Artist Challenge – Day 3

For day 3 I wanted to go back and look at some of my scientific 3D work.  Sometimes the stuff you didn’t think so much about in the moment, looks better when you go back to it.

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HIV Reverse Transcriptase with RNA/DNA
pdb model 2hmi

 

I was nominated by the talented Briana Hertzog to post 3 images a day for 5 days.

Today I nominate my VCU  and UIC partner in crime Jennifer Rogers !! I also nominate another BVIS alumi who has magical work and was amazing support for our two years in grad school, Natalie Doolittle. ♡

Light in the modo tunnel

My animation is seemingly becoming shorter, and I almost gave up on modo but it turns out I was just being an impatient user.

I am liking the feel… even without any materials.. but I think I will play around with the shaders. 

The main molecule, reverse transcriptase, is a low-poly version of PDB’s reverse transcriptase 2hmi.

Going into the molecule from the left of the image is single stranded RNA created from nucelotide PDB files ( obtained through mMaya tutorial : DNA: Variations on a theme) . I created a model for A, T, C, and G nucleotides. Then I randomly instanced one of the four models and using the maya pathAnimate function, the nucleotide was assigned to animate on a curve. I did the same with the DNA strand, however I created a model for each pair which would exists and randomly instanced the pair. I didn’t get to use particles like I wanted… to create a ‘blob’ effect however I think it is turning out very nice.

As soon as vimeo catches up with me you can see part of the animation here:

WIP Reverse Transcriptase

Reverse Transcriptase

I like small things. I like the things that affect us and we can’t see. It amazes me that viruses, bacteria, living and non-living entities which we can barely see can coexist with us, or really ruin our day.

The CGSociety is sponsoring a challenge put on by Autopack, the autoPack Visualization Challenge.
I do plan on submitting an image to the challenge, but I mainly used this as inspiration for my animation this semester. Originally I wanted to depict the entire life cycle of HIV. So I started storyboarding:

After I wrote and drew the steps out I realized this was a lot of information to cover in a 30-60 second animation.  I am still learning animation techniques and to learn all of the techniques in three months would have been pretty ambitious ( especially with project research in the background).  So It was agreed that I should focus on a part of the viral life cycle.

 

At this point I started thinking about HIV, and pondered “what really makes HIV so dangerous?” The answer is in the proteins HIV caries with it. One of these proteins is reverse transcriptase (RT). HIV uses RNA to carry genetic information. In order to infect its host HIV needs proteins like RT to make DNA out of the RNA. The new DNA is later integrated into the host DNA by Integrase (a character for separate HIV tale).

My main character, HIV Reverse Transcriptase, isn’t perfect. A lot of the time it screws up. One may wonder how this messy virus lives so long and infects so many. In fact, the constant mistakes made by RT works to HIV’s advantage. This ever so slightly will modify the envelope proteins, making them unrecognizable to the body’s immune system.

 I need to storyboard again and figure out exactly what will happen throughout the animation. But at least for now, I have my star.

HIV Reverse Transcriptase with RNA/DNA
pdb model 2hmi

The Omega Desk

OmegaDesk Displaying a Neutrophil

I am stoked to tell you about my independent study. This semester I signed up with Luc Renambot to learn how to use a multi-modal work station through the creation of an interactive. To build the interactive I am working with Victor Mateevitsi and Alessandro Febretti. This OmegaDesk lives in UIC’s Electronic Visualization Lab (EVL).

For this project I started with the idea of the heart. I thought since I was building an interactive for my research project, I might be able to reuse assets and focus on the interaction. But I don’t have all of the heart yet, and so I moved on to components in the blood. The two forms I am showing today are a neutrophile (above) and an active state platelet (below). I really enjoy building these microscopic components. They look very inhuman, but whenever I make them I feel something happens that gives them personification.

Active Platelet, which I thought turned out looking like a head crab. Victor said it looked like a [full raw] chicken (lolz). Now I can’t unsee it.

Stay tuned! I still have a few more blood components to create and implement!

From Sketch to 3D

Earlier in the semester I introduced my final project for Computer Visualization (Origination). I decided to create an environment to display the bacteria Giardia Intestinalis. This is a pretty intense little critter. I learned about this guy while taking Medical Microbiology at Towson University. It is amazing how many microscopic creatures surround us constantly!

After I came up with my idea, I needed to roughly figure out what I wanted my scene to look like. I created the following sketch as a general composition and color scheme. I didn’t want to make the sketch too detailed, as I was sure bits of the image would changed as I started modeling and texturing in 3DS max.

Once I had the sketch I proceeded to create the scene. One of the goals of this assignment was to demonstrate an understanding of render passes. Render passes, generated in a 3d modeling program when you render your scene, allow output of different channels. This allows for post-processing, or editing, in Photoshop. One of the benefits of this technique is ease of post render modifications (i.e. – its a big time saver). My gallery provides most of the passes I rendered out such as alpha, lighting, specular, ambient, diffuse and zdepth .

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Then after hours of modeling, texturing, lighting, rendering AND Photoshop editing I was able to create this master piece:

As a tip to compositing newbies, don’t hesitate to generate a channel using matte. I didn’t do this when I rendered my ‘main Giardia’ render pass, so the environment in this render pass had all parts rendered, including parts unseen in the beauty pass. I was able to paint this out in the alpha channels, but had the shape been more complex I would have re-rendered with a matte layer.  Another tip, try placing your zDepth as an alpha channel in Photoshop. Then blur the image using lens blur filter ( once in the filter options, you have to select the channel from a drop down menu). This magical trick keeps from having to use depth of field in the camera settings and saves time rendering.  I also really liked working with the lighting channel. I can’t really explain how, but it does nice things.

As always there are edits I would like to make, but like any good artwork I learned a lot during this process. The overall color scheme changed however I am okay with that. The image needed to look darker and feel more unpleasant. In this sense the lighting worked out, and overall I think it came out better then I originally sketched. I hope you enjoy!

UPDATE:

I made some minor modifications

Working at a Molecular Level

The molecular world is a fascinating place. What captivates me is the visuals we accept as a part of the molecular environment tend to be theoretical. This environment is outside of a human’s visual capacity, therefore in order to better understand the form of the chemical compounds we come up with visual mechanisms to understand their structures (of course we use math and very expensive equipment to verify our theories).  After establishing a foundation in chemistry, human understanding of chemical properties led to the capability of visualizing complex chemical structures. A few of the visual mechanisms developed are backbone, ribbon, ball & stick, space-filled and surface models. Through apprehension of structural form, a chemical compound’s functional mechanisms can be better understood.

© 2008 Nick Woolridge

This passed Wednesday our class learned how to extract and manipulate files from the Protein Data Bank and use them to visualize chemical models. We explored different methods and programs such as Chimera and mMaya. Another program we did not go over, but worth exploring, is BioBlender.

The model I have decided to play with is the human growth hormone (GH). This hormone is manufactured in the anterior pituitary gland, then released into the blood stream where it then travels to the liver. In the liver GH stimulates the production of  insulin-like growth factor 1 (IGF-1). IGF-1 then leads to the growth of long bones as well as facilitate growth of muscle cells.

After extracting the data from the Protein Data Bank website, I slightly modified the surface model in Chimera. I played around with the colors of the different chemicals, and tried to understand how each molecule was broken down. Sometimes the protein can be divided into different chains.

Link to WebGL - Human GH Surface Model

Link to WebGL - Human GH Ribbon Model

My next step is to use take the extracted PDB file and display the molecule in a 3D environment. Stay tuned for sweet visualizations ahead!