Monday, November 17, 2014

Book chapter on my flipped classroom

I am writing a book chapter on my flipped classroom for a book on university pedagogy.  Normally I decline invitations for book chapters of any kind, but I was working on a web-book anyway so I thought I could just reformat part of that as a chapter.

Here is a draft.  Comments welcome.  Use either the comment function in Google Docs or the comment section below.

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Sunday, November 2, 2014

Teacher of the year, a year later

Harald at home on top of the bookshelf

Last November I received the teacher of the year award from the University of Copenhagen. This led, directly and indirectly, to some interesting experiences this year.

November (2013)
The award is announced, I receive my porcelain owl, and shake hands with the Queen (minute 66 on this webcast)

I am interviewed for the school paper with separate photo-shoot in my office.

I am interviewed (over the phone) for ForskerForum - the monthly newsletter for a series of academia-related trade unions.  The interview can be found on here on page 20.

I participate in a roundtable discussion on good teaching at the university, at the Ministry of Science, Innovation and Higher Education.  The then-minister of education (now minister of taxation) moderated the discussion and the current minister of education was also there.

I give a talk to the chemistry department at the Danish Technical University about active learning. Here's a re-recording of the talk.

I am invited to give a talk on teaching at a local Rotary club.  It's in the evening so I decline.

I am invited to write a book review for the alumni newsletter.  You can see a draft of the review in English here.

I am invited to write a book chapter in the flipped classroom for a book on university pedagogy.  I am already planning a web-book on this, so I say yes provided I can write it in English.

I participate in a panel discussion on blended learning at the minister of education's annual meeting. The meeting is in Kolding, so I have to get up at some ungodly hour to catch a train.

I give a talk to the Department of Physics, Chemistry, and Pharmacy at the University of Southern Denmark about active learning. This turns into a 2.5 hr marathon discussion!

The ministry of education gives me a free ticket to attend the EDUdisrupt2014 meeting.

Henrik from the Faculty of Science's IT Learning Center comes by and films my use of peer instruction in a course (here and here).  Afterwards we do a little interview.

I invited to asked write a comment on an (paywalled) article on the use of clicker in STEM education at the University of Southern Denmark in MONA - Matematik- og Naturfagsdidaktik, a Danish journal for research in STEM education.  You can find the English draft here.

I give a talk to the Faculty of Science's IT Learning Center about active learning.  That afternoon I give the same talk to the teachers of 1st year chemistry courses in my department.

I give a talk to the School of Pharmacy about active learning.

I give a talk to the Department of Computer Sciences about active learning.

I am invited to participate in a workgroup on the design of teaching portfolios for the Faculty of Science.

I am a keynote speaker at the Make a difference - teach and learn with technology conference.

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Saturday, October 18, 2014

100K views on my YouTube channel

I passed the 100,000 views mark on my YouTube channel. That's not very much by YouTube standards but I'm still surprised given the pretty dry videos I tend to make.  Most of these videos were made for teaching of some kind, so I am happy that a few other folks found them useful.

Anyway, here are the top 5 videos with number of views.

Illustrating Entropy  19,674 (20%)

Tunneling and Scanning Tunneling Microscopy 10,331 (10%)

The Computational Chemistry Movie 9,203 (9.2%)

Molecular basis of differential scanning calorimetry 5,450 (5.4%)

Four simple examples of the Schrödinger equation 5,438 (5.4%)

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Sunday, September 28, 2014

PM6, DFTB, GAMESS, enzyme design, protein-ligand binding, and protein structure validation

The publication of this paper got me thinking and this blog post is an attempt to organize my thoughts.

A while back my group developed a method for high-throughput calculation of the effect of mutations on enzyme barrier heights.  The newly developed PM6 method was key to this: it was fast enough and predicted the right reaction mechanism, which AM1 and PM3 did not.

Around that time Mike Gilson and Stefan Grimme published studies were they predicted good absolute binding energies of host-guest complexes using hydrogen bond- and dispersion-corrected PM6. Again PM6 was fast enough to compute the vibrational frequencies needed for the free energy correction.

Parallel to this we have been working in protein structure determination using chemical shifts.  I am starting to suspect that the best way to validate the predicted position of key side chains is to compute their chemical shifts ab initio.  The first step this process might be a complete or partial geometry optimization using something like PM6-D3H+, followed by an QM/MM-like ab initio chemical shift calculation.  Or perhaps a similar check of all side chains.

Using PM6 in MOPAC gave all sorts of problems. At that time the only other option for PM6 was Gaussian, without dispersion and hydrogen bond corrections. So the only option was to put PM6 in GAMESS, or more precisely:
1. implement PM6
2. implement dispersion and hydrogen bond correction
3. interface to PCM
4. linear-scaling FMO implementation.
5. interface to QM/MM?

