Tuesday, October 29, 2013

Advancing Science in Tandem with Colleagues in Japan… (#ACS #PRE #justpublished)

Sometimes features in my projects appear to come in waves. Intellectual discourse with distant groups appears to be a running theme at the moment. As with our recent work on roaming reactions, my recent article in Physical Review E involves a bit of back and forth with colleagues around the world. This time, it's my friends Kawai and Komatsuzaki at Hokaido University.

Since the start of my independent research career, I have been working on developing a series of models to describe the motion of particles in solvents that change with time. It's like trying to describe how a returner will run during a football kick-off without fully specifying the details of where all the blockers are and will be. The truth is that the blockers will move according to how the kick returner moves. This coordinated response between the chosen system—the returner or a molecule—and it's environment is not so easy to describe, and has been the object of much of the NSF-funded work by our group. We have managed to develop several models using stochastic differential equations that allow us to include such coupled interactions to varying degrees. While we were able to describe the response of the blockers to the returner in ever more complicated ways, for the most part they never seemed willing to talk to each other. A few years ago, Kawaii and Komatsuzaki found a formal way to extend the environment—that is, the blockers—so that they are able to affect each other as they respond to the system motion. In order to do this, though, you have to make some strong assumptions about the environment that are hard to satisfy for typical systems. In our latest paper, Alex Popov and I show that the our formalism is able to capture some of the generality of their model while still accommodating more general particles and environments.

The discussion between our two groups is a bit technical, but the back-and-forth is helping us all advance our understanding of the theory as well as enable its applications. The discourse is also not restricted to paper (in ink or bits) as our groups are now meeting regularly at workshops (such as in Telluride), and at our respective institutions (such as in my upcoming visit to Hokkaido university.)  Again, it's the opportunity for open discourse that makes it fun to keep advancing science!

The title of the article is "The T-iGLE can capture the nonequilibrium dynamics of two dissipated coupled oscillators," and the work was funded by the NSF. It was released recently at Phys. Rev. E, 88, 032145 (2013). Click on http://dx.doi.rog/:10.1103/PhysRevE.88.032145 to access the article.

Friday, October 25, 2013

Checks and Balances in Science… (#ACS #JPC-A #justpublished)

Science is self-correcting in a number of ways. It's true that sometimes the progress of science gets off the rails, seemingly falling into sink holes. Other times, it appears to find its course only through the jolt of a paradigm shift. However, most of the time, it moves forward with errors or missteps corrected naturally (or incrementally) by the community along the way. In our case, we recently made one (albeit small) such misstep. Specifically, in our recent article on roaming and transition state theory in the ketene isomerization reaction, we had a factor of 1/2 in the wrong place. (Check out my earlier blog post describing our earlier work.) Trouble was that the same factor had been mistyped in an earlier article by Gezelter and Miller, and we, like others before us, hadn't noticed it. Wiggins ran across our article before it was available in print, noticed the typo, and wrote to me about it. After some back and forth, including Miller, Gezelter and a few others, we agreed that the factor should have been there in the first place. The results of Gezelter and Miller's original article are o.k. because the typo was only in the text, not in their calculations. This left us wondering about our calculations. We reran them. The precise numbers changed, but fortunately all the qualitative results remained the same. Nevertheless, we just published a correction in the Journal of Physical Chemistry to clean up the issue and remove any doubt about the results.

Long story short, the scientific process worked. We published our results in an open setting. Someone across the Atlantic discovered an error that had endured in the literature through to us. He brought it to the attention of the community and us. We fixed it, and science moves on. There has been much talk in the common press in the past year about the persistence of errors in science. Indeed some of them persist because the internet tends to retain a memory of them. Sometimes searches find the article and not the subsequent correction. For the most part, though, these are rare events. I, like others, are just happy to get it right at the end of the day, and the scientific system works to help us get there.

The title of the article is "Correction to `Effects of Roaming Trajectories on the Transition State Theory Rates of a Reduced-Dimensional Model of Ketene Isomerization'" and the work was funded by the AFOSR. It was just published at J. Phys. Chem. A, 117, 10567 (2013).
Click on http://dx.doi.org/10.1021/jp408997z to access the article.

