Seeking a joint Open Force Field Consortium / XtalPi Distinguished Postdoctoral Fellow

The Open Force Field Consortium (OpenFF, openforcefield.org) and XtalPi, Inc. (xtalpi.com) seeks a Distinguished Postdoctoral Fellow to perform cutting-edge research in a unique academic-industrial joint effort.

OpenFF is an academic collaboration (based at UC Irvine / UC Davis / UC San Diego / Univ. Colorado Boulder / Sloan Kettering Institute in New York) that seeks to develop next-generation molecular mechanics force fields and associated parameterization software and data infrastructure. XtalPi is a pharmaceutical technology company founded in 2014 that is introducing revolutionary advances in drug research and development, and has established strategic partnerships with several major pharmaceutical companies and recently completed a Series B funding round with Sequoia, Tencent, and Google.

The Postdoctoral Fellow will work with OpenFF and XtalPi to improve the accuracy of molecular mechanics force fields for predicting crystal structures and binding free energies. The work spans the disciplines of force field development/validation and Bayesian inference, and seeks to answer the fundamental scientific questions: 1) What regions of chemical space are critical failures for current force fields? 2) What are the fundamental limitations of (a) current functional forms and (b) parameterization methods?

The position spans a two-year project period that involves a gradual transition from the OpenFF side to the XtalPi side. In Year 1, the Fellow will be hosted for ~9 months in one of the academic groups (to be determined by the OpenFF PIs, XtalPi, and the Fellow) and ~3 months at XtalPi in Shenzhen, China or Boston, MA. In Year 2, the time division will be 3-6 months academic / 6-9 months XtalPi. The Fellow will be considered for full-time employment at XtalPi after Year 2.

For more information, see the full job posting.

Postdoc Gregory Ross joins Schrödinger as a Senior Scientist

We're excited to announce that Postdoctoral Fellow Dr. Gregory Ross has joined Schrödinger as a Senior Scientist, where he will be working to bring his expertise in statistical mechanics and semigrand canonical methods to their suite of molecular modeling and simulation tools.

You can see more fantastic work from Dr. Ross at his Google Scholar page, and check out his recent preprint on semigrand canonical methods for simulating realistic biomolecular salt concentrations on bioRxiv.

Science Communication Boot Camp: The Experience

Guest blog post from postdoc Sonya Hanson.

Earlier this month, I went to Science Communication Boot Camp. It was at the 'Alan Alda Center for Communicating Science' at Stony Brook University. We did not get to meet Alan Alda. That was disappointing. But everything else was really, super awesome. We played a lot of improv games, we did a lot of woodshedding explaining our own science, we learned about how to make stories, we learned about metaphors, and at the end we taped three-minute mock media interviews and talks to try and implement what we had learned throughout the week. It was exhausting, it was embarrassing, it was hard, but it was a blast.

Baseball

I first realized we were someplace special when we started talking about baseball. Now, I am not a baseball person, but that's okay: I know enough. But in the beginning of the first day, they asked us to explain the following to someone who knew nothing about baseball:

'In the bottom of the ninth, Jeter worked a one-out walk and stole second. But the Red Sox's ace reliever got Ellsbury and Teixeira to strike out swinging to end the game.'

And it was super hard. We started explaining baseball: there are three bases, there are these things called outs, you get a point by... That just wasn't working. And then... they put up this explanation:

'The game was almost over, and the home team was losing to its most hated rival. The beloved captain of the home team, playing in his last season, made a last-ditch effort to win. He took a big risk, and it looked like it might pay off. But when his teammates tried to help him score, a key player on the other team shut them down. The game ended, and the home team went down to bitter defeat.'

Suddenly you understand the stakes. Suddenly you understand why someone might care about baseball.

Yes, and...

Don't worry, the rest of the camp was not about baseball. Time-wise, the plurality of the boot camp was spent doing improv games. Why, you may ask? What do science and improv have in common? Why would you do improv, where the whole point is that you're just making stuff up, to become a better scientist, where the whole point is precisely that you do not just make stuff up? Because improv is about connecting. Improv is about 'Yes, and..'

Not 'No, but...', not 'Yes, but...', but 'Yes, and...'. Agree and add something. Find how to connect to someone and then add to that. At the beginning the improv games were not science related. Zip-zap-zop, the mirror game, the ball game, the positive side of ranting, etc. My hypothesis is that they're to get us talking. To get us comfortable with talking about anything, anything at all. To find our own rhythm, and try to connect that rhythm to whoever you're communicating with. In one of the most powerful games, we were told to take a blank piece of paper and describe a picture. It was intense. Almost everyone talked about something deeply personal. A picture of an important family space or pet that got you through hard times. There were no instructions to 'do your best to make everyone cry', but somehow that's what happened. And this was all without any preparation. Somehow, we already had these stories inside of us, but how could we use them *dun dun dun* FOR SCIENCE?