+Jimmy Charnley Kromann has done 1-2 and +Casper Steinmann has done 3, both for elements up to F. Heavier elements require d-functions.  We have the d-integral code.

Now Nishimoto, Fedorov, and Irle have implemented dispersion-corrected DFTB and FMO2-DFTB in GAMESS, leaving the implementation of a hydrogen bond correction and interface to PCM.

Where does that leave us?
Is DFTB as good as PM6?
For binding and frequencies the answer appears to be "yes" (see for example Table 5 and Table I). For TSs I'm not really sure, but perhaps a little better (Table 4).  We should definitely test this on our little database.
One worry is that DFTB is available for fewer elements than PM6.

What's more work: implementing PM6 for the remaining elements, and d-integral PCM implementation, and FMO2 or implementing hydrogen bond corrections and the PCM interface for DFTB? 
I think the latter.  However I should definitely ask the authors if they have similar plans and when we can get our hands on their code.  Should we decide to go ahead with FMO-PM6 this paper will be very helpful.

What about QM/MM?
AMBER now has dispersion and hydrogen bond corrected PM6 and DFTB, complete with interface to a continuum solvent method and, of course, the AMBER FF. Do we really need to treat all the atoms with SE-QM?  If not, we could go straight to applications!

One problem is that we have no real experience with AMBER. How easy is it to use? Would we get the help we need if we get stuck?  How easy is it to modify the code?

There is really only one way to find out.

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Friday, July 25, 2014

Flipping your classroom: getting started

Completely flipping your classroom with videos, clicker questions, etc. is a lot of work.  One way to make it happen is to do it in stages.  It is better to do a little bit than nothing at all.

The alarm clock approach
The most common use of clicker-questions is to give a multiple choice clicker question about half-way through the lecture to wake students up. This begs the question "why put them to sleep in the first place" but it's better than letting them sleep.  It also gives you some feedback on how much the students have absorbed.

If you feel you can't even spare 5 minutes for a clicker question because you are always hopelessly behind in the lectures then there is something seriously wrong with the way you teach.

An experiment: is lecture necessary?
1. Make a 2-3 question reading quiz on a topic you would like to skip in lecture and that you feel the book explains well.

2. Give 1-2 in-class clicker questions that, if answered correctly by >75% of the student, makes you comfortable skipping the topic in lecture.

3. Repeat a very similar in-class question on same topic next week (yes, you'll need to repeat material to make it stick).

Convinced? Good, now:

The first year
Look through your lecture notes and replace part of lectures where you mostly repeat the textbook with reading quiz and in-class questions.

The second year
Record video lectures where you deviate from the textbook and use the entire lecture period for questions.  This will also free up time for review questions on previously covered topics.

The third year
Rethink the course in light of what you have learned. Is the book helping or hurting the course? Does it cover what you want in the order you want it? If not, consider getting rid of the textbook and replacing it entirely with video lectures. When doing so, consider reducing the curriculum compared to the textbook.

Clicker questions. In my experience I get through about 6 good clicker-questions per 45 min period: about 3 review questions and 3 questions on new topics. It's OK to re-use or only slightly modify questions that you haven't used for at least a week (if you don't believe me, try it).

It's hard to write good clicker questions. Be prepared to replace questions that are too easy or too hard the following year.

Reading quizzes. You need to give a reading quiz before every lecture period where you give clicker questions on new material. The reading quiz shouldn't be more than at most 7 easy-to-answer (if you have done the reading or watched the video) questions. I often use true/false.  It usually takes me 15-20 minutes to write such a quiz.

Video lectures. The optimum length for a video is about 7 minutes. If you already have lecture notes or Powerpoint slides and are comfortable with the recording software you use then making a 7 minute video takes about 15-30 minutes depending on the amount of editing you do. This does not include the upload to Youtube, which can be up to 30 minutes depending on internet speeds, but you can do other things during that time.

Recording live lectures
Another option is to record your live lectures in year 1 for use in subsequent years.  If you lecture with Powerpoint you can use screencasting software to record and use an external microphone.  If you lecture on the blackboard you will have to get someone to record it with a video camera.  Ask your university e-learning office to borrow one.

In either case you should edit the recording into shorter videos no longer than 10 minutes. It is just a boring and off-putting to watch a 45 minute lecture on-line as it is live. If possible insert a question at the end of each video to activate the students.

Other universities have recorded lectures on put them on-line, so you might be able to find what you need just by Googling or searching on Youtube.  Notice that if you only want the students to see part of a video you can specify the start time in the Youtube link.

This post is part of an ongoing series of post on teaching tools and tips collected here.

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