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

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

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

Physics Today - front cover

My work is on the cover of "Physics Today" (March 2010 Vol 63, Iss 3, pp.8-80)! The featured article is " Universal insights from few-body land" which starts on pg 40 (check it out!). I worked closely with JILA Fellow Chris Greene with the data for the cover image and I used Seth Rittenhouse's POV-Ray data files. This is my first Physics Today cover.

cover caption: "The four cobralike forms here represent one view of a wavefunction for a collision between two weakly bound dimers composed of fermionic atoms. The calculations underlying the figure are at the forefront of theoretical work that explores universal properties in few-body systems—that is, features that are independent of the details of particle interactions. Chris Greene’s article, beginning on page 40, surveys universal physics in few-body systems, from a startling prediction offered in 1970 to recent theoretical and experimental advances."

Chris Greene came to me in October to talk to me about helping him make the cover image for submission to Physics Today. We discussed several ideas and processes, but there were some factors that I had work around. The main one was that I was already working several other projects for some other Fellows, the deadline for PT submission was soon, and Chris's project involved a lot of 3D work (which are never quick projects to do). Even though these factors were daunting at the beginning of the project, I was super excited about it. I never work with his 3D data before and I thought Chris's and Seth's original models were interesting representations of their research. The idea was just weird enough that I had to do it. It has Cobras!!? naturally im into it and I couldn't pass up this opportunity. (shout out to my GDC crew!!!)

The project started with Chris giving me the POV-Ray files and showing me what he was doing with them. You can check out the older renderings of the cobras here. The POV-Ray model data files were Seth Rittenhouse's. Seth was graduate student at JILA, but I didn't realize he finished his thesis and was now at Cambridge, MA when I emailed him about doing some data re-renderings. He mentioned that files I was working with took 1.5 weeks to process (pure continuous processing on a pretty fast computer cluster at JILA (i think)). So doing some re-processing of the given models wasn't going to work with the time frame that I was working in.

Production Notes:
I work with a lot different 3D environments and softwares, but I typically avoided using POV-Ray. POV-Ray (Persistence of Vision Raytracer) is a great open source command line driven render, but I would rather work in more robust 3D package like Maya that have some great standard renders and mentalRay (i typically like to render with MentalRay if i can). Don't get me wrong, you can definitely render some beautiful things with POV-Ray, but it takes a veteran 3D coder (the recent versions of POV-Ray have been really impressive since the last time I checked out POV-Ray in 2004.) Also POV-Ray is primarily a render and lacks other functions that a lot of other 3D software come standard with (part of the beauty and downfalls of POV-Ray). The work flow of POV-Ray immediate brought back memories of me coding/modeling with OpenGL environment back in 2004. At the beginning I was working with POV-Ray's script files and I was getting some good results (I was running it on both the PC and Mac environments), but the work flow was really tedious and not efficient use of time to master POV-Ray's rendering commands and work flow process. I needed a better work flow that could use POV-Ray files and that could make some great renderings with a lot of easy to change controls. So I decided I need to incorporate Maya in this work flow which meant I needed to export/convert the model data. So I spent a lot of time reading forums about other people trying this and it appears that its not the easiest thing to do (or that common with the Maya and POV-ray communities). There weren't a lot of scripts or programs that would do this well (and cheap as in free). I was checking this software called Moray (which is kinda of GUI interface for POV-Ray), but it didn't really have what I needed. Then I found this program called 3DWin. At first 3DWin didn't look that promising or if it did do it, it was going to make the model come out looking like garbage. But I was surprised and super excited that it converted the model data pretty well (i still had do some operations to it). Now I was able to work in Maya's 3D environment. Unfortunately it took a while to convert the files and a lot of the rendering techniques and processes I was planning on working on for this project was going to take too long. So the final rendering that PT selected is hybrid of mutliple renderings using POV-Ray and Maya. I am glad I was able to work pretty closely with POV-Ray and actually incorporate it my work flow process of making a pretty good rendering.