Tuesday, October 22, 2013

Theoretical Chemistry at Georgia Tech (@GT_CHEM)

Last Tuesday, we staged Theoretical Chemistry Day at Georgia Tech. As the School of Chemistry and Biochemistry was footing the bill, we limited the local faculty featured in the program to essentially those within our Center of Computational Molecular Sciences and Technology (CCMST). This sadly excluded a number of faculty members who are card-carrying theoretical chemists but are located in other schools such as Chemical and Biochemical Engineering, Biology, Materials Science and Engineering, Physics, etc. Nevertheless, the five of us, Jean-Luc Brédas, Angelo Bongiorno, Ken Brown, Rigoberto Hernandez (me), and David Sherrill, comprise a fairly large theoretical and computational chemistry subgroup in comparison with others around the country. The plenary talks by exemplary guests, Roald Hoffman, Peter Rossky, George Schatz, Josef Michl and Mark Ratner, provided a highlight to draw the attention of the campus for the day (as was the intention.) Meanwhile, the activity of the CCMST scientists and students is led by our insiders, and continues every day.

The CCMST started back in 2000 founded by David Sherrill and myself. Our then Vice-Provost for Research, Charlie Liotta, made a large bet on these two Assistant Professors in matching a Shared University Research Grant from IBM to help us bring a large supercomputer (an IBM SP2) as a cornerstone of the center's resources. We were also lucky to hire Edward Valeev as our first CCMST Scientist. (He's now an Associate Professor at Virginia Tech!) Our primary priority has always been to maintain a stable platform allowing computer jobs to run for a long time (like months to years!), and to continue executing through upward compatibility whenever possible. In parallel with the founding of the CCMST, Jean-Luc Brédas (then at U. Arizona) was also awarded an SP2. It was natural to have a merger of our HPC resources in expanding the CCMST in 2003 with his arrival. Since then, we have secured two different NSF Chemistry CRIF grants allowing us to add a few more newer clusters. We also grew to include two additional faculty members, Angelo Bongiorno and Ken Brown.

The funny thing about this story is that none of us were here 17 years ago. Indeed, at the time that I arrived, there were no full-time theory and computational professors in chemistry. It should be surprising that we went from essentially zero to a national presence in theoretical and computational chemistry in that little time. After all, it's the strength of the faculty in rejuvenating itself that typically maintains its rankings. Our recipe for success is simple. Mostafa El-Sayed, though he is an experimentalist, identified theory and computational chemistry as a critical growth area for our school and made it his mission to make it happen. I like to think that he was right!

Friday, October 11, 2013

What do you see? (Part II) @OxideChem

The empiricists (think Locke, Berkeley and Hume) and the rationalists (think Descartes, Leibniz and Spinoza) have debated forever about whether science is something to be observed or constructed. As I'm a theorist, you might think that I would land entirely on the side of the rationalists. However, I believe that no matter how well constructed, a theory must still be tested by experiment. It invariably also rests on experiment and may even be guided by experiment. Indeed, roughly half of my group's work involves simulations because it provides us with observations to guide our theory development. This does not detract from the fact that the theory can and must predict phenomenon that have yet to be observed. All to say that I, like most working chemists, believe that there is a significant place for observation, and our training as chemists has involved a sharpening of our observational skills. As such, most chemists (and likely also most physical scientists) pride themselves in their ability to accurately observe, analyze and synthesize all the data around them.

How can we reconcile this with the social science data that routinely shows that we all have implicit biases shaping our decisions? To make this question more concrete, it is helpful to consider Amy Herman's work on the Art of Perception that I discussed in my last post. Clearly, she has found that the average person has difficulty in accurately observing signals and discerning them from spurious information. Providing training for specific settings, she is able to help individuals improve their ability to see. I would claim that most chemists, through their training and experience, are already very good (if not exceptional) at seeing the signal in the data of their experiments. The problem is that we have seldom been trained to see or judge candidates (for positions all the way through the academic ladder) without employing implicit biases. But we're so good at rating the quality of a given science that it's hard to accept that we aren't equally good at rating the quality of a given scientist. The latter, though, is perhaps much more complex and a lot harder to see. As observers, we must also recognize that our current practices have led to faculties whose demographics are far from being representative of our nation. And this suggests that we need to change the way we see scientists....