STORIES, DISTILLING, AND METAPHORS

The first night, guest speaker Carl Safina told us about (among other things) his 'Spray can theory of science communication': he used to be pissed off that you buy a can of spray paint and it's only 2% paint, but then he realized that the paint is no good without the 98% propellant. The story is the 98% propellant. The science is the 2%. Sorry, guys. That means it pays to find that 2% of your science that is really what you want to communicate. Unsurprisingly a lot of what we learned when we weren't doing improv was how to 'distill our message'. We would go around in small break-out sessions and have one minute to describe our work. One of the first things I learned was, "bring cancer up front". Apparently in my first run-through I left it to the very last sentence. Another was "tell them what you're going to tell them, tell them, then tell them what you told them". I think this is more powerful than it seems. It forces you to decide what you're going to say, and decide your goal instead of just rambling off a laundry list of facts that probably don't mean anything to the person you're talking to, anyway.  Relatedly, getting rid of jargon was surprisingly difficult. In retrospect, it shouldn't have been surprising, but also I now feel bad for all the people I have explained my science to in the past that had to deal with all those meaningless (to them) words. If anything came out of this camp, I hope I am now better at recognizing when this when it happens.

One of the things that helped a lot in explaining more difficult concepts was using any kind of comparison to a real life thing. Why do we care about semiconductors? How small is an atom? What analogies can you make to other complex, but more commonplace things? Coming up with these kinds of comparisons, I think, is often scary for scientists: we don't want to lose reality in an imperfect analogy. But actually, having any kind of reality to compare to is surprisingly helpful when your other option is just an abstract concept... and you only have three minutes to get your point across. We even did a game to explore how easy it could be to find everyday things to relate to scientific topics: everyone writes down a scientific topic on a piece of paper and puts it in a pile; everyone puts a random object from their backpack or purse in the pile; pick four of each. Surprisingly, after mixing and matching, it is not hard to find reasonable pairs: swiss army knife and adaptive evolution, broken retractable badge holder and the RNA folding problem, sunglasses case and protecting DNA in epigenetics, headphones and being desensitized to the song 'Happy' for antibiotic resistance, etc. The hardest part, it turned out, was not pairing a scientific concept to an every day object, but telling a story around it.

The media interview

So that was a lot of fun. We got a bit better at improv and finding our rhythm. We got a bit better at distilling our scientific message. But then they got out the big guns: time to record it. This was definitely invigorating, partly because it was actually at the Stony Brook journalism school where they had real lighting and real cameras, and the Alda Center brought in some totally legit interviewers (they were kind of a big deal: googling Marcy McGinnis or Rory O'Connor is a good way to misplace a few hours of your day). It was also pretty nerve-wracking. I for one felt like an idiot because I was wearing a black shirt in front of a black background. What a noob! See my little interview below for your viewing pleasure:

Eh? If you liked that, it is probably just because I've heard my boss say those same things over and over and over again... Also I did do a bit of (extremely professional) editing and cut out some parts I messed up. Anyway, it's certainly not perfect, but maybe I managed to put into practice the bits and bobs mentioned above. Hopefully, now you know more about what the Chodera lab does!

Closing remarks

One of my favorite things about all this is that from these short (1-3 minute) talks, I now understand the science of other boot campers  better than the work of scientists I've seen talk for 15 minutes or more at conferences! While this is great, there are still things that bother me about a lot of these techniques of communicating science. What if what you want to communicate is the history of the material of the bases and how that has had an impact on the game of baseball. Something smaller, something that is harder to make seem important. I think most of us were able to make our science personal by talking about how it effects human health, and I would have loved to see more diverse ways of making science personal. I would have loved to take a crack at explaining why we care about the Higgs boson.

This hits on another issue we ran into several times during the course: we don't want to oversimplify. And I think we didn't cover how far is too far very well. On the first day we picked an abstract of someone in the course (Hi, Tali!) to explain to a lay audience: a study on Archer fish (the link is a sweet NYTimes ScienceTake video) that seemed to indicate that fish could do conflict resolution even though they don't have a brain with a prefrontal cortex, which is where humans and mammals do conflict resolution (while this particular abstract is not published yet, here's a link to a related study from the same lab/author). The resulting impression the audience had was: "This research says that an injury to the decision-making section of the brain, may be curable." This made the abstract's author cringe. To me this is exactly what we want to avoid, and I think I am still a little scared of this, and as a result might still fall into jargon sometimes when I explain my research because my instinct is that it is better to communicate poorly than to communicate wrongly. Ideally, we wouldn't do either. 

These are some of the more complex nuances that I don't think we quite got to cover and clarify in the class. But that's fine. No one said this was going to be easy. One of the most important things we learned, I think, is that we all have our own rhythm and our own stories and that tapping into those is all we need to communicate science effectively. We don't all need to be Bill Nye.