Thursday, September 26, 2013

Molecular Dynamics Sonification and Music Hack Day Chicago

I went to Music Hack Day Chicago this weekend ( It was the first time I ever went to a Hackathon but was looking forward to spending 30-40 hours coding out something cool. Of course these hacks were supposed to have something to do with music and I decided upon programming a mechanism to sonify data from Molecular Dynamics simulations.

I recently received a grant from the national supercomputing center for computer time on Stampede at UTexas, currently ranked the sixth fastest super computer in the world ( I have been running some equilibrium molecular dynamics simulations of proteins to understand conformational change pathways and basically figure out how proteins work the way they do. The amount data from these simulations is huge and complex and it is very multi-dimensional because not only are you looking at how each atom in the protein is moving in 3-dimensions but you are also looking at the physical forces that control this.

Normally one uses a variety of analysis software and also watches the simulations to try and observe obvious changes. As you can imagine simultaneously trying to understand any portion of this data is a crazy task visually so I set out to to use more senses. I wanted to sonify the data and play it back while watching the visual part of the simulation. Harnessing our auditory ability to pick out unique sounds.

So I created a layered musical arrangement that allows someone to listen for more subtle conformational changes while watching video of the simulation. This is different then most any other form of data sonification that I have found because it uses easily recognizable musical instruments whereas most data sonification just uses frequency shifted sine waves.

It surprisingly work really well and is really cool to experience. Code for demoing it is available here (

The sounds that one can hear in the video:

The piano key in the beginning represents the radius of gyration of the protein as it becomes higher in pitch the radius of gyration is becoming larger, as it becomes lower the radius of gyration is smaller. The radius of gyration is a measure of movement away from a center of mass, so basically if the protein is expanding or shrinking (

The beeps represent the RMSD of each residue as compared to frame 1 of the simulation. As the RMSD from the starting structure become higher the pitch becomes higher. Each beep is for each residue and they are performed in order. RMSD is basically how far each residue moved from it's initial position in relation to the protein(i.e. minus translation motion) (

To determine where a residue is located listen for secondary structure cues.

The percentage secondary structure as calculated by dssp is the background sounds.
This is an explaination of secondary structure (

A violin is played for the first quarter of the protein and represents the amount of structure in the whole protein, a combination of alpha helix, beta sheet and turn. It becomes higher in pitch as the number goes up and lower as it goes down.
The second quarter of the protein's background sound is Monks making an ohhh noise(according to MIDI tables) it is a representative of the percentage alpha helix. It becomes higher in pitch as the number goes up and lower as it goes down.
For the third quarter of the protein the background sound is a guitar it is a representative of the percentage beta sheet. It becomes higher in pitch as the number goes up and lower as it goes down.
The final quarter is a Sci-Fi noise (called so by MIDI tables), it represents percentage coil. It becomes higher in pitch as the number goes up and lower as it goes down.
So for instance if you hear a group of high pitch beeps during the violin you know they are in the first quarter of the protein.

The protein is HIV protease is a dimer(i.e. composed of two of the same protein). This means the sonification of the first half will be one half and the second half will be the other. Being a dimer doesn't mean that the conformational changes are symmetric either so the two halves can sound different.

Listen to the sounds a see if you can identify where in the protein the conformational changes are occurring. 

What one can tell is that the high pitched beeps are in the beginning and end also the middle of each half.The beginning and end of proteins, the termini are often very flexible and so change alot but are often not related to protein function. However, the high beeps in the middle(residues 40-60) are the flaps of the HIV protease that open up to allow substrate binding and cleavage and allow the virus to be active. It is pretty cool that this works!

Saturday, September 7, 2013

Scientific American

So this week has been crazy. Two articles were published online that were widely read and accessed based on the Chromochord. One in Scientific American by Nona Griffin that Karen Ingram did some cool artwork for!

The other was by the awesome Katie Drummond at The Verge . She was super cool and so much fun to do the article with. 

I will be honest. All the the attention was fun. It was cool to interact with new people and I even was able to interact with Zoe Keating ( my favorite musician! She wants to do a duet with me! hah. If only I could actually play good music on The Chromochord.

I think my main goal from the press was to try and leverage it in some way to acquire more press and to make connections that I can use now or in the future. Partly to try and fund this Indiegogo Campaign I have been working on with Francisco Castillo Trigueros the composer. I probably emailed every major news organization but no one picked it up . It was fun while it lasted but now I need to continue moving forward. My 5 minutes of press are up.

I do think it was good though. It was inspiring. Inspired me to fix some software bugs in the Chromochord. Inspired me to work on new projects and Inspired me to keep doing what I am doing because it really is a productive path. I am excited to see how far my mind can take me! Just need to keep thinking of new ideas and how to implement and keep working to implement them.

Monday, September 2, 2013

Is Being a Scientist Cool?

Sorry, Roger Tsien, you're my boy but you look like a huge nerd.

You walk into most academic institutions and go and meet the Scientists and they look like huge nerds. Now there is nothing wrong with looking like a huge nerd. People should feel like they can be themselves and people should not be judge by what they wear and how they look. Let's be honest here though if you met these people would they inspire you to be a Scientist?

What do people aspire to? Well obviously positions in which they will make lots of money but besides that people aspire to things that look cool and sound cool despite what the actual work consists of. Why do so many people want to work for all the Facespaces and Googles? Sure, there is pay and benefits and such but I am sure a job at Yahoo or Zipcar pays similarly. It is because of status.

In the late 90s and early 2000s I worked at Motorola as an engineer and programmer for the iDEN cell phone network. I wasn't paid an overly large sum of money about $30k but I wouldn't have left there if some company came and offered me $50k to do web development. I didn't want to do anything but work for Motorola. My cool ID badge and RSA secureID card and access to cell phone systems. For a technology nerd I was living the dream. A job with a really famous technology company giving me access to important data and control over cell phone networks. It was awesome.

So why would people rather work for Facespace with their job description revolve around trying to make people click ads rather than work in academic Science and Technology doing something so much "cooler".

Why isn't being a Scientist cool? I mean, being an Astronaut is barely cool these days. A couple thousand applicants for the last Astronaut application cycle? Survivor receives more applications than that!

Iron Man the movie has started to bring some coolness back into Science and Technology. The other day I was at the Grocery store and I heard a kid say that he wanted to be Iron Man. Hopefully because he wanted to invent cool things and not just because he wanted to beat people up but you take what you can get.

I dare you to show me a picture of a Scientist that would make someone in high school or younger think "Wow, that person is cool I really want to be like him or her". Why do we pay footballers and rap stars so much money? Because everyone wants to be them. They look cool, they act cool and they live what seems like a fun life. Their tweets are entertaining and funny, they are enjoyable people.

Is it just the life of the Scientist to be absorbed so much in their work and their head that they don't really care how they are perceived by other people?

I mean everyone loves people like Neil deGrasse Tyson but does anybody really aspire to be him and wear a suit everyday and act pretentious?

Is it our job as Scientists to make Science cool, Accessible, and seem like it is a fun job?

I don't know.

I am in no way endorsing that I am cool and other Scientists are not at least not outright but why do most of us seem so boring? TV shows and movies portray Scientists as ugly and nerdy and boring. Well except Iron Man. Are they portraying Scientists the wrong way or is that the way we all really look and act?