I want to thank for Seth and Chris for the original files and for letting me work on this project. The project deadlines originally took place in October, and after a few months of not hearing back from PT, I was little worried we wouldn't get our submission selected for the cover. Physics Today has a pretty wide circulation and some pretty amazing past cover imagery. Physics Today's covers are pretty competitive to get and I am really happy that Chris and Seth's research was selected as the cover feature.

Clients: Chris Greene and Seth Rittenhouse

Related Links: Physics Today - March 2010, JILA Research Highlight article

Carl Lineberger's cover - Journal of Physical Chemistry A

Lineberger Research Laboratories in JILA Basement, 2001. Watercolor by visiting fellow Zdeněk Herman.

The Journal of Physical Chemistry A did a special cover and preface issue where they did a tribute W. Carl Lineberger (January 28, 2010,Vol 114, Iss , Pg 1225-1602). Check it out!

Carl asked me about scanning JILA visiting Fellow Zdeněk Herman's watercolor painting, and preparing it for print for JPC-A. He told me about the idea of using Herman's watercolor painting, and I thought it was a fantastic idea for cover layout. Scanning it was bit difficult due to the size of the piece but I was pretty careful when I was dismantling the frame and handling the art. I made sure the colors were mastered correctly and maintain high fidelity scans.

If you ever been to JILA before, you may have noticed visiting Fellow Zdeněk Herman's art work hanging in the JILA tower and in various Fellow's offices. It was one of the first things I notice when I first went to the top floor of the JILA tower. I expressed my admiration for the Herman's illustrations and Carl loaned me his personal reprint of Zdeněk Herman's sketch book that I could check out. It was pretty funny seeing the history of JILA through Herman's sketch book. When I get extra time, I am hoping to scan it to make digital version of Herman's sketch book and make it avaliable to the staff and faculty at JILA (and maybe for JILA's website).

People: Carl Lineberger

Related Links: The Journal of Physical Chemistry A : Tribute to W. Carl Lineberger

Ana Maria Rey & Jun Ye - NIST Annual Report

This was a photo shoot with Ana Maria Rey and Jun Ye for the NIST Annual Report (2008-2009) which is slated to be published and available in mid 2010.

Client: Jun Ye Group and Ana Maria Rey

Related Links: NIST Annual Report (2008-2009) [pdf]

Measuring red blood cells elasticity

This was a project where I was 3D modeling (using Maya) a microfluidics device that was being used to measure the elasticity of red blood cells. This was for JILA Fellow Ralph Jimenez's group. I did version of this a few years ago (see posting titled "Mircofluidics Device"), so it was interesting to follow the updates/changes to this particular experimental apparatus and the applications it is being used for.

Client: Ralph Jimenez

Related Links: JILA Research Highlight article

PNAS: Phase-matched (coherent) addition of the high harmonic X-ray fields

I worked with Fellow Margaret Murnane and Dr. Tenio Popmintchev from the Kepteyn-Murnane Group on this figure for PNAS. The paper was titled "Phase matching of high harmonic generation in the soft and hard X-ray regions of the spectrum". It was published June 2009, but I just recently found the article was finally published.

Caption: "Fig. 1. Extreme nonlinear upconversion of a femtosecond laser light to
shorter wavelengths. Phase-matched (coherent) addition of the high harmonic
X-ray fields emitted by many atoms in the medium is shown."

• Clients: Kapteyn-Murnane Group


• Related Links: PNAS article (30 June 2009, Vol 106, No. 26, pp10516-10521)

Facing Heisenberg at the nanoscale

Nature Nanotechnology version

I worked closely with John Teufel (who now works at NIST) and with JILA Fellow Konrad Lehnert on making this graphic for the JILA Research highlight and for the JILA AMO site, JILA main site, and for JILA Light & Matter Winter 2010 issue. Then project expanded to have the visual for Nature Nanotechnology, and the article is called "Measurement: Facing Heisenburg at the nanoscale" (citation: Nature Nanotechnology 4, 796 - 798 (2009)doi:10.1038/nnano.2009.368). The top image is the Nature Nanotechnology version which was modified to meet the design/style guide for their journal. The second image is the original design that was mainly made for the spread layout of upcoming JILA Light & Matter issue (it looks pretty good in the layout) Check it out Nature Nanotechology article if you want find out more about visual and research. the links are below.

