Thursday, May 19, 2011

Peer instruction: radial distribution functions

These slides show questions I used when teaching radial distribution functions using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

Some comments about specific slides:
Slide 8: The hint is given after the first vote.

Slides 11-18 show results from two Molecular Workbench exercises, which you can download here and here, once you have installed Molecular Workbench on your computer.

Slide 11: First I run the solid simulation, then pose the question and have a couple of votes, then click on the "show pair correlation function" in the MW simulation.  Note that you have to run for at least 100,000 fs to get good statistics (i.e. relatively smooth curves).  Then I explain the answer (slides 12 and 13)

Slide 14: Same procedure as slide 11, but for the liquid.

Slide 16: No vote, since the answer is pretty obvious, but I do ask where the peak at r = ~1.5 Å comes from.  Of course it comes from the attractive part of the Lennard-Jones potential, and you can clearly see some particles sticking together in the gas simulation.  To check, I change the depth of the well from 0.1 eV to 0.001 eV (simply double-click on any of the particles, and you will see what to do), re-run the simulation, and show the radial distribution function (summarized in slide 17).

See all posts related to peer instruction here.

Wednesday, May 18, 2011

Peer instruction: entropy

These slides show questions I used when teaching entropy using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate. Any questions, just leave a comment.

The slides refer to two Molecular Workbench simulations, which you can access here and here, and read more about here and here.

Specific comments to the slides
Slides 1-5: Here I start the simulation without removing the separator.  Then pose the question, two rounds of votes (usually not needed for the first simulation with 100 particles, as more than 80 % submit the correct answer), then remove the separator and explain.

Slides 10-15: Here I run the first simulation (small volume, low temperature) and carefully explain what the recorded times mean and how they correlate with probability.  Then I pose the first question (slide 10), two rounds of votes, then run the double volume simulation, then summarize the right answer (slide 11), and explain it (slide 12).  Same process for doubling the temperature.

See all posts related to peer instruction here.

Related blog posts
Illustrating entropy
Entropy, volume, and temperature
Simulations in teaching physical chemistry: thermodynamics and statistical mechanics

Monday, May 16, 2011

Peer instruction: force fields and energy minimization

These slides show questions I used when teaching force fields (slides 1-4) and energy minimization (slides 5-8) using peer instruction. The slides are in Danish, but I hope you get the idea and there is always Google translate.  Many of the equations are discussed in Sections 1.5 and 2.1 of Molecular Modeling Basics.

I also use the Avogadro program when teaching force fields.  See for example this post.

I have made a Jmol model to illustrate energy minimization, as discussed in this post.

See all posts related to peer instruction here.

Saturday, May 14, 2011

Molecular modeling and peer instruction

Last Tuesday I had my first go at using peer instruction.  Peer instruction is a fancy term for a relatively simple process:

1. Put up a multiple choice question
2. Ask the students to come up with an answer without talking to each other. Give them 2-3 minutes.
3. Have a vote (more on how below)
4. If 80 % or more get the right answer, show the right answer, give a short explanation, and move on.
5. If less than 80 % get the right answer, ask the students to discuss it with their neighbor. Give them 3-5 minutes.
6. Have another vote.
7. Give them the right answer and explain it.

Voting using

The screencast (best viewed in full-screen mode) shows how I use the website for the voting.  It requires the students to have access to a browser, so I ask them to bring a smartphone or a laptop to class.  It is also possible to submit votes by SMS, but Polleverywhere only provides a British phone number for Europe, so this gets pricey in Denmark.

The free version of can register up to 30 votes.  For larger classes your department needs to buy a six or 12 month subscription, the latter is about $900.  You just create an account on the site, create your poll, and you are ready to go. 

All my questions have four options labelled A, B, C, and D, so I just create one poll per course.  The example in the screencast is used in a course called KemiF1, so the codes for the options are kemif1A - kemif1D.  You do need to create completely unique codes.  The site assigns you numerical codes by default, so you can also just use those.  The website with the question is here.  Option D is "don't know".  It is important to have that option so that everyone casts a vote every time.

