This week in pchem we are discussing the energy minimization techniques that are used in computational chemistry. The students will build a mock energy function that models the dihedral rotation of 1,2-dichloroethane. Then three methods (The Monte Carlo Method, Newton minimization, and Metropolis simulated annealing) will be employed to solve for the preferred (lowest energy) dihedral angle (a).
A performance plot will also be generated that shows the lowest energy and its root mean squared deviation RMSD from the known minimum structure (a = 180 degrees). This plot clearly shows Newton’s propensity to get stuck in local minima. It also clearly shows that the Monte Carlo method will always find the global minimum, but with increasing inefficiency. And finally, the Metropolis simulated annealing technique is found to be flexible enough to accurately locate the minimum energy structure every time provided that the step size and temperatures are “tuned”.
Stay “tuned” for a planned video of the spreadsheet in action.
You can participate! Download the Rosetta@home screen saver, and solve protein folding problems in your sleep. (I have no official connection to the Rosetta at home folks, but their work is great! http://boinc.bakerlab.org/rosetta/)
As my research group began to enter into the world of precision cleaning, we needed to come up to speed on contact angle measurement. In doing so, we met Anselm Kuhn who was a great help and mentor. Together, we produced an inexpensive way to standardize contact angle measurements using spherical ruby lenses. We also evaluated the many freely-available contact angle measurement programs that act as plugins for ImageJ. This work was published in the German metal finishing journal Galvanotechnik.
Williams, D. L.; Kuhn, A. T.; Amann, M. A.; Hausinger, M. B.; Konarik, M. M.; Nesselrode, E. I. Computerized Measurement of Contact Angles, Galvanotechnik, 101, 2502-2512, (2010)
Measurement of contact angles often provides valuable information as to the cleanliness of a surface as well as the ease of wetting of a surface with a coating such as paint or other organic species. Previous methods based on use of a sessile drop were subject to considerable operator error. In order to minimise such errors, the computer-based analysis of drop shape has been developed. The use of such software which is Windows-compatible and easy to learn, is described, giving results where operator-error is minimised. The method has considerable potential for Quality Control in surface finishing.
I have always been bothered by subjective references to color, especially when used in acceptance specifications or quality evaluations. One specification spelled out that the product must be burnished gold. Great. What exactly is burnished gold.
This sent me down the path toward colorimetry, and since this was lacking in my B.S. and Ph.D. chemistry curricula, I decided to include it in the Physical Chemistry course at Sam Houston State University. Here are the abstracts for two articles I wrote for the Journal of Chemical Education. Continue reading “Quantitative Color”
I built this NXT robot and equipped it with a dream-gear wireless game controller from mindsensors.com and a radiation sensor from Vernier.com. This video shows it detecting the radiation coming from an old piece of Fiestaware that used uranium as a pigment. This was prepared for the Austin Science Festival 2010, but I also use it to teach object-oriented programming to my spring physical chemistry class at Sam Houston State University.
Continue reading “Radiation-Sensing NXT Robot”