Wednesday, December 24, 2014

Engaging with Your Audience No.2: Think-Pair-Share

What’s wrong with delivering a research lecture as a sage at the stage? It is after all the format that research seminars have always been delivered in. It's also the equivalent of TV's talking heads. In the humanities, the lecturer typically reads from carefully crafted prose while sitting in front of a desk at the front of the room. In the sciences, we go comparatively rogue by standing and presenting extemporaneously using our slides to provide visuals and pacing, but otherwise remain standing far in front of our audience. Either of these delivery mechanisms are stately, befitting the seriousness of our enterprise. Unfortunately, it also creates a barrier between the speaker and the audience. Using interactive approaches does more than keep your audience awake, it also helps them internalize the material.

My current favorite teaching modality is the so-called think-pair-share method. It can be implemented using clickers, but it's just as easy to use a sheet with large preprinted letters or even with hands showing varying numbers of fingers. I often use the latter when I give research seminars. It's an unexpected request of the graduate students and professors. Perhaps not surprisingly such an audience is inclined to make it a competitive sport in which they are most concerned about getting the right answer. If my answer doesn't agree with theirs, they will sometimes argue to the contrary. I actually don't care if they get the right answer at the start, but rather that they become engaged in finding an answer and subsequently learn the answer. Similarly, in my classroom, it also helps break the stress of lecture while giving my students an opportunity to reflect not just on the question but also the entire narrative of that day's lecture.

I'm sure that my implementation of think-pair-share is noncanonical. I start by reading the question. I then poll students. If nearly everyone gets it right, I summarize the correct reasoning behind the answer and move on. If not, I will ask them to pair with a classmate, and give them some time to discuss. If they collectively get the right answer after a second poll, then I summarize the rationale and move on. Otherwise, depending on the question and the distribution of their answers, I give them an opportunity to share with the class, give them hints, repoll, etc. Eventually, we're all on the same page, but more importantly the process itself allowed them to learn the concept. Thus think-pair-share is neither an assessment tool nor an extra part of the lecture. It is the way in which we discuss a particular concept for the first (and likely last) time.

N.B., I’m also not afraid to interact with my audience through visual metaphors such as stunt punching a volunteer audience member (as described in an earlier post), or using them as props in describing Brownian motion...

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.

Monday, August 18, 2014

Taming the multiplicity of pathways in the restructuring of proteins

The average work to move molecular scale objects closer together or further apart is difficult to predict because the calculation depends on the many other objects in the surroundings. For example, you might find if easy to cross a four-lane street of grid-locked cars (requiring a small amount of work) but nearly impossible to cross a highway with cars speeding by at 65mph (requiring a lot of work.) When the system is a protein whose overall structure is expanded or contracted, there exist a myriad possible configurations which must be included to obtain the average required work. Such a calculation is computationally expensive and likely inefficient. Instead, we have been using a method (steered molecule dynamics) developed by Schulten and coworkers based on Jarzynski's equality. It helps us compute the equilibrium work using (driven) paths far outside of equilibrium. The trouble is that the surroundings get in the way and drive the system along paths that get out of bounds quickly.

In previous work, we tamed these naughty paths by reigning them all in to a tighter region of structures. Unfortunately, this may be too aggressive.  The key is to realize that not all paths are naughty. That is, that there may be more than one region of structures that contribute significantly to the calculation of the work. We found that we could include such not-quite-naughty paths and still maintain the efficiency of our adaptive steered molecular dynamics. I described the early work on ASMD in my recent ACS Webinar.

This research project was truly performed in collaboration. My recent graduate student, Gungor Ozer, did the work while he was a postdoc at Boston University. Tom Keyes hosted him there and gave great insight on the sampling approach. Stephen Quirk, as always, grounded us in the biochemistry.

The title of the article is "Multiple branched adaptive steered molecular dynamics.” The work was funded by the NSF. It was just released at J. Chem. Phys. 141, 064101 (2014). Click on the JCP link to access the article.

Saturday, August 9, 2014

Lost in Projection

Life is full of cycles. For the American Chemical Society (ACS), there’s a National Meeting held every 6 months. With that as my time constant, it feels as if it was just the other day that I gave the Keynote Lecture at the ACS Committee on Minority Affairs Luncheon at the last National Meeting in Dallas. Last March, I framed my remarks through the title of this post. I knew that it was a good title because my wife liked it. But she also wondered what in the world I would talk about under such a title. This seemed fortuitous. It meant that I could say nearly anything without disappointing the audience. After all, they couldn't possibly have any expectations. In truth, the title wasn’t advertised as evidence by the large turnout.

What is lost in the projection of how others frame you? That is, there is a potential disconnect between what others expect of you and the person who you believe yourself. To what extent are you bound by what others expect of you? Such expectations may arise from how others have seen you in the past or perhaps by who they see on first impression. I came to the United States as a child, a Cuban immigrant who spoke no English but proud to be able to count from one to ten without too much of an accent. Children grow and learn so surely I cannot be bound by that early frame. As adults, we may not grow physically, but we also learn. And yet, we have a tendency to hold others to the frames that we first see of them. Even more dangerous to each of us is the fact that the frame is often projected onto us by others, and not always correctly. There were several young scientists in the room. During the question and answer period, they echoed the angst of having felt bound by such projections in the past. I hope that I succeeded in encouraging them to find their way in breaking those projections and choosing their own frame.

