Thursday, May 26, 2011

Outline Jan's edu-seminar: Using simulation and visualization in chemical education

Here are the main points of my seminar which I give tomorrow:

Chemistry deals with complicated three-dimensional structures and the complex motion of many particles, both of which are usually reduced to static two-dimensional structures on blackboards and Power Point Slides when teaching.  This is one of the things that makes chemistry a "difficult subject".  In the talk I show some examples (listed below) of how this can be overcome using three free software packages called Jmol, Molecular Workbench, and ChemDoodle Web Components.

I discuss four ways of using simulation and visualization when teaching chemistry:

1. Make an e-resource page (for example on Absalon) with links to simulations or visualizations you find on the web.  Examples: the DGU site and Jean Claude Bradley's page.
Try Googling "jmol and xxx" where xx is your topic of interest, such as "inorganic chemistry" or "chirality".  Or look through the library of simulations that come with Molecular Workbench.

2. Use them in lecture. Examples: illustrating energy states and molgrabberOther examples in physical chemistry.

3. Use them in peer instruction.  Examples: cyclohexane and illustrating entropy. See more examples hereSee two videos on peer instruction here.
I use for voting.  It is free for 30 or less students.  I have bought a 1-year license for larger courses.  If anyone at KIKU or COMS wants to use it, contact me for login instructions.

4. On-line quizz or practice pages.  Examples: cyclohexane, chirality, and molgrabber.

If someone in KIKU or COMS is interested in pursuing some of this further, please contact me.  We have money to hire student helpers.

Sunday, May 15, 2011

Peer instruction without clickers

I have written about my first experience with peer instruction over at Molecular Modeling Basics.  Click here to read, and please leave any comments over there.

I have bought an instructors version of polleverywhere.  If anyone at KIKU or COMS is interested in using it, just contact me.

Wednesday, May 11, 2011

The importance of being indexed

Playing around with iAnnotate for iPad and talking about it with Jan, I realized the importance of being able to swiftly navigate through documents. While reading an article or reviewing a manuscript it is important to be able to check quickly the content of figure 3 and then jump back to where one was in the text. iAnnotate has the possibility of including personalized bookmarks to a PDF document, but it is extremely boring, tedious, and time consuming to go through an entire document first to mark all the important features. PDF documents can have an embedded outline, as well as cross references to figures and tables. I found out that latex can do that for you almost effortlessly! One just need to include the hyperref package in the preamble. For example here is what I used while preparing my latest manuscript:

\usepackage[hypertexnames=false, naturalnames=false, dvips, colorlinks=true, linkcolor=black, citecolor=black, hidelinks]{hyperref}

Automagically all your \section, \subsection, \begin{figure} etc. commands will also produce a cross referenced link. In the mentioned example I hid in the text any sign of the links, but it is also possible to specify to have differently colored links or with colored boxes around.
In order to be able to use the "hidelinks" option one has to use the very latest version of hyperref. Think about it when preparing your next manuscript!

Thursday, May 5, 2011

Creating interactive chemistry ebooks

Well not quite. But I am getting started. See more in my latest post over at Molecular Modeling Basics. HTML experts especially welcome :).  Please leave any comments there.