Tuesday, October 8, 2013

What do you see? (Part I) @OxideChem

When you look at a piece of art, do you see the same thing every time? Or do you, perhaps, see something that your neighbor does not? Are there items that you notice only because of where you are in your life? For example, if you see a painting in a landscape (not the one pictured here!) with two people walking along a park path, do you notice the eight-year old of the pair or the attractive older companion? A child might note exactly which toy the eight-year old is carrying, whereas I might only remember the kind of techno gadget the adult is fiddling with. Someone else might guess the time of day based on the position of the sun and the fact that it was a weekday because of the date printed on a newspaper tossed on the ground. Why does that matter? Because it would be incongruent to see a kid out of school. Or would it? Oh, and did you wonder why the kid was walking with the adult?

As part of Georgia Tech's diversity symposium (that was the subject of my previous post), Amy Herman provided a discussion of the art of perception. She didn't actually present the example above. Instead she walked us through a large number of famous and not-so famous paintings and images on other media. In each case, her constant refrain was the title of this post. Invariably, we got the answer wrong, or more precisely, we missed items that were important or we added information that was not there. Either way, many of us made assumptions either to fill in the detail of the image or to categorize so as to simplify the detail. Why does this matter? Well, if you are in the business of solving crimes (as many of her customers are) then you must finds clues to solve the case in the context of a large amount of spurious data. Learning how to see exactly what is there, nothing more and nothing less, forms the basis of solving a case. For this reason, Amy Herman's perception training has been highly sought out. But the import of her work goes much further.

When you sort through a sea of resumes or curricula vitae, what algorithm do you use to pick the handful that you will read precisely? To what extent does that sorting algorithm rely on the information that you are filling in? When you are interviewing candidates for a position (on a faculty or work group for example), how do you project their future growth? Any Herman's message is that you must limit the projection to those forecasts that are based only on what you see in the application. That is, you need to train yourself to not make assumptions based on your perception of the facts about the candidate that are extraneous to the job description. Not an easy thing to do, but very necessary in order to remove inequities that may lie in the hiring process.

Friday, October 4, 2013

Celebrating Diversity at GT

Two weeks ago, Georgia Tech celebrated the advances we've made in creating an atmosphere of inclusive excellence on our campus. (Given the time delay, it should be clear that I'm still catching up on my blog posting and everything thing else!) Only three years ago, the office of the Vice-President for Institutional Diversity (VPID) was created. Dr. Archie Ervin was appointed the first VPID (as announced by President Peterson on October 5, 2013). It was a privilege for me to be involved in the search for his position. He had us at "hello" and he's been catalyzing our community ever since. He's built a staff of extremely talented people. He's created much needed mechanisms to coordinate the many diversity activities that had already been taking place on campus. Not only is the sum greater than the parts, but it has allowed for the creation of new policies and programs to improve the atmosphere on campus. The now-annual Diversity Symposium is a capstone bringing attention to these advances.

The keynote speaker was Dr. France Córdova. She's a true rocket scientist, having been appointed as NASA's Chief Scientist in 1993. She's the former President of Purdue University, and she's currently working at the Smithsonian. Through this latter position, she has a connection to Georgia Tech. Her boss, Dr. Wayne Clough, is the much beloved President who preceded President Peterson. Interestingly, she's presently not accepting speaking invitations. She honored ours only because she had accepted the invitation prior to Obama's announcement that she will be the next Director of the National Science Foundation subject to Congress's approval. Evidently inclusive excellence has to be timely, too! Dr. Córdova's message was simple. We need to increase the public's science literacy and awareness. As evidence, she shared her personal story and directed us to the recent National Academy's report on "Changing the conversation: Messages for Improving Public Understanding of Engineering." Notably, the chair of the committee that wrote the report was Georgia Tech's own former Dean of the School of Engineering, Don Giddens. Why is this message relevant to a Diversity Symposium? Because one of the biggest obstacles to inclusive excellence is the fact that not too few children are dreaming of becoming a scientist. Sadly, the barriers to science don't stop there. Progressing through his or her career, the realization of the dream to advance science tends to be obstructed in ways that affect people from different backgrounds inequitably. What Georgia Tech is doing to change the atmosphere on campus is critical to lowering such obstacles for everyone. For example, students and faculty presented with clear and transparent guidelines for success (in facing tests or tenure promotion, respectively), are thereby provided with the confidence (in the system) necessary to be successful regardless of their diversity make-up. The presence of such success stories, in turn, makes it easier for young people to see that the STEM career pathway is truly accessible to them.