Lyons. This is another classic geared towards counting experiments but also covers general topics in data analysis. This book is a favorite of Dr. Boeglin.
3. "Experiments in Modern Physics 2nd Edition" (ISBN: 0124898513) by A.C. Melissinos and J. Napolitano. This is another classic and a good read. The book describes in detail the Millikan Oil drop experiment and describes pulsed NMR. The last few chapters include are on probability and statistics as applied to measurement including likelihood and least-squares fitting.
4. "Measurements and their Uncertainties" (ISBN: 019956633X) by Ifan G. Hughes & Thomas P.A. Hase. Another excellent reference on experimental techniques and measurements.

Lab Notebook

You should purchase a bound notebook to keep detailed notes about the experiments that you are working on. You should include data that you obtained, notes about the techniques, lists of references, etc. Notes should be dated so that you can cross-reference things in the notebook with other materials you may get or produce during your experiments. A good researcher usually has five times as much information in the notebook than needed--but you never can be sure what you are going to need once you sit down to analyze your data.

To encourage this practice, lab notebooks will be collected from time to time and inspected for completeness.

Lab Reports

After you complete taking data on a given project you will have about one week to complete the report for the lab. The reports should resemble a journal paper. Each report should have an introduction, a description of the procedures and equipment used, a description of analysis procedures, tables and/or graphs of the data collected, and a discussion of the results. Proper use of significant figures and statistical analysis is expected. All graphs and tables should be well labeled and properly displayed. You should cite all references used in a bibliography. I've attached below a couple of recent paper examples from Journals: A Physical Review Letters (PRL) paper on yet another discrepancy between the recent faster than light neutrino results and known physics PhysRevLett.107.251801.pdf and a recent paper on Upsilon resonance production at the LHC by the CMS collaboration PhysRevD.83.112004.pdf. Look to these as samples of what I expect. In addition, the arxiv.org website also has many tex templates most of which I will accept. You may also search the APS site for word templates if you so desire or create your own based on the sample paper attached below. I will add templates as I find them to this TWiki. There is some freedom in how you lay out your paper but please consult the Physical Review journals PRL, PRB... guidelines for proper formatting and rules regarding the layout. Your report should include these sections:

• (5pts) Abstract: A single paragraph, only in rare situations, and never in this class, would there be a need for additional paragraphs. Each element of your abstract should be concise and short (one or two sentences) and consist of the following: what was done, how it was done, your primary result or results, and finally, any major conclusion drawn. If numerical results are obtained you should quote those prominently in your abstract, particularly those that are most important. If you think it is relevant you may summarize important intermediate results but usually, this is not necessary for an abstract. The rest of the paper is better suited to this sort of information. Always make sure to include uncertainties, and that all values have their proper number of significant figures. And of course, the units of any numerical result should be quoted. Your conclusion(s) can be summarized in the last sentence or two. Remember your abstract is not your introduction so it shouldn't read like one. A general rule of thumb is that a good abstract is one that provides a reader with enough information to allow him/her to decide whether it is worthwhile to read the paper that follows. Regarding tense and use of pronouns. Use past and present tense where appropriate. For example, as the experiment was already completed use past tense when describing things that were done and use present tense to describe general ideas or conclusions or when appropriate. As an example, your abstract could begin something like this "We determined the magnetic moment of a small disk.. ". While this is okay usually in scientific papers a more formal and less personal tone is taken, for example: "The magnetic moment of a small magnetic disk was determined... "
  