John Teufel use to be in Konrad Lehnert's group at JILA, but he recently graduated and started working at NIST. I worked with him before, so it was nice to have another project working and talking to him about his latest work with Konrad. It started out with emails and phone chats discussing the concepts and visual challenges of "how to explain" the research (Konrad's group always have a good visual challenges for me). John dropped by my JILA office a few times for a few discussions (its nice that NIST is only few blocks down the road from JILA). John made some schematic like figures how the device worked and had some SEM images of the device which was great start. I proposed isometric perspective style illustration which would help the visual with the scale and space a little easier. The device was dense with detail and John and I wanted to emphasis the nanowire area, but not loose sense of the whole device's architecture. I did all the line work in Illustrator using the SSR Method and then used Photoshop for the final touches and layout. Eventually I would like make a flash animation of the device to help explain the vibrations of the nanowire and zoom in and out of the areas of the device to explain how it works.

Client: Konrad Lehnert and John Teufel

Related Links: Nature Nanotechnology (News and Views) article, JILA Research Highlight article

Angewandte Chemie - front cover

My art work is on the cover of "Angewandte Chemie" (2009 International Edition: published online Oct 6, DOI: 10.1002/anie.200905074). I worked closely with Carl Lineberger (at JILA) and Takatoshi Ichino (at University of Texas) in designing the cover image. It is my first cover for this international journal.

Cover and article description:
"Photodetachment of the oxyallyl radical anion leads to formation of the oxyallyl diradical, an elusive transient molecule involved in many organic reactions. As described by W. C. Lineberger et al. in their Communication (DOI: 10.1002/anie.200904417), the photoelectron spectrum reveals that the oxyallyl ground state is singlet and the lowest triplet state is only 55 meV higher in energy. The spectral profile indicates that the planar singlet state is the transition state for ring opening of cyclopropanone, while the C-C-C bending motion is activated upon photodetachment to the triplet state."

I want to especially thank Carl Lineberger and Takatoshi Ichino for entrusting me to work on this project and for working collaboratively with me. This project would not have been as successful nor would it have been completed if the project had not been approached with a team work mentality (working collaboratively is my favorite work style!). I also want to make a special mention about Takatoshi's contribution with helping with GNUplot surface plots and being available during that Saturday and Sunday to trouble shoot the graphics outputs from GNUplot with me.

Read the paper on the Angewandte Chemie journal website! Links below (check back for updated links and sourcing). For everybody else, yes it is rather complicated to explain, but JILA will be doing a research highlight this winter and I recommend reading that to get a general audience version of the research details and visuals (again check back for updated links).

THE SHORT SIDE STORY behind this project:

It was a pretty fun and intense project with a quick turn around of 3-4 days. I was working on several projects at once for several different Fellow groups at JILA. Also I was trying to make major advances on the JILA website overhaul to a CMS design and platform. I was pretty stressed about how I was going to manage all these projects at once and they ALL had really tight deadlines. So I arranged my project queue based on deadline and prioritized importance. Carl's cover project had the most immediate deadline, so I hyperfocused on his project. My project planning and time management skills made it possible to finish this project and stay on top of my other project productions (future posts coming soon!)

Usually when I start a project like this, I work in extreme close communication with the Fellow(s) and all researchers involved all the way through the project until it is finally submitted. The only problem was that Carl was going to be in Europe during the project and Takatoshi was in Austin, Texas. This particular communication setup initially opened up some logistic barriers, but I carefully figured out my game plan, and how we were all going to stay connected and work through this. How you might ask? extensive active Email threads (I think all of us were constantly checking our email accounts every 10 seconds) and cell phone calls (just got my iphone all app'ed up and ready to go). I figured out everybody's time zones and when the best times were to shoot off communications. Fortunately Takatoshi's time zone wasn't as drastic as Carl's. All n All, everything worked out just fine.

