The translation stage ‘Standa 960-0060’ sells for $399 and offers a full-step resolution of 1.25 micrometer (200 steps/turn, 250 micrometer per turn). With factor 8 or 16 microstepping, the resolution should be sufficient for interferometric experiments with visible light (156 or 78 nm resolution). The stepper can be easily controlled with an Arduino-based USB controller for a cost of less than $40, but a little soldering is required. (more…)

Problem: We need to track environmental variables in our laboratory to identify parameters that affect our measurement results

Solution:  We read out sensors using Arduinos and transfer the sensor data to PCs for storage and analysis. We programmed sensors to analyze temperature, humidity, air pressure, acceleration, and motion. For some sensors (e.g. temperature sensors), the program just involves reading sensor values. For other sensors (e.g., the BMP180 pressure and temperature sensor), a library is required to handle the communication with the sensor. Some programs were written in older Arduino IDEs and they may have to be adapted to work with the new IDE. (more…)

Scientific seminars follow ancient routines. The speaker speaks for his allocated time plus a generous 15% bonus and then the big-shots in the first row ask a few questions. But have you ever noticed that they always ask the same questions? It’s called experience, i.e., they made up their question some 20 years ago. Time for you to get up to speed and participate with your own highly original questions! Don’t have an idea what to ask? Just select one of the generic categories offered  in the PDF file below, and pay attention for some 5 minutes before napping off. Try different questions until you find the one that suits you best! Before you even recognize you will sit in the first row, being a proud member of the establishment!

Writing scientific publications seems to be a science on its own for most of young researchers, but there is no magic behind scientific writing! By following simple rules, everybody can improve his writing skills. I summarized these rules in a cheat sheet for scientific writing.

Of course, you should not expect a miracle. Your principal investigator will always find something to complain about. 😉

If you want to read further on The Science of Scientific Writing, please refer to the article.

Ab initio packages for starters

	PCGamess: Ab initio code for your Windows PC
	MacMolplt: Nice visualization of Gamess output
	Arguslab: Visualize or draw molecules, optimize with molecular dynamics, useful to generate starting geometries
	Mopac: Molecular dynamics and semiempirical methods

Suggested sequence for simple structure calculations:

(1) Draw your molecule in CHEMSKETCH and push the ‘optimize 3D’ button, save it in .mol format

(2) I used OPENBABEL to convert the .mol coordinates to Gamess input format.

(3) Perform a PM3 calculation in Gamess Firefly to get a better structure (fast calculation). A sample input file is here: Toluene_PM3_geometry.

(4) Use the PM3 structure result to start a DFT (B3LYP) calculation with the Gaussian 6-31 basis set (fraction of a minute calculation). A sample input file is here: Toluene_B3LYP-6-31G_geometry.

(5) Use the DFT-6-31 structure result to start a DFT B3LYP calculation with a larger basis set (e.g.,Dunnings augmented correlation-consistent valence-triple-zeta basis set. This basis is about as good as it gets, so this will be the final structure.) A sample input file is here: Toluene_B3LYP-accpVTZ_geometry.