The cycle continues this weekend with the start of the ACS meeting in San Francisco. If you are here, I encourage you to go to Monday’s CMA Luncheon where Madeleine Jacobs will be speaking. The issue of implicit bias and the effects that has on academic careers will also be a large piece of the Symposium on Advancing the Chemical Sciences Through Diversity to be held at the Hilton San Francisco Union Square Hotel all-day on Tuesday. I hope to see you there!

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, "Revisiting roaming trajectories in ketene isomerization at higher dimensionality,” 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.

Monday, April 28, 2014

The Academic Juggle: Hallows or Horcruxes

Every day, entering the office, I face the question of whether to write papers or grant proposals amidst the flood of other tasks. Yes, we all have to deal with managing time lines. But the question is akin to the one that Harry Potter faced when trying to decide between chasing after horcruxes or hallows. The horcruxes represent the immediate problem. The hallows offer the possibility of solving this and any other problem. In the fictional case, the hallows are also the temptation to become evil. Focusing on them would likely be done at the expense of ridding the world of the latest evil, Voldemort, and would also lead Harry to become evil. This is the Faustian bargain revisited. Like Goethe before us, let's remove the unfair rule that one isn't dammed just for playing. The question then centers on how we should balance our time on the short-term versus the long-term. That is, without papers, you won't earn the next grant, but if you never write grants, then you won't have funds to do the research that you will document in your next journal article.

Some researchers love to write articles because it is part of their process to do the research, diving deeply into the details that you have to get 100% right or else the logic of the paper falls. Some researchers love to write grants because they enjoy thinking about the possibilities that have yet to be explored without having to worry about the details that might muck it up. Still others enjoy neither because they dislike the toil of writing let alone the fact that it takes you away from actually doing the research. Or perhaps you prefer to do something else entirely, like writing blog posts? Regardless, you have to choose between hallows or horcruxes, not just the one time as Harry did, but every day.  It is the daily need to make a conscious choice over the prioritization of articles, grants, and everything else that makes being an academic researcher both challenging and exciting. We're not Harry Potter. We don't have a wand. We can't make (unexplainable) magic. We don't have the glasses. O.k., maybe we do have the glasses. But we do get to choose our own adventure as we as advance the limits of our understanding.

Friday, March 14, 2014

Failure is an option

Most of the time, baseball batters strike out. Many football passes end in incompletions and sometimes interceptions. Dunks sometimes bounce out. Goals get scored past goalies. Yet the players still remain on the field. That's because without the possibility of these failures, they wouldn't be able to make great plays. The lesson is that the players on the starting squad aren't there because of their lack of failures, but rather, because they make enough outstanding plays to make up for their comparatively infrequent failures.

So why is it that we tend to expect that our research scientists (and professors) be infallible? Except for public performances (like when we are teaching or lecturing), we do have the opportunity to edit and refine our work before it is embedded in the literature thereby avoiding some failures. Nevertheless, typos, misplaced theories, erroneous results, incorrect analyses, and other such failures manage to be written by us. But this is not the worst offense. I would put forth that the biggest problem is that we don't have more magnificent and more frequent failures. After all, such bright failures can only arise if scientists launch truly ambitious programs that just went too far outside the box. But the risks are too great for most scientists to make such bold leaps. If she or he fails, then there will surely never be funding for another idea (no matter how conservative.)

The trouble with highlighting examples to give this blog topic substance is precisely the fact that failures are not  reported and the victors rarely want to discuss the torturous path it took them to get there. Here lies the fundamental problem inhibiting the next generation of truly innovative research. At present, the funding models are too conservative. Review panels focus on preliminary results —read several papers already published— and proven accomplishment —read established lab with over 10 years of operation. It's hard to fault them because the risks for both the individual researcher and the individual sponsor are great. It's simply too risky to include failure within the realm of possible outcomes even when the potential is high. The true loser of this game is society because the growth of science is partly stunted. The solution has to be for institutions and funding agencies to provide a safety net for researchers that stray far outside the box. And failure has to be an option.

Saturday, February 22, 2014

Seeing chemistry through an Olympic lens and beyond

If science were an athletic pursuit, then chemistry would be a sport. Each of our chemistry departments would be like a team in the Olympics (think Nordic skiing). In chemistry departments, each faculty member competes in a given event such as organic chemistry (think biathlon), analytical chemistry (think cross-country) or computational chemistry (think jumping). To be successful we must conduct our scientific programs to be world (or better, international) class. The commitment that each faculty member must put in towards success is priceless. She or he must work countless hours, read and write papers, read and write grants, and sharpen their skills to see what has never been seen before. Scientists don't do this alone, of course. They build research groups of students and professionals that are critical to doing the work and advancing the ideas while at the same time they are being trained towards their own career objectives. The sacrifices are consequently not borne exclusively by the principal investigator. Looking at the winter Olympics over the past couple of weeks, it is clear that while any given athlete wins a medal, there is a corresponding team of people that is essential to the success and who share in the excitement of victory.

