Students have long had better access to wireless internet than staff in the Department of Chemistry. But this changed when we got our new and hard to remember user names. It's just that no-one (I am looking at you, Science-IT) bothered to tell us. Having said that, when I asked Science-IT I got the following helpful tip:
Follow the instructions for students on this site, and substitute <ki-id>@ku.dk for <ki-id>@alumni.ku.dk.
Monday, February 28, 2011
Friday, February 25, 2011
Web applications in KemiKS: Quiz and Hückel
This week, we have tried three new visual features in KemiKS.
a) The students were strongly encouraged to use Maple in the solution of one problem, where they are supposed to draw the wavefunction of the hydrogen molekyle ion. This exercise was previously solved by hand, but now was supposed to be solved by using Maple. The students responded positively to it, although they had lots of problems in remembering how to use Maple. But when they finally had plotted the wavefunction, they really liked the fact that they now had created themselves the figures shown in many textbooks.
b) Janus had found a website at http://undergrad-ed.chemistry.ohio-state.edu/H-AOs/index.html, with a good discussion of atomic orbitals up to f-orbitals and a nice quiz. The student were asked to do the quiz in the first exercise class on monday as a repetition of what they had learned in the week on atomic orbitals. We will later in week 7 follow up on this idea and give the students in the beginning of the week a quiz on the key points of the week, which they probably will not be able to answer. At the end of the week, the students will then repeat the quiz and hopefully can see what they have learned in this week. Janus will look for appropriate tools in order to make a quiz with high score and solutions outside of Absalon.
c) as illustration of the discussion of the Hückel method, we have now incorporated two java based Hückel programs (see description in previous blog), which can be run over the net or can be downloaded and run directly on ones computer. This was thought to have the big advantage that we can study much larger systems, which previously were out of question, when one had to diagonlize the Hückel matrices by hand. The students were then asked to use these tools in two of the problems of this week. One problem was newly made and the other was modified so that the students now use these Hückel programs instead of doing it by hand. Talking to the teaching assistants helping the students the response is mixed. On one hand the Hückel programs are nice tools, but the danger exist that the students loose the understanding of how the Hückel matrix should look like, because in these Hückel programs it is generated automatically for them after drawing the molecule in the GUI. Therefore, it might actually didactically more effective to let the students write down the Hückel matrix by hand and then use Maple to diagonalize it, which is without computers typically the limiting factor or to have to exercises: one with the Hückel matrix by hand / Maple approach for a medium size molecule and one with the Hückel programs for a large molecule.
a) The students were strongly encouraged to use Maple in the solution of one problem, where they are supposed to draw the wavefunction of the hydrogen molekyle ion. This exercise was previously solved by hand, but now was supposed to be solved by using Maple. The students responded positively to it, although they had lots of problems in remembering how to use Maple. But when they finally had plotted the wavefunction, they really liked the fact that they now had created themselves the figures shown in many textbooks.
b) Janus had found a website at http://undergrad-ed.chemistry.ohio-state.edu/H-AOs/index.html, with a good discussion of atomic orbitals up to f-orbitals and a nice quiz. The student were asked to do the quiz in the first exercise class on monday as a repetition of what they had learned in the week on atomic orbitals. We will later in week 7 follow up on this idea and give the students in the beginning of the week a quiz on the key points of the week, which they probably will not be able to answer. At the end of the week, the students will then repeat the quiz and hopefully can see what they have learned in this week. Janus will look for appropriate tools in order to make a quiz with high score and solutions outside of Absalon.
c) as illustration of the discussion of the Hückel method, we have now incorporated two java based Hückel programs (see description in previous blog), which can be run over the net or can be downloaded and run directly on ones computer. This was thought to have the big advantage that we can study much larger systems, which previously were out of question, when one had to diagonlize the Hückel matrices by hand. The students were then asked to use these tools in two of the problems of this week. One problem was newly made and the other was modified so that the students now use these Hückel programs instead of doing it by hand. Talking to the teaching assistants helping the students the response is mixed. On one hand the Hückel programs are nice tools, but the danger exist that the students loose the understanding of how the Hückel matrix should look like, because in these Hückel programs it is generated automatically for them after drawing the molecule in the GUI. Therefore, it might actually didactically more effective to let the students write down the Hückel matrix by hand and then use Maple to diagonalize it, which is without computers typically the limiting factor or to have to exercises: one with the Hückel matrix by hand / Maple approach for a medium size molecule and one with the Hückel programs for a large molecule.
Sunday, February 20, 2011
Smelling vibrations: why do isotopomers have different smells?
An interesting paper (I assume, I haven't read it yet) led to an interesting blog post (I did read that one) with an interesting discussion (be sure to check out the comments below, including those of the paper's author).
Science in action and science in the open.
Science in action and science in the open.
Saturday, February 19, 2011
Symmetry: Ancient Knowledge Rediscovered
There are things in this world you never learn. You either wish you never will, or thought you never would. When the topic concerns symmetry of molecules, I've used (and keep using) the good old C1 for quite some time without any hassle. Excuses for not exploring it have been many, but when I had to be assistant teacher in a course (KemiKS) which the Department of Chemistry at the University of Copenhagen offers, I had to sit down and buckle up. Visualising it in 3D proved to be the hard task, so I went on the web to find the symmetry@otterbein website. It has interactive pages where you can rotate around the molecules to get a good feel for where axis and planes are. It also includes a challenge so you can learn to use the flow charts that follows every book on the subject.
Now symmetrize a molecule!
COMS Seminar Calendar
A COMS Seminar Calendar has been created. You can add it to your favorite calendar program by using the link. This will be maintained by Casper Steinmann.
