Successful Ph.D. Defense!

This past Friday was a huge milestone for me – I successfully defended my Ph.D. work! It’s been a long five year journey but I’m incredibly proud of what I’ve been able to accomplish with the help of many friends and collaborators, both in the Martinez Group and externally!

My goal has always been to use technology to create better tools for research and increase the accessibility of science to the general public. My efforts in my Ph.D. work center around the development of the TeraChem Cloud framework, which enables writing high-level Python code on a laptop while getting all the speed of GPU-accelerated electronic structure calculations. I applied this framework to several group workloads (automated reaction network discovery, energy transfer in light-harvesting complexes, and dataset generation).

While TeraChem Cloud makes life easier for researchers, I also wanted to improve ab initio interactive molecular dynamics simulations, which allow users to push and pull on molecules in a digital playground and watch the atoms respond with full quantum mechanics in real time. With the help of a few others, I used virtual reality to create an immersive interface for these simulations and developed a curriculum for both undergraduate and high school students.

One upside of conducting the defense over Zoom is that the whole thing was recorded! If you are interested, you can watch the public portion below.

Upside of Zoom: automatic recording of my defense!

I’m very thankful for all the support that has gotten me this far. I’ve been slacking on the blog posts, but hopefully I will catch up and keep you appraised as I move on to the next phase of my career.

Falling Walls Lab 2019

I was lucky enough to compete in the Falling Walls Lab 2019 finals this past week in Berlin, Germany! Falling Walls Lab is an international scientific innovation competition where one has two slides and 3 minutes to pitch their research (and answer questions!) to a jury and audience. There are two rounds: the first was a series of local competitions, which chose 100 finalists from around the world. In the second round, the finalists gather in Berlin for the second round of competition.

Luckily for me, my local Falling Walls Lab competition was hosted at SLAC in September! I was unsure of whether I was going to apply because the deadline for application was the day after I got back from the OMSC workshop, but man am I glad that I did! My local competition featured talks on the cutting-edge science done at SLAC to a startup centered around carbon sequestration, but my virtual-reality interactive simulations just managed to eke ahead and I was able to take first place.

Thanks to the official SLAC Twitter for tweeting about me after the local competition!

After a round of feedback from my local jury members, I submitted my final slides in early October, and before I knew it, it was November and I was off to Europe again! The first few days were an opportunity to mingle with the other competitors and also to learn about the scientific research opportunities in Germany. I got to visit the Fritz-Haber Insitute, a world-class chemistry research facility and one of the campuses of the Max Planck Society, and was even able to see their free electron laser setup. Theirs is designed for infrared radiation and so fits in a large basement, unlike the one at SLAC designed for X-rays – in fact, I’ve been inspired to try and make a post about the two soon!

The Fritz-Haber Institute was first opened for Physical Chemistry and Electrochemistry by Kaiser Wilhelm in 1911.

Finally, the day of the competition was here. This year’s Falling Walls conference is particularly meaningful as it falls on the 30 year anniversary of the Berlin wall coming down. Our competition opened with a moving interview of Professor Jens Reich, a molecular biologist who gave a speech during the Alexanderplatz demonstration on November 4th, 1989. After his sentiments that science should be pursued regardless of what obstacles stand in our way, the morning was packed with three minute presentations spanning the fields of chemistry, physics, biology, medicine, and the environment. I really enjoyed the rest of the talks as well – despite the vast number of them, I found I was actually able to stay alert and interested for the whole 5 hours of presentations throughout the day.

The stage and ever-present timer for the Falling Walls Lab finals.

I came on in slot 41, directly after the lunch break. I was very happy to be first in the session since it gave me less time to overthink my presentation. While not as smooth as some other presenters, I had no major stumbling blocks and was able to answer two questions very succinctly. While I didn’t win, I was very proud of this effort and am very grateful to have the opportunity to share my research on such a prestigious stage!

The following day was completely packed with exploring Berlin. I saw the Reichstag and Brandenberg Gate, walked through 3 museums and one university, saw the Berlin Wall, and ate sausages and sauerkraut. Unfortunately I fell sick the next day and had to cut my exploration short, but overall it was a fantastic experience: meeting new people from all over the world, hearing about their innovations for the future, and exploring a new country and city.

Thank you Falling Walls for the opportunity, and to everyone for listening to my ideas on how we can bring quantum chemistry into schools, museums, and one day even into homes.

Open Molecular Science Cloud Workshop at EUCO-CTC 2019

Throughout the years, I’ve given many posters and had many engaging conversations at chemistry conferences. Today marks another landmark for me as I gave my first conference talk as a part of the Open Molecular Science Cloud workshop at the 12th European Conference on Computational and Theoretical Chemistry (EUCO-CTC 2019)!

