Tuesday, August 30, 2011

Saturday, August 20, 2011

Education at its best: my poster for the assessment meeting

Here is my poster for the assessment meeting for the Education at its Best (Den gode uddannelse, DGU) initiative.

Here is a translation with links and supplementary information:

Simulation and Visualization (tools and resources being developed with support from DGU)
* Vibrating molecules
* The Quantum Calculator
* Student wiki-projects
* Video software manuals
* Link collections for courses

Active learning and peer instruction
* Web clickers (two videos about peer instruction)
* Web lectures (pencasts, Khan Academy type videos)
* Simulation based peer instruction questions

Other activities
* Web quizzes
* Using MAPLE in chemistry teaching
* Interactive chemistry e-book prototype
* Mini seminars on education

What was the money used for?

Student helpers
* Janus Eriksen
* Toke Fritzemeier
* Anne Schou Hansen

* Polleverywhere (web-clicker)
* Screenflow/Camtasia (screencast software)
* iPad apps

* Wacom Bamboo tablet
* iPad
* Web server

Suggestions for future funding
* Fund people instead of projects
Example: Hughes investigators. "By appointing scientists as Hughes investigators, rather than awarding them grants for specific research projects, the investigators are provided with long-term, flexible funding that gives them the freedom to explore and, if necessary, to change direction in their research. Moreover, they have support to follow their ideas through to fruition—even if that process takes a very long time."

* Make outreach a funding requirement
To continue to receive funding you should demonstrate that you are sharing your new teaching techniques with your colleagues.

* Students should be required to have a laptop
This is self-evident but apparently it needs to be said: You cannot incorporate IT deeply into your teaching unless you can be sure that all students have a laptop.  Why isn't the University of Copenhagen doing this yet?
* Power in classrooms and exams
If we want the students to use their computers we must provide them with basic necessities like power.  Right now most classroom have 1-2 power outlets, and the students do not have any access to power outlets during exams. 

* Control over internet access at exams
Many exam rooms do not have WiFi, so we can't write exams that require internet access to complete.  Conversely, many more teachers would embrace the use of computers if they can be sure access to the internet (for example using 3G) is not possible during exams.  This can be done with with "WiFi jammers".

Thursday, August 18, 2011

COMS Seminar: Anders Steen Christensn

 Towards protein structures that agree
with spectroscopic data

Chemical shifts assisted protein structure refinement

Download the slides from my talk Aug 18, 2011 here:

Protein G MC simulations - OPLS/AA with NMR restraints

Top: OPLS/AA + CamShift 1.35
Bottom: OPLS/AA + H(N) Chemical Shifts

Wednesday, August 10, 2011

New Paper: BioFET simulation with a multiple charges model

Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensor

De Vico L., Iversen L., Sørensen M. H., Brandbyge M., Nygård J., Martinez K. L., Jensen J. H.

Nanoscale, DOI: 10.1039/C1NR10316D

Abstract: A single charge screening model of surface charge sensors in liquids (De Vico et al., Nanoscale, 2011, 3, 706-717) is extended to multiple charges to model the effect of the charge distributions of analyte proteins on FET sensor response. With this model we show that counter-intuitive signal changes (e.g. a positive signal change due to a net positive protein binding to a p-type conductor) can occur for certain combinations of charge distributions and Debye lengths. The new method is applied to interpret published experimental data on Streptavidin (Ishikawa et al. ACS Nano 2009, 3, 3969-3976) and Nucleocapsid protein (Ishikawa et al. ACS Nano 2009, 3, 1219-1224)

We analyze how appropriate combinations of buffer conditions and charge distributions and orientation may lead to a counter-intuitive signal in BioFETs.