I thought it would be cool for the students to see the votes coming in live, but they felt it biased their vote too much, so it is better to leave the question up as they vote, and show the results when the vote is done.  You can monitor the progress on the vote on another device such as a smartphone or iPad.

Why use peer instruction?
Much has been written about peer instruction (just google it), but I find the two videos posted here especially informative.  And think about this: if you lecture on organic chemistry and less than 80 % of your students understand what you mean when you draw a hexagon, is there really any point in going on to more complicated material?

Peer instruction and molecular modeling
The real challenge when using peer instruction is to come up with good questions and I think molecular modeling and visualization can contribute a lot here.  For example, the spinning models in the example  reinforces the fact that cyclohexane is not planar.  Note that the students can go to the page and interact with each model as they mull their options.

I will show more examples of using molecular modeling and peer instruction in future posts.

Monday, May 9, 2011

Interactive chemistry ebooks: interactive figures

Here is version 2 of my ebook mockup page (see here for a description of version 1).  Actually there are two versions: one using Jmol and one for the iPad.

The Jmol version is how I would like the page to look.  The static figures are replaced with interactive Jmol versions embedded right in the page, and the figure captions contain links (denoted by ">>") to larger version of the figures on a separate page, that also contain extra features such as animations (Figure 3.1) or overlays (Figure 3.2).  An alternative design would have been to keep the static images, but insert links to the larger figures.  I think I like the current look better.  But for pages with more figures loading-time could become an issue with Jmol.

The iPad version is what is currently possible for the iPad with ChemDoodle Web Components.  We are waiting for two things to happen: 1) WebGL in Mobile Safari, which will allow real 3D representations of the molecules, and 2) Implementation of contours and surface maps in ChemDoodle Web Components.

For the iPad version I generated the necessary ChemDoodle Web Component HTML code using the ChemDoodle software package, as I show in this screencast.  The mol2 file I start with is generated with Avogadro.

ChemDoodle costs $60, and normally I restrict this blog to free software, but I am making an exception here because I think iChemlabs deserves to be supported since they made ChemDoodle Web Components open source.  Furthermore, since I have access to the source code I could probably figure out the format for the HTML code, if I wasn't so lazy.

Related blog-posts:
Interactive chemistry ebooks: highlight and annotate
Interactive chemistry ebooks: let us start now!
ChemDoodling: now in 3D, but not (yet) on the iPad
ChemDoodling on the iPad and the future of interactive chemistry text books
iPad: even 3D molecules that can be viewed from any angle

Sunday, May 8, 2011

Interactive chemistry ebooks: highlight and annotate


In a previous post I argued that the best way to get started on making interactive chemistry ebooks is to do it on the web with straight HTML, rather than wait for the epub technology to catch up.  But how would one highlight text and scribble notes in such a book?

One solution is to use Diigo, which is a free add-on to your browser as well as a free iPad app.  The picture above show a screenshot of annotation I added to the web page mock-up I talked about earlier.  Notice the "Web Highlighter" in the bookmarks bar, which, when clicked, gives you the blue tool bar you see.  The highlights and annotations are stored in the cloud, so they can be seen and modified from any browser where you have installed Diigo.  It also appears possible, though I haven't tried it myself, to share your notes with a group of people you define, which sounds like a very interesting study tool.

The computer version of the Diigo browser plug-in also has a "read it later" option, where the web page is saved and can be read in the Diigo app off-line.  For some reason this option is not there when using the iPad browser.  It also not possible to annotate in the Diigo app.  But I wouldn't be surprised if both options would appear in future releases.

Related blog-posts:
Interactive chemistry ebooks: interactive figures
Interactive chemistry ebooks: let us start now!

Thursday, May 5, 2011

Interactive chemistry ebooks: let us start now!

The problem
Henry Rzepa writes thought-provoking blogposts and his latest, entitled What is the future of books?, is no exception.  He describes the current state-of-the-art in science e-publishing and the very limited options and steep learning curves facing aspiring authors in this area.