My journey to EUCO-CTC 2019 actually began when I attended the ACS Spring 2019 conference in Orlando, FL and was drawn to the Sustainable Software session being hosted by the Molecular Sciences Software Institute (MolSSI). I am sympathetic with MolSSI’s attempts to cultivate proper software development practices in the computational chemistry community and saw an opportunity to potentially connect my work with some of their efforts (i.e. my TeraChem Cloud with the QCEngine component of the QCArchive project).

With MolSSI more prominently on my radar, I was pleasantly surprised to see an announcement for a travel grant to attend an Open Molecular Science Cloud (OMSC) workshop at EUCO-CTC 2019. I applied in June and was awarded the travel grant in July, and so come September, I was off to Perugia to give a talk on TeraChem Cloud!

Badge and certification of presentation to my first conference talk!
Conference hall was pretty large, with a projector and screen to match. (Photo credit: Grier Jones)
Always more things to improve on: looking at the audience during the start of the talk! (Photo credit: Grier Jones)

After the MolSSI contribution section, we learned how the University of Perugia was using OpenStack to test HPC on cloud resources and their efforts in creating a distributed repository of lessons for chemistry education. The second half of the week was spent back in Rome, discussing potential paths forward for computational molecular sciences with cloud computing.

Second part of OMSC workshop in the Biblioteca Accademia Nazionale delle Scienza in Rome.

I think the most valuable experience for me was getting to connect with my fellow young academics through MolSSI during this trip. It was awesome to hear about their efforts in using high-throughput calculations for automatic force field parameterization (@JessMaat), using machine learning to build correlation energy corrections (@vwcruzeiro), or recycling electronic structure intermediates to speed up expensive calculations (@JonesGrier). It was also a great opportunity to learn more about QCArchive from the project lead himself (@dga_smith).

Post-workshop discussions in Perugia with a beautiful view. (Photo credit: Sara Tortorella)
The full MolSSI crew in St. Peter’s Square during post-conference exploration.

I am extremely grateful to Professor Antonio Laganá of the University of Perugia for organizing the OMSC workshop at EUCO-CTC 2019 and to MolSSI for making it possible for me to attend. Interacting with all these amazing people working on the future of computational chemistry has been a fantastic experience, and I look forward to seeing what comes out of the friendships and ideas built this week!

Stairway to Heme

Nowadays, it’s even easier to get started with machine learning and art. The Martinez Group recently had an internal competition using the neural_style package and a pre-trained VGG net to transfer art styles onto pictures of molecules we are studying.

Myoglobin, with secondary structure (dark gray) and heme group (center) emphasized.

I chose this image of myoglobin I generated for a benchmark paper I am writing as it is one of the most composed molecular images I have generated so far. The actual structure is shown in the transparent ball-and-stick style, with the heme group (an iron atom in a porphyrin ring) displayed as thicker and more opaque. Due to the size of proteins, it is common to visualize a cartoon-y ribbon style that shows secondary structure, such as the various alpha helices shown in dark gray.

Relativity by M.C. Escher (1953)

I wouldn’t say I know a lot about art or art history, but you don’t need an encyclopedic knowledge of artists and art styles to try and make something cool. In this case, the ribbon representation of the alpha helices reminded me of the stairs looping around in Relativity by M.C. Escher. I thought it would be cool if the stair pattern could be imprinted into the alpha helices of the myoglobin, so I chose this piece for the style.

In the end, the net was fairly simple to run, assuming you have Anaconda installed on a machine with a GPU and are somewhat comfortable on the terminal:

git clone
conda create -n neural_style
conda activate neural_style
cd neural-style
pip install -r requirements.txt
curl -o imagenet-vgg-verydeep-19.mat

python --content myoglobin.png --styles escher.jpg --content-weight-blend 0.2 --pooling avg --style-scales 0.2 --preserve-colors --output stairway_to_heme.png

Only the content, styles, and output keywords are needed for the net to run. However, I played with a few other keywords to get something closer to what I was looking for:

  • I lowered content-weight-blend to transfer more of the style since I didn’t care about the fine detail structure of the myoglobin
  • I lowered style-scales to try and match the size of the stairs in Relativity with the alpha helices
  • I switched pooling from max to avg to go for a more abstract look
  • I used preserve-colors so that the nitrogen (blue), oxygen (red), and iron (orange) have a chance to pop out

I didn’t get exactly what I was imagining, but for half an hour of playing with some command line arguments, I’m pleasantly surprised by the results. I call it Stairway to Heme, and challenge you to try it for yourself!

Stairway to Heme

Website Migrated to WordPress

My previous site was a foray into DIY web-hosting using GitHub Pages in combination with Jekyll, originally inspired by this post. It was a great first step: got me playing with Ruby & HTML again and creating some easy DNS records to route my domain to GitHub Pages.

However, I’m happy with the decision to migrate my website hosting to WordPress. Moving forward, it should be easier to provide some more content on personal milestones and my thoughts on events in chemistry, tech, or anything else I find interesting!