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Running Chemistry Simulations on the TNTECH HPC Cluster
The two most commonly used HPC applications in chemistry research on our campus are Gaussian ’09 (for ab initio and semi-empirical quantum mechanics), and NAMD (for classical molecular dynamics). To manage the queue of different computational jobs on the cluster, … Continue reading
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Tutorial: Windows vs. UNIX/Linux File Formatting Tips
For the most part, files generated in Windows will be compatible and readable on a UNIX/Linux system. One of the first key things for users to understand is that UNIX filenames are case-sensitive, while Windows filenames are not. So there … Continue reading
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Tutorial: Printing on the Poster Printer in LSC-2335
The HP DesignJet T530 is a high quality, large format printer capable of printing up to 36″ wide for scientific posters. This printer is available to faculty and student researchers in the Department of Chemistry. The printer is located at … Continue reading
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Molecular Modeling Laboratory Now Open in LSC
The molecular modeling laboratory is now open in the new Laboratory Science Commons, room 2335. This laboratory is a shared research resource with eight Linux workstations and a variety of molecular modeling software such as MOE 2020, NAMD, VMD, Gaussian … Continue reading
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Chemistry Demonstration: Shaving Cream Swirls
Introduction The experiment demonstrates the interactions between hydrophobic and hydrophilic substances. Hydrophobic substances repel water – the name comes from the Greek word, “Hydros”, for water, and, “phobos”, for fear. Hydrophilic substances (the Greek stem, “philic”, means “love”) attract, or … Continue reading
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Chemistry Demonstration: PVA Slime
Introduction Multi-colored slime can be created using a solution of poly-vinyl alcohol (PVA) and borax. This experiment demonstrates the ability of borax to form chemical cross-links between molecules of the PVA polymer. The chemical structures below show a molecule of … Continue reading
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Chemistry Demonstration: Molecular Modeling with Candy
Introduction This is a fun demonstration that teaches students how to build simple molecular models using colored candies. It is relatively simple to prepare and set up, and easy to maintain. The basic principles of building small molecular models of … Continue reading
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Chemistry Demonstration: Molecular Modeling with Avogadro
Introduction This is a simple and fun, hands-on activity that demonstrates the basic concepts of computer-based molecular modeling. Using molecular mechanics, small molecules may be modeled by treating the atoms as balls and the bonds connected them as springs. We … Continue reading
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Chemistry Demonstration: Marker Butterflies
Introduction Some artists use the way paint moves on a surface to produce interesting shapes and designs. Many artists paint on a canvas, a type of fabric that is very absorbant. Before painting on canvas, most artists treat the surface … Continue reading
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Chemistry Demonstration: Iodine Clock Reaction
Introduction The iodine clock reaction is a classical chemical clock demonstration that displays chemical kinetics in action. It was first discovered by Hans Heinrich Landolt in 1886, so many texts may refer to it as the Landolt Reaction. In this … Continue reading
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