Cavity-Enhanced Direct Frequency Comb Spectroscopy

I worked close with Florian Adler from the Jun Ye Group. Florian requested a schematic of their experiment setup to help explain the process how the Jun Ye group performs tomography on a supersonic expansion. Florian explained he need the visual for Annual Review of Analytical Chemistry which will be officially printing their article "Cavity-Enhanced Direct Frequency Comb Spectroscopy: Technology and Applications" (early online review release available now) on June 15, 2010 as part of 2010 Vol 3.

I worked on this visual over the summer 2009. Florian explained to me what he wanted for the visual and he brought me physical pieces of hardware from his experimental apparatus that I could use to model from. I started with an old-fashion sketch up the scene that Florian and I discussed. After that I decided this was going to be an extensive Maya project since I could use previous models I already built and texture/rendering scripts that I made for other projects. I essentially modeled the whole scene from my sketch layout and used the physical pieces Florian gave me. I used Illustrator and Photoshop to incorporate the labels and composite the overall layout. I think it came out pretty well and everybody seemed pretty happy with the end results.

If you are interested in learning more about research that Jun Ye Group and other JILA groups a doing in this area, I would recommend you checking out the JILA Research Section; Molecular Fingerprinting and Control.

  • Clients: Jun Ye and Florian Adler

  • Related Links: Annual Review of Analytical Chemistry Article (early online review release)- Cavity-Enhanced Direct Frequency Comb Spectroscopy: Technology and Applications, JILA Research Section; Molecular Fingerprinting and Control
  • 4/4/10

    Visuals for "Life from an RNA World: The Ancestor Within"

    Michael Yarus (aka Mike) came to me about helping him create all the insert visuals for his new book "Life from an RNA World: The Ancestor Within". The book is published by Harvard University Press and is now available on their website and on Amazon. Harvard University Press produced the cover visual (Ill find out who did that image once I get a copy of the book). The visual inserts that I rendered are below and I provided the B&W and colored versions together. The inserts for the book were printed in B&W.

    Production notes:
    After several meetings with Mike discussing the data and concepts for the visuals that to be included in the book as inserts, I had to do a bit of research finding the data and which visual scientific software I was going to use in my production workflow. I used PDB data file "2gis.pdb" for the model data which can be downloaded from the Protein Data Bank website. I was familiar with VMD (Visual Molecular Dynamics) software in past projects at JILA. I typically use VMD in coordination with Maya where I would use VMD to produce the models and then use Maya for its rendering environment. I like VMD, but I found its interface and functions to be difficult to use (it is an older piece of software). I heard about PyMol which is an open source molecular visualization system. I thought it might be a good software to use for this particular project because it has pretty sweet openGL rendering environment that I could use on Mac and PC computers. PyMol had better support and controls that I could use to create different visual representations of the data! I also discovered that it could render out some beautiful renderings without necessary having to port data model to Maya which help save me a lot of time in my work-flow (when compared to my work-flow with VMD and Maya). I still wanted to export the model data from PyMol and incorporate Maya, and PyMol made this much easier than VMD. I essentially export model data in PyMol by exporting it as VRML format (.wrl files) which I could then open in Maya. The hardest part about this project was learning how to use PyMol in a few days. I used Illustrator and Photoshop for layout and vector line work.

    After completing the inserts and preparing them for print, there was some question about making a visual for the cover of the book. The editors at Harvard University Press had some plans already about creating the cover for the book and they did not really tell me about what they wanted to do for the cover. I am not sure who created the cover image or how the visual was created. I think it is an artist's conception of RNA. (ill find out which studio rendered that image eventually and update this posting) Regardless I wanted to attempt making a visual for the cover based on the data that was used for the inserts. I thought the possibility of using the data and visual that was already used for the inserts would help tie the book design together. The image below is my attempt. It is a multiple rendering of 2gis.pdb data file where you can see stick figure representation combined with the space filling representation. The rendering below was not published with the book, so it is for sale to anybody who wants to use it as a cover or visual for something. Just contact me. I still like this image and it has my art/design style. It is my interpretation of book title "Life from an RNA World: The Ancestor Within" as rendered from data. I think the editors at Harvard University Press probably thought the visual was too scientific or technically complex to be used as a cover visual. They wanted a more main stream visual that would probably sell more books. I thought cover image they used was pretty eye catching and will probably help promote their book sales.This was a fun project and I wanted to thank Mike Yarus for letting me work with him on the visuals. I also want to give special thanks to Julie Fiore from JILA for her help with giving me a quick crash course with PyMol!

  • Clients: Dr. Michael Yarus

  • Related Links: Buy the book at Amazon OR buy it from Harvard University Press
  • 4/1/10

    Journal of Physical Chemistry A - front cover

    My work is on the cover of "Journal of Physical Chemistry A" (April 1, 2010 Vol 114, Iss 12 Pgs 4017-4470) ! The featured article is "Vibrational Autodetachment−Intramolecular Vibrational Relaxation Translated into Electronic Motion" which starts on pg 4017–4030. I worked closely with JILA Fellow Mathias Weber with the data for the cover image. This is my first offical Journal of Physical Chemistry A cover.

    Cover Description: "Vibrational excitation of CH stretches in nitromethane anions leads to vibrational autodetachment. The photoelectron spectra of autodetachment processes encode the underlying dynamics"

    Mathias came to me August to talk to me about his research and potential cover for JPC-A. I wasn't familar with his current research, so I read his research paper to poured over his scientific poster that his group put together. Mathias explained his research findings and showed me his MOLDEN simulations. Once I understood his research and data visuals that I had access to, I had to figure out how visualize his research on JPC-A cover which essentially a perfect square area in the middle. Mathias and I chose visualize the research in 3 part story panel. This led me to format the layout in the square with 2 vertical columns (column 1 shows the molecule structure and column 2 show details enacted on the molecule structure) and sequence the story with 3 horizontal rows. Row 1 shows the molecule getting hit with hv(IR) laser that causes vibrational excitation. Row 2 details the vibrational excitation and the specific areas of the molecule that vibrate. Row 3 details the end result of vibrational autodetachment and how it compares to direct detachment (the 2D spectroscopy data). I was pretty happy with this design layout and I think it describes Mathias group's research pretty clearly and effectively.

    Production Notes:
    I started this project opening the data in a program called MOLDEN. MOLDEN allowed me to view the simulations/animations that Mathias had collected. Unfortunately MOLDEN's rendering environment was a bit dated and the quality I desired was going to be difficult with MOLDEN. So I switched to gOpenMole for modeling and rendering the data. I performed multilple layer renderings with gOpenMole of the molecule structure to allow me the most visual control. I then used Illustrator and Indesign for the layout. Mathis introduced me to a new piece of software called Image-J which has some really interesting functions (like the Interactive 3D surface plot). I am hoping to incorporate this imaging tool for various future projects. I am probably going to play around with this tool for some various creative experimental applications.

  • Clients: Mathias Weber

  • Related Links: The Journal of Physical Chemistry A - (April 1, 2010 Vol 114, Iss 12 Pgs 4017-4470), JILA Research Highlight article