  
• (10pts) Introduction: Here you will introduce the paper, describe what is being measured in detail and why it is interesting. Background information should be included in this section and any theoretical motivation for the work. This section will likely be the most heavily cited so make sure you cite your sources and include references in the "References" section. Properly formatted, check sample papers, or use the AIP style guide linked below.
• (10pts) Experimental Procedure: Describe the experimental setup in detail in this section. This is where you would describe the equipment used and its function, with as much detail as you think relevant. Assume here that the reader is not familiar with the equipment. Long and complex equipment can be cited to a manual, as there is no need to re-write what is already available. If you cite web pages make sure these conform to proper formatting guidelines. Make sure you include relevant figures and photos if needed. Also, describe in detail how the measurements were performed, procedures, assumptions made, particularly describe difficulties encountered and how you estimated uncertainties that result from any and all measurements. This is also where you can detail the experimental uncertainties and any steps taken to reduce them. Many experimentalists move a complete discussion on experimental uncertainties to a separate section as this is as if not more important the main result of your work. Remember the idea here is to provide as complete a description as you can so that others can reproduce your work, this is usually the approach taken in a never-before-done experiment. In this class, I will take into account that what we are doing is practice.
• (10pts) Results and Conclusions: ( Results ) As per the title of this section here you describe the result(s) obtained. Included a summary of important final calculations. Do not just include numbers in loose itemized lists instead use properly formatted tables, plots, and or figures to describe the results. Never have a section that only has data tables and plots WITHOUT a narrative describing what is being presented. This can not leave the interpretation of data completely up to the reader, no matter how expert you believe they are. Here is where you would include any statistical analysis conducted to obtain your results, models used to fit data, statistical inferences, discussion of the goodness of fit parameters, confidence levels in the agreement between your data and your model assumptions, t-values, and/or any other relevant statistical analysis performed. A full summary and description of your uncertainties; both statistical and systematic should be included here unless it was moved to its own section, somewhere else in the paper. (Conclusions) For the conclusions part of this section, you should give context to your results what they mean and how to interpret them. Discuss how they relate to theoretical predictions or known values you are comparing your results with, other measurements, or previously accepted determinations. You could also discuss possible improvements to the experimental procedure especially if your results are inconsistent with expectations. However do not freely speculate and try your best to quantify your statements, for example by changing this I can improve the uncertainty in that by how much. If you can not easily quantify these statements they are better left unsaid. You may also want to discuss the precision of your result particularly if these are poor and if there are ways in which that can be improved. For example with a longer experimental run, measurement of input parameters with different equipment, or the use of improved techniques.
• (5pts) References: Citations should be included in your paper and be properly formatted, consistent with standard practices in physics journals, such as PRL or PRD (use the AIP style guide linked below. If you don't want to read that style guide just copy the sample papers linked below). I prefer the use of square brackets, [1] to cite a reference and require you to use separate reference bibliography started on its own page. If you use the style templates below they provide you with proper formatting for your citations automatically. But you need to know how to use it. It pays to learn this sooner rather than later. You can use online sources but only if you cite them properly. If you cite a webpage, which I allow, make sure you reference it properly in the bibliography. I also allow Wikipedia sources but you should avoid the use of these as much as possible as they are usually not allowed in real papers. It is probably a good practice to check the reference in the wiki page article and read through that as an original source. With this warning in place, I will not penalize you for using Wikipedia citations. But make sure you reference it properly. Remember anyone can post to a Wikipedia page, so it may not be true. I know pages are usually monitored closely by experts, but they may have been away when someone posted...
• (5pts) Formatting -Not really a section: Your best bet is to look through the sample paper linked below to see how to properly format figures, captions, tables margins etc. I am expecting a publication-quality paper from you and if it doesn't look right it's actually a lot harder to read comfortably, this is partly why journals impose strict style guides on papers they publish. Below you will find a latex and word template. Try to avoid using other word processors as they tend not to be universally supported. The best is latex but there is a rather larger and steep learning curve so MS Word is good enough. By the way, the AIP style guide, 4th edition, linked below doesn't just address formatting issues it is a general guide that helps you improve your technical writing but within the AIP style.
• (0pts) Appendix: You can include one of these if you need to but it is not necessary.

A grading rubric GradingRubric will be applied to each lab using the criteria above to assess your performance. Your lab reports (papers) grade will constitute 80% of your final grade for the course. Reports will generally be due one week after you have completed the experiment. Reports that are late will have their grade reduced by approximately one letter grade if not turned in by the due date shown in the google calendar. After two weeks late the lab report will not be accepted and a zero will be assigned. Typically no grades for one lab report will significantly impact your course grade as there are only five lab report grades and one presentation grade in this course. If you miss more than one lab report your chances are pretty good of earning a C- or worse. That would mean you would have to take the class again before you graduate with a degree in Physics.

You can use the Journal of Physics: Conference Series guidelines to format your paper in. But if you prefer to use some other physics journal guidelines you are more than welcome to do that instead. We provide below zip files with the guideline/templates from the JPC for your convenience.

Presentation

At the end of the semester, you will be required to give a 20-minute presentation on one of the experiments you did or a topic of your choosing related to some physics of interest to you. In the past students have presented work they've participated in during Summer research projects at FIU or elsewhere. For example: at Jefferson Lab, with the Biophysics group, etc,. In any case and to avoid conflicts all students need to have their topics approved by me a week before the presentation is scheduled. The presentation will be graded and will constitute 15% of your course grade. The ability to convey and communicate your topic through oral presentations is a critical part of my work as a physicist.

The maximum time for each presentation is 20 minutes, plus 5 minutes for questions and discussion. The grading on your presentation is based on the following aspects:

1. (20 points) Smoothness and clearness of your talk.

2. (20 points) Structure and organization of your slides (should include: Introduction, background, motivation (significance), method, results, conclusion/summary).

