Chemistry's Community Spaces

There was a time when book stores and libraries were the places where you met others. Like in today's universities, in which librarians can't get rid of books fast enough, students still go to libraries to study in their carrels. Unfortunately, the flattening of the printed word through electronic delivery is decreasing the need or motivation for you to physically visit bookstores or public libraries. Meanwhile, next-day (and next-hour!) deliveries de-motivate you from going to retail shops at your local mall. But we still need community spaces, like the Mexican zocalos, to see and meet other people. Coffee houses and fitness centers, necessarily serve products or services that you and others must experience physically, and are increasingly serving the need for community gathering spaces while proving that brick-and-mortar can still be profitable.

So where do chemists gather? Increasingly academic buildings are being created with coffee houses in mind. Sure, it's cheaper for me to make an espresso with the machine in my office. But if I walk down to the coffee shop, I have the extra benefit of running into students and colleagues. The upcoming National Meeting of the ACS in San Diego also serves this need. Going there, I get to hang out with over 15,000 of my closest friends. I can't, obviously, see them all, but I don't have to make many, if any, appointments. The chemists with whom I have common interests naturally attend the same receptions, governance meetings and scientific sessions. These chance run-ins are devilishly short and sweet. The follow-up often occupies my activities and seeds my next innovations over the next six months and beyond.

Of course, old and new gathering mechanisms can overlap. In San Diego, the Multidisciplinary Program Planning Group (MPPG) selected Computers in Chemistry as the theme. Working with my colleagues on the associated symposia, we introduced a special break from 10:00 AM to 10:30AM on mornings from Sunday to Wednesday called "Café con Ordenadores." We hope to leverage your need for coffee to discuss how computers can enable your chemistry. I look forward to my chance meeting(s) with you in San Diego starting on March 13th!

Check out my old post on some tips for making a large conference, like the ACS meeting, feel exactly like the small conference you want to attend.

This post was reprinted on the Sustainable Nano Blog on March 8, 2016. 

Counting to 41,044,208,702,632,496,804 and beyond...

Counting is a rather simple thing. You increment a given number by one just like in the journey of one thousand miles you take a step and repeat. Trouble is knowing when to stop. Ultra runners might not stop until they get to 100 miles (about 180,00 steps), but few will be able to tell you exactly how many steps they took. It's just too annoying to keep the count up and enjoy the view. Regardless, this gives us a good estimate of how high a person might be able to count in a day (if they count really fast). To get to the number in the title, it would take such a person over 600 billion years...

Now consider how long it would take to count the number of possible distinct non-recrossing paths following the edges of a square between the opposing corners along a diagonal. That's two, and it takes you less than a second. Suppose that you make it a two by two square. The number of possible distinct non-recrossing paths now comes up to 12. You might then ask about a 3 by 3 square or larger. Or maybe not as that might seem a little too mathematical. Dr. Minato and his colleagues followed this train of thought and made a YouTube video to illustrate how quickly the count grows. It's in Japanese with English subtitles and already has well over a million page views!

While this is a very fundamental question, it's useful to recognize that knowing how to count paths (particularly using Minato's clever algorithms) on an arbitrary network has lots of cool applications. Among these could be the determination of the sum of chemical pathways between reactants and products. That's the problem that I'm interested in, but it's a little harder because each path has a different weight (or cost.) The cost isn't necessarily the same for each of Minato's subsets and consequently it isn't trivial to reuse his existing algorithms. But here lies a challenge to a possible advance in the field of chemical physics.

Check out "The Art of 10^64 -Understanding Vastness-Time with class! Let's count!" on YouTube.

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!

Looking inside the black box of computational chemistry

This week, I'm teaching faculty from Primarily Undergraduate Institutions (PUIs) about the underlying concepts behind molecular dynamics simulations. This seventh workshop on computational and theoretical chemistry is part of the cCWCS workshops aimed at STEM education dissemination and undergraduate research capacity building. Our first workshop was held in 2002, now more than a decade ago! I cover statistical mechanics, David Sherrill covers electronic structure, and Tricia Shepherd covers the hands-on labs. We alternate (roughly) between holding them in Atlanta and in Salt Lake City. Both have their charms. The Westminster Campus is a great venue because it's an idyllic oasis in the middle of the city. It has the open greens and architectural gems that you would expect from a private undergraduate liberal arts school. It also has the requisite high-caliber undergraduate students and facilities to do first-rate science. Holding the workshop here thus makes it easier for participants to see that the computational tools we sample can be replicated at their home institutions.

This workshop, however, is different than most such computational chemistry workshops because our emphasis is on the underlying theory in the computational codes, and not just on how to run a particular computational package. There's nothing wrong with doing the latter. However, we feel that it's useful to understand when computational chemistry calculations or simulations are meaningful or not. To that end, one needs a bit deeper knowledge of how exactly the algorithms are working within the codes. In part this means knowing the underlying equations. In equal measure, it also means understanding the underlying concepts. So the lectures in our workshop tend to focus (a lot!) on the theory. In like fashion, we also want to help participants understand how the algorithms are implemented. Although the labs are run on Apple laptops (which is known for its fancy graphical user interfaces), we guide them into the unix layer, editing files and running jobs from the command line. Thus our goal is to have participants be more comfortable with what the calculations are doing and how they are being done within software packages, whether they're computing energetics or dynamics. In knowing what's inside these black boxes, they should be in a better position to set-up computational experiments and to mentor their undergraduate students and researchers to do likewise. The fact that the workshop continues to be oversubscribed gives me hope that we are achieving at least some part of this goal.