Wednesday, July 30, 2014

Getting to the shore when riding a wave from reactant to product

Suppose that you were trying to get across a floor that goes side to side like a wave goes up and down. If you started on the start line (call it the reactants), how long would it take you to cross to the finish line (call it the products) on the other side? In earlier work, we found “fixed” structures that could somehow tell you exactly when you were on the reactant and product sides even while the barrier was waving side to side. Just like you and I would avoid getting seasick while riding such a wave, the “fixed” structure has to move, but just not as much as the wave. So the structure of our dividing surface is “fixed” in the sense that our planet is always on the same orbit flying around the sun. This latter analogy can’t be taken too far because we know that our planet is thankfully stable. In the molecular case, the orbit is not stable. We just discovered that the rates at which molecular reactants move away from the dividing surface can be related to the reaction rate between reactant and products in a chemical reaction. (Note that the former rates are called Floquet exponents.) This is a particularly cool advance because we are now able to relate the properties of the moving dividing surface directly to chemical reactions, at least for this one simplified class of reactions.

The work involved a collaboration with Galen Craven from my research group and Thomas Bartsch from Loughborough University. The title of the article is "Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields.” The work was funded by the NSF, and the international partnership (Trans-MI) was funded by the EU People Programme (Marie Curie Actions). It was just released as a Communication at J. Chem. Phys. 141, 041106 (2014). Click on the JCP link to access the article.

Friday, July 25, 2014

When the buffalo roam, do they go over the pass or across the plain?

In one of our papers from last year (recapped in an earlier post), we found that in at least one chemical reaction (the ketene isomerization), the reaction could involve rather distinct pathways. On the one hand, the system could go across the break between the two energetic mountains separating the reactant and product. On the other hand, it could find a flat plain in which it could meander slowly across. The first of these two cases involves a narrow pass that is difficult for it to get through. The other is a wide plain but it costs a lot of energy to get up to it. Chemical reaction rate theory is built on the notion that the reaction always goes across the narrow passage as long as it’s the easiest one to get over. However, in the last decade there has been a lot of work observing that roaming over the flat plain has its privileges.

My postdoctoral student, Inga Ulusoy, and I wondered whether the ketene reaction gave rise to both possible classes of paths. It did! We also wondered the degree to which each path affected the rate in which the molecule reacted. We found earlier that the traditional pathway (over the break between the barriers) was the most important one in a model of the reaction with only two degrees of freedom. This led us and others to question whether our result was an accident of the simplicity of our model. In our recent paper, we extended the model to a larger number of degrees of freedom. Interestingly, the main result was the same. Namely, the reacting partners still have the possibility of roaming, but the direct path over the break between the barriers is still the most important one.

The article, "Recent advances in the dynamics of molecular systems: Classical, semiclassical, and quantum perspectives,” was recently published at Theoretical Chemistry Accounts 133, 1528 (2014). (doi:10.1007/s00214-014-1528-z) The work was supported by the AFOSR. Equally, importantly, it was a real treat to include our work in an issue published in honor of Greg Ezra's 60th birthday. I have followed his work since I was a graduate student, and have learned much from it. While science is immutable, it’s the fact that people are involved in the discovery that makes it humane. And for this reason, it’s particularly fun to be able to contribute to issues that honor the people involved in advancing science.

Monday, July 14, 2014

Inclusive excellence symposium coming up at ACS San Francisco

Two qualifiers, successful and diverse, for the research enterprise are inseparable concepts. And yet, some members in the scientific community have often treated them as orthogonal if not outright destructively interfering. (Please forgive my geek speak here!) I think that the only part that is destructive is the failure to be inclusive. Indeed, as we are broadening participation in the chemical research enterprise, we are drawing more and better talent from all over the world and this should include that which is within our borders. Unfortunately, we aren't quite there yet as is visible through the existing imbalance in the demographics between the US population and the chemical workforce. Achieving parity requires us to be actively engaged.