Carl was around for a day before heading off to Europe, so I quickly started going over the materials with Carl. We talked directly about how to make a cover design about his rather complex research. The title for the paper is "The Lowest Singlet and Triplet States of the Oxyallyl Diradical" which is not the easiest thing to explain visually. I spent a lot of time reading the research and pouring over the powerpoint slides and visuals. At this point Carl and I were emailing and calling Takatoshi about our discussions. The design changed quite a few times, but we all reached a rough consensus about what should and shouldn't be in the cover.

The game plan was roughly simpified as:

• Model the (3D) molecules from data with GaussView in high resolution
  
• Model the energy surface plots from various math equations with GNUplot (which is Linux based software)
• Take the model pieces and combine them in layout, done in Illustrator
• Finalize the design and master the file for print publication

While this seems simple enough, the process was more complex with the work flow process and communications. I never used GaussView before, so I had to install the software on my machines, quickly read the manual, and crash through some quick tests to make sure I was going to be able to use the software for my workflow. Using GaussView worked out perfectly. So far so good.

Then I had to do the same thing for the GNUplot application which I got running on my Windows and Linux. Jim from the JILA computing group helped me figure out how to get GNUplot running on the Linux box and my PC box (Thanks Jim!). Next Takatoshi wrote some GNUplot commands and equations which I was also playing with (again after crashing around GNUplot manuals). Takatoshi and I were in constant communication, swapping GNUplot commands back and forth between each other. Then BAM; GNUplot started being a difficult baby with me. Everything was going well until we all realized that GNUplot was rendering the surface plots kinda oddly at certain perspectives. While it was rendering mathmatically correct plots, they looked extremely odd from the particular perspective angles that we wanted. While it was rendering certain basic perspectives correctly, it could not handle 3D perspectives where any region of surface and contour potentially overlapped. Essentially, it was rendering the plots with contours and surfaces that had both hidden and viewable surface regions; that was causing some 3D optical allusions. While it was still mathematically correct, it was extremely hard to tell which parts of the surfaces were supposed to be in front, underneath, top, and in the back. GNUplot didn't have a ray-trace function to help it distinguish what was supposed to be viewable and what was supposed to be hidden (more-or-less Takatoshi and I couldn't find a corrective function nor did we have time to try to figure how to code one in about a day). This essentially made rendering images at high resolution RASTER worthless to us. So Takatoshi and I investigated the 3D and Vector formats. Takatoshi was able to pump out some pretty hot pdf vector versions. I was trying to do the same thing, but my PDF plugin library for GNUplot wasn't working! At this point I was about to pull out my hair because if I couldn't get the pdf version to work properly, then the whole project was in jeopardy. It was quickly becoming a "DO or Die" situation with GNUplot for the whole project. The pdf versions were extremely important in order to get visuals in a scientifically correct format (color mappings, vector contours, etc) that I could correct for the optical discrepancies with my other graphic software. Fortunately Takatoshi was able to render the pdf(s) from GNUplot correctly....So Takatoshi and I were working all day Saturday (until late in our nights) trading GNUplot code and pdf exports. Once Takatoshi and I were done with GNUplot exports, next came me spending quite a bit of time running corrections on the GNUplots exports. Even though it took a long time to fix the plots, the results were well worth it and the data still remains correct and true. Once the GNUplots were fixed, I knew the cover layout was going to be awesome and exactly the way I was originally planning it to turn out. I like it when I get my way.

After that it was just getting everything together and having a remote round table discussion by email and phone with Carl, Takatoshi and I. Those weren't held at normal business hours due to extreme locations we were all physically at. We all got excited about final results and after a few minor details were adjusted, we were ready for submission (which was hours away). done.

Full citation: Takatoshi Ichino, Stephanie M. Villano, Adam J. Gianola, Daniel J. Goebbert, Luis Velarde, Andrei Sanov, Stephen J. Blanksby, Xin Zhou, David A. Hrovat, Weston T. Borden, and W. Carl Lineberger, Angewandte Chemie Int. Ed. English 48, 8381 (2009).

