Friday, November 21, 2014

Building Pillars of MesoScale Particles on a Surface

Let’s build layers of (macromolecular) material on a surface. If the material were lego pieces, then the amount of coverage at any given point would be precisely the number that fell there and connected (interlocked). In the simplest cases, you might imagine the same type of construction on a macromolecular scale surface with nano sized bricks. The trouble is that at that small length scale, particles are no longer rigid. The possibility of such softness allows for higher density layers and even a lack of certainty as to which layer you are in. This leads to a roughness in the surface due to the fact that the soft legos stack more in some places than others. Moreover, there will be regions without any legos at all which means that the surface will not be completely covered. This led us to ask: What is the surface coverage as a function of the amount of macromolecular material coated on the surface and the degree of softness of that material?

As in our recent work using tricked-up hard particles, we wondered whether we could answer this question without using explicit soft particle interactions. It does, indeed, appear to work in the sense that we are able to capture the differences in coverage of the surface between a metastable coverage in which particles once trapped at a site remain there, and the relaxed coverage in which particles are allowed to spread across the surface. We also found that relaxation leads to reduced coverage fractions rather than larger coverage as one might have expected a spreading of particles due to the relaxation.

This work was performed by my graduate student, Dr. Galen Craven, in collaboration with a research scientist in my group, Dr. Alex Popov. The title of the article is "Effective surface coverage of coarse grained soft matter.” The work was funded by the NSF. It was published on-line in J. Phys. Chem. B back in July, and I’ve been waiting to write this post hoping that it would hit the presses. Unfrotunately, it’s part of a Special Issue on Spectroscopy of Nano- and Biomaterials which hasn’t quite yet been published. But I hope that it will be soon! Click on the doi link to access the article.




Monday, November 17, 2014

Engaging with Your Audience

How far are you willing to go in keeping your audience awake during your seminar? Are you willing to punch one of your audience members? Well not quite punch them, but as in the picture accompanying this article a near miss. Or perhaps you use the Socratic method, hoping that someone will answer? Educational research has shown that active-learning modalities are the most effective way of teaching in the classroom. As lectures are meant to teach the audience about your research (or whatever topic you are describing), why not use them there as well?

At a seminar in UCSD a couple of years ago, I was asked a question concerning the velocity implemented in steered molecular dynamics. The issue concerned how the environment around a protein is affected by the speed in which a protein is literally pulled through it. This is analogous to a fist hitting your mouth. If the fist moves slowly enough, hopefully your mouth will have time to open and adjust itself allowing the fist to fit. But if the fist moves quickly, your teeth will likely be broken. To demonstrate this, without the benefit of this prior explanation, I ask for a volunteer (as I did extemporaneously at UCSD, and then later at Cal State LA where Carlos Gutierrez volunteered as is shown in the accompanying photo) and stunt punch him or her. The students (and the volunteer) are clearly surprised about the action and all are generally relieved that no one was hurt. More importantly, the visual metaphor helps them to better understand the algorithm. Many of them subsequently relay the visual metaphor to their friends and colleagues, undoubtedly also struggling to explain the connection to the science of the seminar. This requires audience members to commit the concepts to a longer-term memory. And this fits with my goal for my seminars which is to help students and colleagues learn and remember the science that my group is advancing. Sage at the stage may be comfortable and without risk, but engaging with your audience offers better rewards!

Sunday, October 19, 2014

Music and Chemistry in Nashville

This weekend, I had an opportunity to do something I have never done before. I introduced the band. SERMACS2014 managed to snag one of the hottest tickets in town. The SteelDrivers have been nominated for three Grammies, four IBMA awards and the Americana Music Association’s New Artist of the Year award. It was yet another sign of the prescient organization of the SERMACS2014 organizing committee that they signed them two years ago.

They were also quite clever in finding a band whose songs encoded a chemical twist. When the SteelDrivers sing one of their hits, "Wearin' a hole in a Honky Tonk floor," I imagine hole transport on graphene. The song even includes a chemical safety twist. In the lyric, "this old bar room suits me fine," I'm envisioning lab coats in front of a fume hood. That is, it's easy to see chemistry wherever you look. On the flip side, Sir Harry Kroto's keynote remarks at SERMACS2014, pointed out that his identification of the C60 structure was made possible by his early exposure to graphic arts and R. Buckminster Fuller's geodesic dome at the World's Fair. Which is to say that it is equally easy to find art in the science that we do. Meanwhile, the SteelDrivers also seemed amused over my opening remarks about their music. At least, they pretended to be as they introduced their song with a line about the newfound chemistry that it evidently contained. Truly bluegrass and chemistry were following the same beat... but alas, I still don't know how to two-step.