For detailed information, look at the appropriate page about the COMS Seminars on the COMS homepage.
Thursday, February 17, 2011
Center of Excellence proposal moves on to round 2
The Center of Excellence pre-proposal I, Thomas Hamelryck, Flemming Poulsen, and Jesper Ferkinghoff-Borg submitted to the Danish National Research Foundation (Danmarks Grundforskningsfond) was one of 27 selected out of 198 for the second round.
The proposal builds on Anders Christensen's Ph.D. project on protein structure determination using chemical shifts.
The proposal deadline is the 28th of April, and we'll know if we made it some time in October.
The proposal builds on Anders Christensen's Ph.D. project on protein structure determination using chemical shifts.
The proposal deadline is the 28th of April, and we'll know if we made it some time in October.
Positions in Irvine and Singapore
Irvine
I have several openings for postdoctoral positions in different areas of theoretical and computational chemistry and physics in my group at UC Irvine. I will appreciate it if you could bring this to the attention of suitable candidates.
Thanks for all your help.
Shaul Mukamel
(A) Computational Biophysics
Simulation of amyloid fibril structures and aggregation kinetics, lipid-protein complexes and antibody interactions and how they can be probed by novel multidimensional spectroscopy ranging from the infrared to the ultraviolet.
(B) Attosecond X-ray Spectroscopy of Molecules
Developing time-dependent many-body approaches to nonlinear x-ray core-electron spectra and their description in terms of real-space and real-time wavepackets of electrons and nuclei. Computational tools will be implemented for the design and analysis of measurements involving multiple ultrafast optical and x-ray pulses.
(C) Energy and charge separation in photosynthetic complexes studied by nonlinear spectroscopy
Developing and applying time-dependent density functional, nonequilibrium Green?s Function techniques and exciton models for computing electronic excitations of molecular assemblies, light harvesting complexes and current-carrying molecules. Connection is made to quantum information processing and manipulation.
(D) Nonlinear Spectroscopy with Quantum Optical Fields
New optical signals which use entangled photons, pulse shaping, and coherent control algorithms are designed and simulated for probing molecular relaxations and exciton transport.
Ph.D. is required. Salary will commensurate with experience. Send a curriculum vitae, publication list and arrange for three letters of recommendation to be sent to:
Professor Shaul Mukamel
Department of Chemistry
1102 Natural Sciences
University of California, Irvine
Irvine, CA 92697-2025
smukamel@uci.edu
949/824-7600 (phone) 949/824-4759 (fax)
http://mukamel.ps.uci.edu (website)
Singapore
A 2 year postdoctoral position is available in singapore, starting from april-june 2011. The candidate should have experience of computational methods in studying protein-ligand interactions and experience with free energy methods will be an advantage. The project is aimed at fragment screening, small molecule screening, peptide design against a protein of therapeutic interest. We have recently designed and patented a peptide against this target for oncology and it is hoped that this will inspire further developments in this project. The work is in close collaboration with experimental labs (biophysical/cell & molecular biology & zebrafish/mouse models) and with the oncology division of the local hospital, with a rapid turnaround time that helps guide design. It is hoped that it will result in a molecule that will be be taken over by a small local biotech after 2 years. For further details please send cv and get 3 letters of reference sent to chandra@bii.a-star.edu.sg
I have several openings for postdoctoral positions in different areas of theoretical and computational chemistry and physics in my group at UC Irvine. I will appreciate it if you could bring this to the attention of suitable candidates.
Thanks for all your help.
Shaul Mukamel
(A) Computational Biophysics
Simulation of amyloid fibril structures and aggregation kinetics, lipid-protein complexes and antibody interactions and how they can be probed by novel multidimensional spectroscopy ranging from the infrared to the ultraviolet.
(B) Attosecond X-ray Spectroscopy of Molecules
Developing time-dependent many-body approaches to nonlinear x-ray core-electron spectra and their description in terms of real-space and real-time wavepackets of electrons and nuclei. Computational tools will be implemented for the design and analysis of measurements involving multiple ultrafast optical and x-ray pulses.
(C) Energy and charge separation in photosynthetic complexes studied by nonlinear spectroscopy
Developing and applying time-dependent density functional, nonequilibrium Green?s Function techniques and exciton models for computing electronic excitations of molecular assemblies, light harvesting complexes and current-carrying molecules. Connection is made to quantum information processing and manipulation.
(D) Nonlinear Spectroscopy with Quantum Optical Fields
New optical signals which use entangled photons, pulse shaping, and coherent control algorithms are designed and simulated for probing molecular relaxations and exciton transport.
Ph.D. is required. Salary will commensurate with experience. Send a curriculum vitae, publication list and arrange for three letters of recommendation to be sent to:
Professor Shaul Mukamel
Department of Chemistry
1102 Natural Sciences
University of California, Irvine
Irvine, CA 92697-2025
smukamel@uci.edu
949/824-7600 (phone) 949/824-4759 (fax)
http://mukamel.ps.uci.edu (website)
Singapore
A 2 year postdoctoral position is available in singapore, starting from april-june 2011. The candidate should have experience of computational methods in studying protein-ligand interactions and experience with free energy methods will be an advantage. The project is aimed at fragment screening, small molecule screening, peptide design against a protein of therapeutic interest. We have recently designed and patented a peptide against this target for oncology and it is hoped that this will inspire further developments in this project. The work is in close collaboration with experimental labs (biophysical/cell & molecular biology & zebrafish/mouse models) and with the oncology division of the local hospital, with a rapid turnaround time that helps guide design. It is hoped that it will result in a molecule that will be be taken over by a small local biotech after 2 years. For further details please send cv and get 3 letters of reference sent to chandra@bii.a-star.edu.sg
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