Clients: Carl Lineberger and Takatoshi Ichino

Related Links: Angewandte Chemie International Edition, JILA Research Highlight article

Ti:S crystal in an optical frequency comb laser

I was asked to come do a photo shoot in Steve Cundiff's lab. Julie has been updating the content on the main JILA website for Precision Optical Frequency Metrology section, and she thought it would be a good idea to get some photos of Ti:S crystal and optical frequency comb laser setup for the website and other potential future uses. John Willits, who is a graduate student in Cundiff's lab, showed me around the lab and helped me with the photo shoot (basically made sure I didn't break anything or touch the lasers). I originally thought I was going to have to do some laser trace photography, but that method was shot down very quickly after a fair warning from John that some parts of the laser arrangement were actually potentially dangerous. The laser setup was really bright bright GREEN, and I was a little worried about how DLSR would handle with this type of light. You could actually see the laser path for the most part, so I wanted to have long exposures in hopes of getting those laser paths to be visible. There wasn't really a lot of room and I was basically balancing ontop of a ladder with a tripod trying to get a steady shot in a dark room. I was getting frustrated with not being able to move around the setup easily, but in the end I got some pretty awesome shots that I am content with. The photos will be on main JILA website (link below) and will probably be used for various presentations and other things. I just wish it could be used for a journal or magazine cover because I think the colors are really vivid and it would make a pretty good print cover.

Client: Steve Cundiff

Related Links: JILA main website; "Precision Optical Frequency Metrology"

Ralph Jimenez Photo Shoot (MOABC website)

Photo shoot Ralph Jimenez in his lab at JILA. Microintegrated Optics for Advance Bioimaging and Control (aka MOABC) needed a lab shot with Ralph for their website. The photo shoot was scheduled pretty quickly. I did not even have the time to bring my lighting kit, so I just worked with the lighting in lab which. We just turned on some lasers (bright green) and I played with the rest of the lights in the lab.

Client: Ralph Jimenez

Related Links: Microintegrated Optics for Advanced Bioimaging and Control (MOABC) website

Subsurface Circulations within Sun's Active Regions

I worked closely with Brad Hindman from the Juri Toomre Group; he came to me about doing some figures for a paper he was publishing titled "Subsurface Circulations within Active Regions" for The Astrophysical Journal. Brad does a lot with Laboratory for Computational Dynamics (LCD) which supports fundamental research on helioseismology and convection and dynamo theory. The scientists at LCD study the dynamics inside stars with helioseismology and design large-scale computer simulations of convection, turbulence, and dynamo processes within stars. They work on a pretty intense TeraGrid network which is basically clusters of supercomputers tied together across the nation. Its pretty neat stuff!

I just realized that this is my first published astrophysics project. I'm breaking into the astrophysics scene!

The full citation for the paper is:
Subsurface Circulations within Active Regions
Bradley W. Hindman, Deborah A. Haber, and Juri Toomre 2009 ApJ 698 1749-1760 doi: 10.1088/0004-637X/698/2/1749

Clients: Juri Toomre Group and Brad Hindman

Related Links: The Astrophysical Journal

Monodromy

I worked with Fellow Heather Lewandowski on making this graphic for the JILA Research highlight and for the JILA AMO site. Heather's group did a series of experiments with the classical system of a pendulum on a spring which has monodromy. Monodromy is a term that has been applied in mathematics to systems that run around a singularity; however, there havn't been too many lab experiments involving monodromy. Heather's group decided to do several experiments in order to see if the systems tested had monodromy. I never heard of monodromy, but it was interesting learning how they were essentially doing these classical experiments which would help give them more insight into how other systems might also display these behaviors. The classical monodromy confirmed in the pendulum-on-a-spring experiment is analogous to the bending and stretching behavior of a CO₂ molecule.

I used Maya for this project because it was the easiest and quickest way to depict this classical experimental setup of monodromy (pretty easy to model the springs in Maya and I didn't want to draw it in Illustrator/Photoshop). In a three-dimensional spherical pendulum, for example, the singularity would correspond to the "straight up" position. However, pure bouncing motions around this position tend to be unstable. Because this instability is straight upward against gravity, any small deviation from purely vertical results in motion that could loop around the singularity. It is pretty interesting stuff and I recommend that you read the JILA Highlight article and article published in Physical Review Letters by Heather's Group to find more about the experiment and monodromy. Eventually I would like to take my Maya 3d file and really animate it. The motion is interesting in the context of monodromy. I hate "never having enough time" for the animating parts of these projects. There is always an endless list of new projects getting in the way (i need another me!).

