State of the Union

I suppose one of the main reasons for vaporware is the unintended situations we all find ourselves in the coarse course of daily events. I wanted to update this blog weekly and have had demands on my time I didn't expect - the first being medical. Definitely not life threatening, it continues to be life coloring. It has hampered my progress in my pursuit of knowledge, my research and of course my software development. I had hope to address a cross-linker software by now. That is my objective this summer in addition to running laboratory experiments in support of my molecular dynamics modeling.

I just finished a two quarter class in Electrodynamics! What a rush! I have to admit many Materials Scientists walk around with one eye shut. One eye on mass and the other shut to charge. If anything my small simulations of DGEBA/IPD showed me the power of partial charges on matter and why Van der Waals forces are necessary for good simulations. I now have a much better understanding of polarization of materials in an electric field. I think it cleared up some questions I had about polarization in chemistry too.  I suggest to all Materials Science majors to take Electrodynamics. Imagine the extra "dog pile" one could add to a molecular dynamics simulator - not "that" kind of dog pile, but the one where all the dogs jump on you because you have a hotdog in your hand. As the geometry of your molecule changes with time the partial charges could be recalculated. The electric field in the material would then change due to the redistribution of charge. The moving charges give rise to magnetic fields which can induce electric fields and vs versa! Griffiths' Electrodynamics text points out the wildly fluctuating fields inside matter at the microscopic level. How these fields affect diffusion, alignment of molecules, whether the fields help or hurt molecules to clump could affect reactions of water with polymers, and how charged molecules behave inside matter. Also, when materials are in a significant electro-magnetic field perhaps fun things happen to the molecules that are diffusing in the materials.

 This summer will provide freedom to work on the following:

• Health - new medication, continue my exercise program
• Research - experiments into a variety of ways to damage siloxane materials and how to model such damage so changes in physical properties can be seen in MD simulations
• Software - build a cross-linker
• Research - how does electrodynamics fit into molecular dynamics simulations
• Research - which force field or potential will work best for simulating siloxane materials such as PDMS

I will present weekly progress on the cross-linker and the technical details. Also, extending existing software into millions of atoms should prove interesting in terms of time efficient algorithms. I strongly believe that MDS could be a great multi-disciplinary teaching project across many fields of study. I look forward to discussing enhancements with all who are interested in enhancing this open source project.