So thank you to the Nashville Section of the ACS for staging a great SERMACS, and for helping me find some cool chemistry in bluegrass!

Wednesday, September 10, 2014

OXIDE's Case for Inclusive Excellence in Chemistry

There's a catch-22 with any attempt to increase the participation of under-represented groups in the chemical sciences, and perhaps elsewhere too. On the one hand, students need to be trained to enter the workforce. On the other hand, they need to make the choice to be trained, presumably because jobs in the chemical sciences are more desirable than the alternatives. There exist many successful programs aimed at the former, but I believe that such programs face an uphill climb because, on top of everything else, they must convince potential candidates that a career path in the chemical sciences is desirable. Sadly, though the odds for success in professional sports are much lower, it appears to be relatively easy to convince someone to follow that dream through college. When it comes to choosing college majors, however, students tend to be more cautious about potential long-term employment opportunities. This is true for everyone, but it's often acutely so for students from under-represented groups who face the possibility of finding diversity inequities along their career path. An objective of the OXIDE effort is to help break the catch-22 by changing the culture so as to eliminate real or perceived diversity inequities. Our hypothesis is that a culture that is accommodating to everyone will lead to departments with demographics that are in congruence with those of the national population.

Our recent article, "A Top-Down Approach for Increasing Diversity and Inclusion in Chemistry Departments," was roughly based on an invited presentation (by the same title) at the Presidential Symposium held at the 246th National Meeting of the American Chemical Society (ACS) in Indianapolis in September 2013. The symposium topic was the "Impact of Diversity and Inclusion" and included several other presentations that were also turned into peer reviewed articles in the recently published ACS Symposium book. I spoke about the work by Shannon Watt and me through our  OXIDE program. She's pictured just to my left in the image accompanying this post.  That picture, by the way, was actually taken at the 248th ACS National Meeting held in San Francisco in August 2014. I included this more recent photo with this post because, in addition to Shannon and me, it features several individuals who have been supportive of the OXIDE effort and who also spoke at the recent symposium on "Advancing the Chemical Sciences through Diversity" and thereby continued the dialogue on inclusive excellence at ACS meetings.

The article was  written with my collaborator, Shannon Watt. The reference is "A top-down approach for diversity and inclusion in chemistry departments," Careers, Entrepreneurship, and Diversity: Challenges and Opportunities in the Global Chemistry Enterprise, ACS Symposium Series 1169, edited by H. N. Cheng, S. Shah, and M. L. Wu, Chapter. 19, pp. 207-224 (American Chemical Society, Washington DC, 2014). (ISBN13: 9780841229709, eISBN: 9780841229716, doi: 10.1021/bk-2014-1169.ch019) Our OXIDE work is funded by the National Science Foundation, the Department of Energy and the National Institutes of Health through NSF grant #CHE-1048939.
We are also grateful to recent gifts from the Dreyfus Foundation, the Research Corporation for Science Advancement, and a private donor.

Monday, September 8, 2014

Advice to high school students ...

Through high school, you are mostly taught the facts. As an undergraduate, you are taught to teach yourself the facts and how to construct answers to questions. In graduate or professional school, you are taught how to ask the right questions. The irony in this construction lies in the common misconception that Ph.D.s know all the answers, when in fact they mostly know the gaps in knowledge. That is, Socrates was not being so humble with his oft quoted saying, "the more I learn, the more I learn how little I know."

At the recent Herty Medal Award Dinner hosted by the Georgia Local Section of the ACS, I was pleased that nearly an entire table was filled by AP Chemistry students from Luella High School in Henry County. One of them asked our medalist, Luigi Marzilli, for advice on her way to college. I took the liberty of conveying the stages I described above. My point is that the mode of learning undergoes a paradigm shift in going from high school to college. My advice to students is thus to be aware of this change and be deliberate in changing their study habits. Indeed students often struggle as they approach the cliff on the edge of what they know coming from high school and the large body of new material that they are now expected to know in a college class. They often respond by trying to memorize every new fact and figure, but the shear magnitude of data makes such a path difficult to follow. Instead, they need to learn the material conceptually so that they can readily process the problems they face on exams and beyond. This requires practicing the problems and making the connections between the concepts steadily through the term, not in a single cramming session the night before the exam!