They apparently used my JILA camera (Panasonic DVX100A) to record video data that they gathered from the experiments. I remember the camera being loaned out for several months (almost a year) which was fine because I wasn't using the camera for any immediate projects myself. I thought it was pretty cool that they were able to use the features/controls of that camera for their experiment. The DVX100A is a notorious camera (known for its low cost and pretty high quality) used widely in the indie film industry and various other productions. Now the JILA DVX100A has another checked "has been used for" use: a classical physics experiment camera.

Clients: Heather Lewandowski Group

Related Links: JILA Research Highlight article

Feshbach Resonances in Soft X-ray–Induced O2 Dissociation

I worked with Fellows Margaret Murnane and Henry Kapteyn from the Kepteyn-Murnane Group. I was originally creating this graphic to be published in an Science magazine article (Science 322, 1081 (2008)). Science is also making this visual available as a PowerPoint slide for teaching purposes.

The graphic explains the Photoionization. After a X-ray knocks an electron out of an O₂ molecule, it takes more than 300 fs before another electron is ejected and the molecule falls apart. The internal state of the molecule prevents the second electron from being ejected until the O nuclei move at least 30 Å (3 nm) apart. Check out the Science article for the research and the JILA Light & Matter article for a more generalized explaination of the research.

• Clients: Kapteyn-Murnane Group


• Related Links: Science article (Science 322, 1081 (2008)), JILA Research Highlight article

Atomic Force Microscope (AFM)

I worked closely with Fellow Tom Perkins, Gavin King, and Allison Churnside. I was initially rendering an image for the JILA Light & Matter Spring 2009 issue and then after I was done, talk of using the image for everything popped up. I was excited about the possibility of getting the cover of Nano Letters, but the publishers at Nano Letters said they already have all their cover images for the whole year or something along those lines. I found this to be kinda weird and was wondering how they actually run their publication. Do they know exactly what research to publish almost a full year in advance? Regardless Science picked up the image for their Editor's choice which was also pretty neat.

I have worked on Tom Perkin's stuff on past projects, so I was familiar with some of the visual and potential animation objectives. The intial meeting with Gavin and Tom was pretty quick. I decided I wanted to use Maya for this project because I knew I could make a pretty beautiful rendering pretty quickly AND I could make an animation from 3D file when I had the extra time. The shapes were pretty easy to model (and I already had some 2D illustrator line work that I did previously to use for the "revolve" procedure in Maya). I spent most of my time working on textures, lighting, and colors. I was pretty happy with my lighting. I hate texturing in Maya, but I was able to get the results I wanted pretty efficiently. Of course I am running Maya 8.5 which is two versions old now and no longer supported by Autodesk. So Maya crashed a multiple times during this project which caused me an extra 2 days worth of Maya time. I think I am going finally break down get Maya 2009 Unlimited because the problems I am experienceing will never get fixed unless I upgrade (UPGRAYED!). I didn't use Mental Ray render because it was artifacting some weird stuff in there and I didn't have time to debugg that (and I would have to redo all my textures also). Hopefully the newer verion of Maya will support my current hardware configuration and work well with the latest OS that I am running on both the Mac and PC systems. All n All the final results were pretty good and I was happy with it. I am glad Perkins Group liked results as well and that NIST picked up the image for their press release thing. Hopefully I will get around to the animation part of the project after I get back from my trip this April.

Clients: Tom Perkins Group

Related Links: Science (Volume 323, Number 5922, Issue of 27 March 2009), NIST Tech Beat, Bio Optics World,In Sciences, Nano Werk, Shanghi Institute of Ceramics Chinese Academy of Science (SICCAS), Thomas Net, R & D Magazine, News Wise, Materials Research Society (MRS), JILA Research Highlight article

SQUID(s) (superconducting quantum interference devices)

I worked closely with Manuel Castellanos-Beltran on this project. JILA had research highlight article for this research, but I wasn't able to make graphic for this research concept at that time because of tight deadlines. Manuel came back to me a few weeks later and he told me that NSF was interviewing him and Konrad about their research. He was asking me about making a visual that would explain their research to wider audience.

