Bucknell Physics & Astronomy

• Random numbers and simple graphs of PDFs html, ipynb,
• Statistics tools (random numbers, distributions, histograms): html, ipynb;
• Hughes and Hayes worked example 3.2.2 html, ipynb;
• Coin toss simulation html, ipynb
• handout on binomial distribution

• Coin Flips and the Central Limit Theorem: html,
• Error propagation: ipynb,

• Introduction to Maximum Likelihood Estimation pdf;
• Skeleton notebook for in-class exercises: Class4.ipynb hdata.dat
• Fitting to a linear model a.dat, html, ipynb;
• Fitting to a nonlinear model: b.dat, html, ipynb;

• Paper Description for PHYS 310
• Latex template with bibliography: templateWithBibAll.zip
• Literature search tools: Web of Science (if off campus, use VPN or Databases link under "Literature Search Tools" below) and Google Scholar

• Worksheet: Journal Paper Narrative (notice that the sections flow down the left side then up the right side)
• Example Journal Papers:
  • Theory/simulation: Chowdhury et al. (Traffic Flow Paper) Vollmayr-Lee & Zippelius 2013 (Defects in glass)
  • Experiment: Yoest et al. 2022 (Swimming microbes) Gowen & Solomon 2015 (Reaction front propagation)
  • Astronomy observation: Villadsen et al. 2014 (Radio Detection of Stars) .
• Figures Intro: Graphical Representation (Prof. I. Sulai, Phys310 talk) (therein figures and summary of [Edward R. Tufte, "The Visual Display of Quantitative Information," 2nd ed. (Graphics Press, Cheshire, Connecticut, 2018)]). Further examples:
  • Maps about US (includes Life Expectancy Map),
  • Research by Prof. B. Marsh (Maps of Institutionalized Racial Inequality),
  • Phase Transition Figures,
  • Ladd et al. Beam Size ,... (2005) ,
  • Villadsen et al. 2014 (Radio Detection of Stars) ; <
  • S.A. Berman, ...,T.S., Phys. Rev.Fluids 6, L012501 (2021) ,
  • KVL, RB, and LMC, PRL 2013,
• Matplotlib examples, Python subplots, Python save figures to PDF (the only line you really need from the example is the plt.savefig line)

• Fitting and \(\chi^2\) error surfaces; Class worksheet with fit to a Gaussian: ipynb,
• Example code for surface and contour plots: html, ipynb.

• Testing whether an exponential function fits a dataset: ipynb
• This time, the exponential model does not fit the data: ipynb
• Testing whether a die is "fixed": ipynb
  Data: die_1000.dat, die_50000.dat

• Note: talks will be 12-15 min this year, with questions at the end instead of during the talk.
• Slides from class,
• How to Give Talks (KVL) , Phys310 handout , further resource: Great Talks (by Prof. A. Graves)
• Talk Examples: Ibrahim (conference talk, 2023), Jackie (Bates College, Dec 2023) (1-hour seminar), Katharina (SiO2 Jumps & Scaling, Ohio 2017), Tom (Dickinson 2017) - PPT,
• Latex Beamer: see last page of How to Give Talks (KVL) , further resource: for uploading on overleaf: beamer_example_All.zip , for latex in linux environment: beamer_example.tex, fig1.eps, fig2.eps, fig3.eps

Experiments

• G: Intro (M. Ligare), Sect5-4 Damped Oscillations [J.R. Taylor, Class. Mechanics]
• Michelson: Guidelines for PHYS 310 students (by T.Solomon), Jenkins & White Ch 13 , Hecht Ch 7 , Hecht Ch 9 , M4 Interferometer Manual (Note: different interferometer)
• NMR: Basic theory of NMR stuff, Getting started manual, Introduction part of manual , Instrument part of manual, Specifications part of manual, Experiments part of manual, Article where the group measures T1 and T2 for some samples.
• Ising: Ising Model & Metropolis Intro (read to get started), Ising Model Jupyter Template, Lecture Notes by Richard Fitzpatrick (UT Austin) about Ising Model (read for additional background and more advanced project ideas).
• X-ray, Part I: General overview and tasks for X-Ray Project I (focusing on x-ray emission and atomic transitions ) Properties of X-rays handout. Intro to X-ray apparatus and getting started. Measuring wavelengths of emission lines for Mo and Cu anodes..
• Radio Telescope: Intro packet (read to get started), Stellarium (free software to plan observations), Data analysis Jupyter template and Test.rad (Example data to use with Jupyter template). Additional info: MIT web page about this project (useful references for a paper!), MIT lab manual for this project (additional background/explanation).
• X-ray, Part II: General overview and tasks for X-Ray Project II (focusing on crystallography) Crystallography reading from Ashcroft and Mermin. Intro to X-ray apparatus and getting started. Debye-Scherrer (Powder) technique. Which planes -- denoted by Miller indices -- are visible for different cubic structures..

