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.
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. ♡
About 2 years ago I needed to make a 3D model of the human heart for my research project.
Then about a month ago I decided to try and 3D print it. The models are SUPER small ( 0.454w x 0.83d x 0.507h (in) ). The following two objects are test prints of the model in strong flexible white plastic (left) and metallic plastic (right).
The models were printed via Shapeways, and the plan was to make necklaces for Valentines Day, but I think I will make miniature wall plaques instead. I will redo the model to create a point to hang the hearts from for the necklaces, and make sure the walls are thicker. I don’t want to mess these precious little hearts up!
Feel free to visit the model’s site here: http://shpws.me/A9oF . While I don’t think others can print the model, because some of the walls are thin, everything seemed to turn out great! Some of the details (vessels) printed a little messy since they are thinner than spec. But I like it, it gives the heart a more organic feel. ❤
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
This semester I am enrolled in the EVL’s game class.
I am a part of a team of 5 creators ( developers and an artist <– that’s me! ), split between UIC and LSU. The concept that we all agreed upon is that of a microbe infecting its host. In reality the game would include multiple levels, but for the sake of the class we will have one level.
The level we are creating is ideally the ‘second to last level’. Here the player attempts to replicate and mutate and grow a colony with select-able attributes which prosper in ‘genetics’ and size. The grid below represents the level. The blood brain barrier is at the top of the map and the green object represent lymph nodes. The lymph nodes are where enemies spawn from. In order to take over the layer the bacteria must take over and destroy the nodes while also collecting nutrients and out competing the immunity.
Capillary Level with Blood Brain Barrier
The diagram above displays how the player may interact with the game and some of the mechanisms it would use to take over the environment.
Below you can see some of the development in process:
Development in Process 1
Development in Process 2
Development in Process 3
I am enjoying creating concept art for the game and trying to think of how to enhance the project. However, I was chosen as the team leader, and I find it difficult to come up with and modify how the game progresses in such a short time span. 8 weeks is not much time to develop a game! But I am definitely please with what we have created thus far.
The website for the game is still under development but can be found here game.encephalostudios.com
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
Documenting your work is just as important as creating work. Lately I find myself working more to refine pieces and figuring out how to display it, in order to share what I have created. So to show for this I have two new videos!
The above is my Blood Components Interactive. With the help of JD Pirtle and others in the UIC – EVL lab, I now have some amazing footage of this application! This interactive was built on OmegaDesk with the help of Victor Mateevitsi, Alessandro Febretti & . The environment I developed for included a 3D viewing screen, a 2D touch screen and Kinect for gestural interaction. My personal objective was to explore designing an application which involved different types of interaction I wanted to think about how you would display 3D assets in this environment and also how to share textual information in the same context. I choose blood components because I like working with cellular and molecular structures. I see them as abstract characters, and while it is a serious subject, you can have a lot of fun with them! I also enjoyed creating the flow of the blood stream. While the irregular movement of the objects can make it difficult at first, I imagine kids would enjoy the challenge of going after the different floating cells. Ideally I see this interactive going in a science or health museum which showcases immunity.
Next I would like to share the video I made using mMaya’s beta-factor to animate the movement of HIV-RT CPK molecular representation. The main star of the animation is HIV’s Reverse Transcriptase (HIV-RT). This little devil travels with HIV’s viral RNA, turning it into DNA which is then integrated into the host cell by HIV Integrase.
This semester I am finishing up research, creating a game in Unity with teammates, redoing my website, and creating an animation in Maya. I hope you will enjoy what is to come!
For a short time you can also visit game.encephalostudios.com for a quick peak at a montage of my work.
Image take you to video of rotating heart, which also shows underlying anatomy
I am still working on finessing the bump map and specular shaders, but I thought I would show some progress
Ready for an update?!
The big challenge lately, for me, has been trying to get these red blood cells to move the way I want in the omegaDesk interactive. I am attempting to make them flow as they would through the bloodstream. Most animations, that do not directly include the heart, tend to show a stream of blood. However, I want my interactive to allude to a pulsing blood stream. First I coded the red blood cells to uniformly and randomly populate across the screen. Then I was able to make them move from left to right, while rotating along individual axis. But now I rejoice as they move across the screen in a more pulse like fashion!
Click to view video
I tested what I was building, using a Processing sketch. There are still some qualities I would like to edit, but I need to keep brushing up on my trig (for all the kids that complain in math class — you need to know the math, to make cool stuff like this happen 😉 ). Here are three screen shots from my processing sketch, showing some movement over time:
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!
I took some time to practice modeling with Molecularmovies.org ‘s Mouse Embryo tutorial (http://molecularmovies.com/pages/bysoftware/ , it is the fourth tutorial under the ‘Maya’ section ).
This tutorial was very helpful, and gave me a better understanding of subsurface modeling. I would say the trickiest part was modeling the toes by extruding along a mirrored axis.