To this end, I just published a Comment in C&EN to advertise the upcoming symposium on "Advancing the Chemical Sciences Through Diversity in Participation." (Earlier, I wrote on this blog about why I publish there and here. You can also check out the ChemDiversity Blog post advertising the symposium.) If you happen to be in San Francisco in mid August, feel free to join us at the Hilton near Union Square. You'll learn a few tips for advancing inclusive excellence and you'll be in the middle of San Francisco. Hard to beat that pairing!

Check out the Comment on page 45 of the July 14, 2014 C&EN at this link. (Apologies if it's closed to ACS members and subscribers only.)

Saturday, July 12, 2014

On my experience delivering a webinar...

I recently participated as a speaker in a Webinar for the American Chemical Society (ACS.) It was only the second webinar that I have delivered. My first was held on January 2013 as part of the monthly meeting series of the Lehigh Valley Local section of the ACS. They were an early adopter of the medium. That is, they were quick to figure out that it's cost effective to host speakers from a distance while also addressing a greater number of their members. The latter is particularly important to them because they cover a large geographic area placing any particular choice of meeting location too far from most of their members. My host, Lorena Tribe, helped me learn how to use questions through the presentation effectively in order to engage their web audience. I found the technique to be so successful that I have retained and used the questions (in think-pair-share style) as I present our work (on the energetics of proteins) at department seminars.

As a consequence, when I was asked to participate in the ACS Webinar, I was initially not phased by the opportunity. That is, until I learned that the audience would include nearly 400 participants. Fortunately, the ACS staff was similarly awesome. They provided all the necessary infrastructure and great user support. All I had to do was put my slides together just like I do for any other seminar. The inclusion of my industrial collaborator, Stephen Quirk, framed my otherwise academic discussion into one that was more accessible for a broader (viz. industrial) audience. Plus he did all the hard work of selecting the questions for me to answer during the Q and A. All-in-all my total time investment was probably less than four hours. Moreover, we reached a large audience and one that I probably would not have "seen" otherwise. That's a high benefit to cost ratio which I consider a big win.

If you missed my Webinar on "Digitally Pulling Proteins: Molecular Dynamics Simulations," you might still be able to hear it at At present, it's available only for view by ACS members.

Wednesday, June 18, 2014

Soft materials made up of tricked-up hard particles

Materials are made of smaller objects which in turn are made of smaller objects which in turn… For chemists, this hierarchy of scales usually stops when you eventually get down to atoms. However, well before that small scale, we treat some of these objects as particles (perhaps nano particles or colloids) that are clearly distinguishable and whose interactions may somehow be averaged (that is, coarse-grained) over the smaller scales. This gives rise to all sorts of interesting questions about how they are made and what they do once made. One of these questions concerns the structure and behavior of these particles if their mutual interactions is soft, that is when they behave as squishy balls when they get close to each other and unlike squishy balls continue to interact even when they are far away. This is quite different from hard interactions, that is when they behave like billiard balls that don’t overlap but don’t feel each other when they aren’t touching.

I previously blogged about our work showing that in one-dimension, we could mimic the structure of assemblies of soft particles using hard particles if only the latter were allowed to overlap (ghostlike) with some prescribed probability. In one dimension, this was like looking at a system of rods on a line. We wondered whether this was also possible in two dimensions (disks floating on a surface) or in three dimensions (balls in space). In our recent article, we confirmed that this overlapping (i.e. interpenetrable) hard-sphere model does indeed mimic soft particles in all three dimensions. This is particularly nice because the stochastic hard-sphere model is a lot easier to simulate and to solve using theoretical/analytical approaches. For example, we found a formula for the effective occupied volume directly from knowing the “softness” in the stochastic hard-sphere model.

The work was done in collaboration with my group members, Galen Craven and Alexander V. Popov. The title is "Structure of a tractable stochastic mimic of soft particles" and the work was funded by the National Science Foundation. It was released just this week at Soft Matter, 2014, Advance Article (doi:10.1039/C4SM00751D). It's already available as an Advance Article on the RSC web site, though this link should remain valid once it is formally printed.

