Yes, yes, I know. After all, I do work for the company. Why WOULDN'T I use the program?! The development of nanoENGINEER-1 is going tremendously well. Now on the verge of another alpha release, I decided, in the interest of seeing what kind of imagery functionality the package might benefit from, to see if I could make the old Nanotech Gallery happen with the new software.
I could not be happier with the results.
The problems to date are all with Povray. That is, my amateur understanding of it. As an order of alignment, I was doing all of my graphic work with VMD, which is still the method of choice for biomolecular images (mostly because I'm still using NAMD/Charmm for my occasional forays into drug development). It's a tall order to replicate the quality of graphics VMD is capable of, but it's clear (to me, anyway) that nE-1 is more than up to the challenge.
Welcoming 2006 with a bang. Or the molecular foundations for a bang, anyway. In the Journal of Physical Chemistry A (J. Phys. Chem. A 2006, 110, 1951). The experimental results were provided by TeraView, Ltd., solid-state calculations with DMol3 from Accelrys.
D. G. Allis, D. A. Prokhorova, and T. M. Korter
Abstract: The experimental solid-state terahertz (THz) spectrum (3-120 cm-1) of the beta-crystal form of the high explosive octahydro – 1,3,5,7 – tetranitro – 1,3,5,7 – tetrazocine (HMX) has been analyzed using solid-state density functional theory calculations. Various density functionals (both generalized gradient approximation and local density approximation) are compared in terms of their abilities to reproduce the experimentally observed solid-state structure and low-frequency vibrational motions. Good-to-excellent agreement between solid-state theory and experiment can be achieved in the THz region where isolated-molecule calculations fail to reproduce the observed spectral features, demonstrating a clear limitation of using isolated-molecule calculations for the assignment of THz frequency motions in molecular solids. The deficiency of isolated-molecule calculations is traced to modification of the molecular structure in the solid state through crystal packing effects and the formation of weak C-H…O hydrogen bonds.
West coast architect Mark Burginger (www.burginger.com) is a brother-in-spatial-learning, having peaked my curiosity almost a year ago with a great design for a unique building block (dare I say "toy?"). The design clicked very quickly once I saw what he was capable of building with it. I suspect formal images and designs will be made available soon on the new website for what are now known as Qubits (the artist formerly known as building block)! I'll let him do the formal introduction, though. I expect to have some of my own designs up once the Qubits hit the market. I'm drawn to anything related to building blocks because one of the many possible pathways in advanced nanoscale engineering or intermediate molecular manufacturing is found in the design and manipulation of simple rigid subunits (which supramolecular chemistry and certain branches of materials science are currently addressing). Towards that end, anything anyone can do to improve other's understanding of spatial relationships is excellent in my book. Molecular models in a student's hands do far more to explain a concept like steric interactions than any diagram could.
One short year later, Mark's won some significant awards and accolades (one notable award being from the Elwood & Stephanie Norris Foundation. In case you missed it, Woody had a pretty good run last year as well). Better still, he managed to wrap the whole Burginger clan (that's Lisa, Garrett, Lyndsay, Hayley) into Team Qubits ("Or else!" he says…). I, of course, wish them all the best. They've got my vote. With luck, they'll soon have my money, too. And don't get me started on that "Geometric Construction Toy for Children" thing.