I remember reading the papers and articles for this research, and I thought it would be a pretty hard to visualize some of the underlying concepts as a single image. Konrad and Manuel already had some pretty nice looking SEM images of the SQUID(s), so Manuel mentioned that an artist conception rendering of SQUID(s) might be a good thing for the NSF article. The SEM images of the SQUID(s) are interesting pictures, but they are kinda hard to interpret the actual shape and structure of the SQUID(s) themselves. So I proposed to make isometric illustration of the SQUID(s) which would see the shapes and pieces of the SQUIDs. Isometric illustrations are common for engineering diagrams, architecture, and manual diagrams. The SEM images kinda make the SQUIDs look like one piece when they are actually made up of multiple (very thin) layers and pieces. I did all the line work in Illustrator using the SSR Method and then used Photoshop for the final touches. I kept my colors palette to greens and blues to relate more to the original SEM images.

Read the NSF article to find more about the SQUID(s) research. The NSF article is pretty good with explaining the concepts to a general audience.

Clients: Konrad Lehnert and Manuel Castellanos-Beltran

Related Links: NSF, Research.gov, Nanotechnology Now, JILA Research Highlight article

JILA MONSTRs laser photography

This was a fun photo shoot involving lasers from the JILA MONSTR system. I actually did this photo shoot the day before I left for the Christmas holiday (i think it might have been Christmas eve) which was a perfect time since everybody was gone and nobody was currently running experiments with the MONSTR system. Twas the night before Christmas, And all through the JILA hallways. Not a creature (or grad) was-ah-stirring. Not even a mouse… ha! sorry i had to do it, but it really did feel like that at JILA on that day...really. Nobody was there EXCEPT for Alan Bristow. Alan helped with the photo shoot so it turned out to be a really fun collaboration (plus he had the keys to the labs). AND he brought his sweet lovely precious, expensive DSLR Nikon camera with a decent lens! I only have SRO's lame Canon Rebel XT DSLR which is no where close to Alan's model. The Rebel XT that I use at JILA is "ok" and it works fine, but it is really a cheaper scaled back version of the more professional standard Canon 20D SLR which is what I currently use for my personal projects (with SIGMA lens). After being familiar with the Canon 20D and 30D models (and even the Nikon DSLRs too), lets just say Rebel XT has many short comings when it comes to its color calibrations, light metering system, and its auto focusing matrix (you get what you paid for is the only thing that comes to mind). I inherited the Rebel XT from my predecessor when I first start working at JILA, and I have been putting a new pro DSLR on my JILA Christmas wish list every year but the JILA Santa fails to deliver a sweet new Canon DSLR under the tree. Anyways......Alan had his camera, so I quickly abandoned the Rebel XT in favor of getting to use his camera. Alan and I were pretty excited about the photo shoot because it was problem solving game. It wasn't just a regular photo shoot where you just set up some lights and point-n-shoot. We wanted to turn on the lasers and doing some laser trace photography.

I heard about some of the methods for doing this, but I never had the chance to actually try it out. Even when the lasers are turned on, you can't see them with the naked eye. JILA MONSTR has all sorts of red and green lasers going every which way. Basically we setup the lights the way we wanted and then opened the shutter for a super long exposure. So we would put a white piece of paper attached the end of a thing stick or wire and trace the path with the paper. The only major problem was the tripod which was "janky" and broken, so it was pretty tough keeping it from falling apart. The shoot went well and we eventually got all the types of exposures I wanted to make my final blend of the images together.

Special thanks goes to Alan Bristow for collaborating with me on this photo shoot and for turning on the JILA MONSTR. If you are curious about what the heck is a JILA MONSTR and why its such a beast, then read the Highlight article below. JILA actually has two of these laser systems machined by the JILA machine shope.

Clients: Ralph Jimenez and Steve Cundiff

Related Links: JILA Research Highlight article