Resources

Python Jupyter Notebooks

• File I/0: html, ipynb, test1.dat, test2.csv
• Tools for Statistics: html, ipynb; Random Numbers, Tools for Distributions, Histograms
• Curve Fitting:
  • Example of nonlinear least squares fitting using curve_fit() from the optimize sub-module of scipy (works for fitting of linear models too) html, ipynb, sample2.dat;
  • Example of linear least squares fitting using curve_fit() from the optimize sub-module of scipy html, ipynb
• Other examples (not necessarily for PHYS 310)
  • Overview of python use for experimental physics applications: external website
  • Linear Curve Fitting using np.linalg.lstsq (based on Jack Gallimore's mlr.py): html, ipynb, sample.dat
  • Vpython: html, ipynb
  • Simple numerical integration (Euler, as in PHYS 211, 212, 221): html, ipynb
  • Numerical evaluation of integrals using quad() from the integrate submodule of scipy: html, ipynb
  • Numerical solution of ODEs using odeint() from the integrate sub-module of scipy: html, ipynb
  • Root finding: html, ipynb
  • Chaos: Driven damped pendulum (PHYS 331): html, ipynb
  • FFTs: html, ipynb
  • Numerical differentiation (including divergence, gradient, curl, etc.): html, ipynb
  • Intro to Sympy (symbolic computation) --- variables, integration, differentiation: html, ipynb
  • Symbolic solution of differential equations using sympy: html, ipynb
  • More symbolic computation examples: nbviewer,
  • Line integrals using sympy (PHYS 333): html, ipynb
  • Astronomy Examples:
    • Downloading image, separating RGB, writing FITS files: html, ipynb
    • Downloading a FITS file: html, ipynb

Writing of Scientific Papers

• The Art of Scientific Report Writing (Oxford)
• Ten Steps to Writing an Effective Abstract
• Preparing a Manuscript for Publication; (Journal of Undergraduate Research In Physics)

Literature Search Tools

• Scientific Papers: Web of Science (accessible from FastX session or Databases next line) and Google Scholar
• BU pages: Library & IT (includes ILL and Journals A-Z), Databases (use to get to Web of Science when off campus; includes social science paper data bases)
• Books: BU Library Catalog (World Cat)
• Physics Sources: APS Journals (PRL,PRE, etc.), IOP Journals, ADS Labs (NASA) search, arXiv.org (preprints)

LaTeX

• LaTeX: Latex (& Xfig) in PHYS 310 (introduction to latex, including how to use the following files),
  for uploading on overleaf: templateWithBibAll.zip ,
  for latex in linux environment: templateWithBib.tex , myRefs.bib , cubic.pdf , samplefig.eps, and see below
• Simpler Paper Template (without bibtex):
  NOTE: These files are written for pdflatex.
  Download the files template2019.tex, samplefig.eps, and samplefigB.pdf. After processing these files you should generate output that looks like this: template2019.pdf.
• Sample file containing many more sophisticated examples of how to typeset a physics paper:
  This file apssamp.tex generates the output displayed here: apssamp.pdf. Comparing these files side-by-side is a good way to learn lots about typesetting papers.
• APS homepage for RevTeX (including links to documentation)

• Tutorials (A random sampling of many that you can find online):
  • Getting Started with LaTeX
  • Beginning LaTeX
  • A beginner's introduction to typesetting with LaTeX
  • The Not So Short Introduction to LaTeX 2e (or LaTeX 2e in 157 minutes)
• Projected Talks with LaTeX:
  • Beamer User's Guide, v3.01
  • Example latex source
  • Example PDF