Currently, there is only one publisher of interactive science e-texbooks: Inkling.  As a result, Inkling has their hands full and is unlikely to be interested in anything but the biggest best sellers in this area.

This means we chemists have to go at it alone, but there a is a big practical hurtle: there a no tools available to us.  The ePub 3 format that will allow interactivity will be released this month.  But when will tools to create and read ePub 3 files become available?

My first, and so far only, attempt at creating an ePub document taught me that the e-editors and e-readers are completely geared towards fiction.  Looking at Chapter 3 of Inklings Biology textbook on the iPad, which is available for free, is very educational.  Their design looks nothing like the traditional book that current e-readers such as Stanza and iBooks try to emulate with page swipes and similar layout considerations.  So we are not really waiting for these apps to become ePub 3 compatible; we are waiting for a science e-book reading app.  Who will write this and when?

One solution
But do we need all this stuff?  Broadly speaking, ePub is HTML in a zip file and ePub readers are hacked web browsers, and both are aimed at letting you read HTML off-line.   If we assume internet access, the need for ePub is mostly gone and this allows us to get started now by doing what we already know how to do: make interactive web pages.  Even if you think off-line access is essential, I hope you'll agree that "web-books" allow to test some design ideas for science e-books in ePub 3 format or book apps.

To kick things off, I have made a web page mock-up of how the section on electron density from my book Molecular Modeling Basics might look in the hands of the Inkling people, using an iPad-friendly template kindly made available by Matthew James Taylor

This is version 1, quite bare bones, and with a few blemishes.  For example, the top bar moves on the iPad (and on Chrome) because Mobile Safari does not respect position:fixed, and the Table of Content menu at the top doesn't work.  I would very much appreciate tips and suggestions from HTML experts on how to improve such things. You are very welcome to copy the HTML and the associated css, and experiment with this yourself.  (I am quite confident that a skilled HTML programmer could make a web page that is essentially indistinguishable from a page in Inkling's Biology book.)

Basic design considerations
Basic layout: The page can be read in both landscape and portrait mode.  The layout ensures that the main window is the same width in each mode, so that the formatting stays the same.  Portrait mode gives you reading without the clutter, landscape mode gives you access to options on the side.  Should the sidebar be on the left?  Should the sidebar scroll independently, and how do I do that?  When publishing Our Choice, Pushpoppress decided on landscape mode only, with a novel navigation, but I not sure this would look good for a real textbook. 

Continuous pages:  The section is not divided up in pages.  This avoids problems like figure captions spreading over 2 pages, but I think I would prefer this layout for fiction books as well: scrolling down on the iPad is a more natural gesture then side-swipe in my opinion.  I don't think I'll change that.

Table of content: Navigating a science textbook is very important.  The menu I have on the top left, will become too big, if I include the entire TOC.  Perhaps a nested drop down menu like this?  Could this be made to appear on a right-click?  Alternatively, I should I simply include a link to a separate page that holds the entire TOC, like iBooks?  Inkling's Biology book has a cool side-swipe feature where the TOC appears, but I have no idea how to do that.

Reading progress: Almost all readers have some indication of far along your are in the book or chapter, usually with dots.  Much of this is a legacy from novels.  In a textbook, you don't really care how much of the book you have read.  Perhaps it's important for a chapter?  Certainly in a section the position of the scroll bar is indication enough?  I don't think this has high priority.

Future plans
My plan for version 2 is to add interactive figures (should they be embedded or in separate pages?), and in subsequent versions I plan to add additional items to the right side-bar.  What should these items be?  Movies? Quizzes?  Again, suggestions are very welcome, as are links to similar mock-ups.

Now is the time to decide what interactive chemistry e-books should look like.  What do you think?

Related blogposts:
Interactive chemistry ebooks: interactive figures
Interactive chemistry ebooks: highligt and annotate
iPad: even 3D molecules that can be viewed from any angle
The Molecular Modeling Basics Electronic Color Supplement

Discussion page for Section 3.1 The electron density

The purpose of this post is to provide a forum for discussion of Section 3.1 The electron density of Molecular Modeling Basics.  Please post your questions an comments about electron density below.