3. (20 points) Your understanding of the topic/research field.

4. (20 points) Interpretation of research/experimental results.

5. (10 points) Completeness of the citation of the sources from which you get the data, image, graph, information, etc.

6. (10 points) Your answer to the questions from your instructor and classmates.

The presentation schedule and topic PresentationSchedule

Exit Exams

To comply with state-mandated requirements, all students will be required to take an "exit exam". This exam covers everything in the FIU undergraduate physics curriculum: Modern Physics, Mechanics, E&M, Thermodynamics, and Quantum Mechanics. The exam is worth 5% of your final grade.

Schedule

You will be rotating through the various labs on a schedule to be determined by the schedule listed below. Typically you will complete 5 labs and your grade will be based on the score you earn on the labs plus the presentation at the end of the semester. The google calender linked belwo will show the lab due date and first draft due dates for your convenience. If there is an issue with the schedule please contact your instructor during the first few times we meet, since once you are on the schedule outlined below it will be difficult to change the sequence of labs. Ultimately you will be graded on five labs plus the presentation.

<iframe frameborder="0" height="600" scrolling="no" src="https://calendar.google.com/calendar/embed?src=c075emqam1c5lr558rkq8ic1hg%40group.calendar.google.com&ctz=America%2FNew_York" style="border: 0;" width="800"></iframe>

Another rendition of the schedule is available here PHY4821LSchedule

Lab due dates are posted on the google calendar above along with due dates for first drafts. The due dates for the first drafts are not enforced, due dates for the labs reports are as follows: 1 point off per day till 1 week late. After one week the lab report will not be accepted. If there is an issue with due dates and your schedule, upcoming conference etc please let me know.

List of Available Labs

Field	Topic	References and Links		Laboratory Instructions	Students
Computational Physics	Monte Carlo Methods, Binomial Statistics, Errors, Uncertainties and fittin	There are sections in both recommended texts related to this lab. Mellesino has a nice section on probability and statistics, distributions, fitting functions and so does Bevington and Robinson. Other sources and links: Helpful information on how to gain access and use the physics server medianoche HowToAccessComputing, A recommend data analysis package called MNFIU or MN_FIT, essentially an interface to CERN MINUIT fitter. Its one of the few precursors to ROOT but is easier to use. The manual and information is available http://www-zeus.physik.uni-bonn.de/~brock/mn_fit.html, The full blown ROOT data analysis package The ROOTt data analysis framework , and Dr. Boeglin's, collection of python scripts and libraries (Labtools) http://wanda.fiu.edu/boeglinw/LabTools/doc/		MonteCarloLab
Statistics and Probability Distributions	Uncertainties, Poisson and Gaussian statistics	"Experiments in Modern Physics" 2nd ed. by Melissinos & Napolitano. Other sources, Poisson Statistics, Poisson fitter, Counting Statistics,[XYZ of Oscilloscopes (Tektronix intro manual)]]		CountingLab
Fundemental Constants	Millikan Oil Drop Experiment	A nice description of this lab is available from Meliesino & Napolitao 2nd ed. The original paper (A must read) MillikanOilDrop		MillikanLab
E&M	Magnetic Torque & Gyromagnetic ratio	Teachspin website: Magnetic Torque		MagneticTorqueLab
E&M	Magnetic Force	Teachspin website: Magnetic Force		MagneticForceLab
NMR	Pulsed NMR, finding FID	Teachspin website: Pulsed NMR		NMagneticResonanceLab
Astro/particle physics	Cosmic Ray Flux distribution			CosmicRayLab
Condensed Matter Physics/Nanoscience	Quantized Conductance in nanocontacts	This is a newly developed experiment for students interested in condensed Matter Physics, nanoscience and nanotechnology. The experiment will be carried out in Professor Jin He's lab (CP 277) and will be supervised by a graduate student.		QuantizedConductance

-- JorgeRodriguez - 2012-01-02

• HiggsDiscoverPaper-xarch-1207.7235v2.pdf: The Higgs discovery paper published by the CMS Collaboration in 2012.

• PhysRevLett.107.251801.pdf: A PRL paper on the faster than light neutrino results obtained last September by the OPERA collaboration.

• PhysRevD.83.112004.pdf: A recent PRD paper from the CMS collaboration on Upsilon production at the LHC. This longer paper includes lots of figures, tables and equations.

• LaTeXTemplates.zip: Lab paper template/guidelines for latex

• wordguidelines.zip: Lab paper template/guidelines for word

• aip_style_4thed.pdf: aip_style_4thed.pdf

• PhysRev.2.109-MillikanOilDrop.pdf: PhysRev.2.109-MillikanOilDrop.pdf