Friday, August 22, 2014

Pitching molecular fastballs through a hurricane

The first course I taught at Georgia Tech was a graduate course in statistical mechanics. I quickly discovered that a big barrier for my chemistry students was a lack of understanding of modern classical mechanics. Actually, this has also been a problem for them in learning quantum mechanics too. It might seem odd because classical mechanics is everywhere around you. It is simply the theory that describes the motion of baseballs, pool balls, and rockets. The details of the theory get amazingly complicated as you try to address interactions between the particles. Baseballs don't have such long range interactions so no worries there. But molecules do, and these interactions need to be included to understand the full complexity of molecules in classical (and quantum) mechanical regimes. In order to address this gap, I created a primer on classical mechanics that I have been sharing with my students ever since. But this document was not available to anyone beyond my classroom. So when I was asked to submit a review article on modern molecular dynamics, it was a no-brainier to include my primer at the front of the article so as to bring up readers up to speed on the classical equations of motion beyond Newton's day.

We didn't stop there, of course. The advanced review article, written with my collaborator, Dr. Alex Popov, also describes modern theoretical and computational methods for describing the motion of molecules in extreme environments far from equilibrium (like, for example, a hurricane). There are lots of ways in which this problem involves many moving parts (that is, many variables or degrees of freedom.). One of these involves the approximate separation in the characteristic scales of electrons and nuclei for which the 2013 Nobel Prize in Chemistry was, in part, awarded. Another involves the three-dimensional variables required to describe each atom in every molecule for which there usually are many. Think moles not scores. This increasing complexity gives rise to feedback loops that can explode (just like bad feedback on a microphone-speaker set-up), collapse or do something in between depending on very subtle balances in the interactions. Slowly, but surely, the scientific community is beginning to understand how to address these complex multiscale systems far from equilibrium. In our recent article, we reviewed the current state of the art in this area in the hope that it can help us and others advance the field.

The article was written in collaboration with Alexander V. Popov. The title is "Molecular dynamics out of equilibrium: Mechanics and measurables" and our work was funded by the National Science Foundation. It was recently made available on-line in WIREs Comput. Mol. Sci. 10.1002/wcms.1190, "Early View" (2014), and should be published soon.

Wednesday, August 20, 2014

LiCN taking a dip in an Ar bath

We all know that it’s easier to move through air than water. Changing the environment to molasses means that you’ll move even slower. Thus it’s natural to think that the thicker (denser) the solvent (bath), the slower a particle will swim through it. More precisely, what matters is not the density but the degree to which the moving particle interacts with the solvent, and this can be described through the friction between the particle and the fluid. Chemical reactions have long known to be increasingly slower with increasing friction. The problem with this seemingly simple concept is that Kramers showed long ago that there exists a regime (when the surrounding fluid is very weakly interacting with the particle) in which the reactions actually speed up with increasing friction. This crazy regime arises because reactants need energy to surmount the barriers leading to products, and they are unable to get this energy from the solvent if their interaction is very weak. A small increase of this weak interaction facilitates the energy transfer, and voila the reaction rate increases. What Kramers didn’t find is a chemical reaction which actually exhibits this behavior, and the hunt for such a reaction has long been on…

A few years ago, my collaborators in Madrid and I found a reaction that seems to exhibit a rise and fall in chemical rates with increasing friction. (I wrote about one of my visits to my collaborators in Madrid in a previous post.) It involves the isomerization reaction from LiCN to CNLi where the lithium is initially bonded to the carbon, crosses a barrier and finally bonds to the nitrogen on the other side. We placed it inside an argon bath and used molecular dynamics to observe the rate. Our initial work fixed the CN bond length because that made the simulation much faster and we figured that the CN vibrational motion wouldn’t matter much. But the nagging concern that the CN motion might affect the results remained. So we went ahead and redid the calculations releasing the constraint on the CN motion. I’m happy to report that the rise and fall persisted. As such the LiCN isomerization reaction rate is fastest when the density of the Argon bath is neither too small nor too large, but rather when it is just right.

The article with my collaborators, Pablo Garcia Muller, Rosa Benito and Florentino Borondo was just published in the Journal of Chemical Physics 141, 074312 (2014), and may be found at this doi hyperlink. This work was funded by the NSF on the American side of the collaboration, by Ministry of Economy and Competiveness-Spain and ICMAT Severo Ochoa on the Spanish side, and by the EU’s Seventh Framework People Exchange programme.