Saturday, June 7, 2014

Old-World Publishing in the New Age

Through the web, we can self-publish pretty much anything at any time. This doesn't guarantee, however, that anyone will read it. Actually no venue can guarantee that. Old world platforms such as newspapers, trade publications and journals do have a circulation among their audiences that effectively guarantee a certain number of page views. On the other hand, all-electronic open access journals can serve as such amplifiers as well. Some blogs have become so popular that their number of page views exhibit viral-like growth. So why should anyone publish on the old-world platforms?

That's a loaded question, and truly one that has many possible good arguments to support it. I'll rest on providing one answer by example.  I recently published a Comment in C&EN. The piece was quite a bit longer than my usual blog post. As such, it would have been appropriate for my EveryWhereChem blog only if I broke it up into about three posts. There is one more key difference. I was able to work with an editor who helped me to focus the piece while allowing me to retain my "voice." My prose was probably a bit too breezy, but she embraced it and made it better. Trouble is that editors need to be paid and one might argue that authors do too! While this and other quality control mechanisms are not exclusive features of the old-world publishing model, they are certainly a large part of the service that authors and readers enjoy from them. They also serve as curators of the pieces that they publish. And this means that a good editor can exert a meta-level quality control that adds value to the readership. There's also a role for blogging as otherwise I wouldn't be writing this too. My postmodern view of the so-called traditional publishing venues is that they remain valuable even if we aren't sure how to monetize it as readily as we once did.

My C&EN Comment focused on Mentoring and the key role if fills in advancing young scientists into their careers. Most new faculty learn the job on the job. As the demands and the tenure decision pressure have grown, it is nearly impossible to figure out the job without help. This is where mentoring can play a big role.  The New Faculty Workshop is one attempt to institutionalize mentoring across all of the chemistry research- active departments. I wrote about my experience at last year's New Faculty Workshop in two earlier posts on July 6 and July 16. The next workshop being held on July 31-August 2, and I'm looking forward to meeting the newest cohort of young faculty.

Check out my my March 24th Comment in C&EN on “Mentoring New Faculty—It Really Works!” and John Schwab’s letter to the editor on May 19th reiterating the “Importance of Mentoring” in response to my Comment.

Monday, May 5, 2014

Stability within field induced barrier crossing (#APSphysics #PRE #justpublished)

Suppose that a 5' foot wall stood between you and your destination. In order to determine if and when you got to the other side, all you'd have to do is stand at the top of the wall and check when you got there. (Presumably falling down to the other side from the top would be a lot easier than getting to the top.) If, instead, there was a large mob of people trying to get across the wall, we'd have to keep track of all of them, but again only as to when each got to the top of the wall. This kind of calculation is called transition state theory when the people are molecules and the wall is the energetic barrier to reaction. The key concept is that the structure—that is, geometry—of the barrier determines the rate, and this geometry doesn't move.

If the wall were to suddenly start to slide towards and away from where you were first standing, then it might not be so easy to stay on top of it as you tried to cross over. Certainly, an observer couldn't just keep their eyes fixed to a point between the ends of the room because the wall would be in any one spot only for a moment. So is there still a way to follow when the reactants have gotten over the wall—that is, that they are reactants—in the crazy case when the barrier is being driven back-and-forth by some outside force? My student Galen Craven, our collaborator Thomas Bartsch (from Loughborough University), and I found that there is indeed such a way. The key is that you now have to follow an oscillating point at the same frequency as the barrier but not quite that of the top of the barrier. In effect, if the particle manages to cross this oscillating point, even if it hasn't quite crossed over the barrier, you can safely say that it is now a product. There is one crazy path, though, for which the particle follows this point and never leaves it. In this case, it would be like Harry Potter at King's Cross station never choosing to live or die. That's the stable path that we found in the case of field induced barrier crossing.

The title of the article is "Persistence of transition state structure in chemical reactions driven by fields oscillating in time." The work was funded by the NSF, and the international partnership (Trans-MI) was funded by the EU People Programme (Marie Curie Actions). It was released recently as a Rapid Communication at Phys. Rev. E. 89, 04801(R) (2014). Click on the PRE Link to access the article.