Just like Olympic events, some areas of chemistry are more "exciting" than others at any given moment. From time to time, new events such as materials or sustainable chemistry come along and they receive special attention (both in terms of funding and presence in the hot journals). That means that depending on your event (or research area), there are varying amounts of support available. But you can't work any less hard if you are to be the best in any given event. And there lies the problem. You have several teams of chemists in a department, all undertaking world-class research, but some have more money than others to do it. It's clear that Olympic sporting committees face the same problem. A few figure skaters, for example, are pulling in millions of dollars in endorsements while some of the bobsledders practically had to pay their own way to Sochi. So in the Olympic spirit, it is essential to look for ways to fund all the scientific events and their "athletes" well so that we are competitive across the board. The payoff for investing in science (and chemistry in particular) goes beyond the medals as the solutions that we create literally transform the human condition.

Monday, January 27, 2014

Keep your outline to yourself! (A random walk through how I run my lab, Item 3)

The best talks (presentations) are the ones that look completely unrehearsed, but for which the speaker's extemporaneous talent somehow causes them to hit every high and low dead on. That can only be achieved with tremendous preparation. To that end, I encourage my students to practice their presentations often. I ask them to present at least once, often twice, in one of our research group weekly meetings, to present it in front of my research group (without me present) at least once more, and to send me the slides several times for feedback. Depending on the importance of the venue, I also ask them to practice it in my office. In that setting, I often video record them. This ensures that they are not as relaxed as they would be in a one-on-one setting. It also gives them a recording that they can use to self-analyze their performance. Repetition alone is not enough because inherent mistakes will persist unless they are checked. As such, it is important that every practice presentation be followed by a lengthy critique.

Here follows a necessarily incomplete set of suggestions on how to deliver a better science presentation:

  1. Lead with an example that is cool and illustrative of the problem that you are solving in your work. (Make sure to tell the audience the problem that you are trying to solve!)
  2. Tell the audience your solution of the problem early on. This is not a detective story.
  3. An outline slide should consist of phrases unique to your presentation. There is no need to have a bullet called "introduction" because you are evidently already doing this. There is no need to have a bullet called "conclusion" because everyone in the room knows that you will eventually stop talking. Don't have a bullet called "method"; instead write the name or names of the unique methods that you are using. 
  4. Don't wear anything that will distract the audience.
  5. Don't wear anything that will distract you. 
  6. Your presentation is an opportunity for you to teach the audience about the work that you have done. It doesn't matter if there are one or more Nobel Prize winners in the room. You are the only expert about your work in the room.
  7. Busy slides are worse than no slides at all.
  8. Each slide requires at least one minute of air time, if not more.
  9. Colored text should be used sparingly and intentionally to highlight or associate text.
  10. Animations should be used sparingly and intentionally to highlight or associate concepts or transitions in your presentation.
  11. Text should be used as cues to you and the audience in an abbreviated form, and not in long narratives to be read. (Occasionally important quotes may be necessary.)
  12. Text and figures should be large enough to be visible in the back of the room.
  13. Each slide (particularly those showing data, a figure, or some other kind of result) should be shown for a reason. Make sure to include prompts or bullets for each such reason.
  14. Appropriate literature citations should be included within each slide, not at the end. 
  15. All images and movies not created by you should be appropriately credited with references. This includes the ones that you "borrowed" from Wikipedia.
  16. Do not speak in a monotone; a little enthusiasm goes a long way.
  17. Look at your audience. If they appear to be inattentive, then throw in some relevant metaphor to bring them back in at the next pre-planned point in your presentation. (That means that you should have such examples at the ready to be dropped in at various places in your presentation.)
  18. Detailed equations, algorithms, methods and/or lab set-ups are cool and you worked really hard to make them. But nearly no one wants to see them in a brief presentation. Try to have at most one such slide so that you may indicate how it was done without losing your audience in a quagmire of details. Have extra slides at the ready in case someone asks for such detail during Q and A.
  19. It's hard to keep anyone's attention longer than 5 minutes or so. This means that you need to stop once in a while to remind the audience where you are in the story you are teaching them.
  20. Good lecturing is good teaching. Think about using techniques from research-based education research (DBER) in your presentation. (For example, active learning!)
  21. Feel free to violate any rule above if it makes your presentation better as long as it is not intellectually dishonest to do so.

I welcome more tips to be added to this list through your comments!

(This is the third post in a series of items on how I run my lab. Check out the list here.)

Tuesday, January 21, 2014

The relaxation of striped spheres… ( #AIP_JCP #justpublished )

When was the last time that you took a bunch of pool balls, suspended them in a thick oil, and watched how they assembled? Pool balls being what they are, they will simply stack on themselves, though there is some question as to how efficiently they do so. If you start to shake the container, thereby maintaining some average kinetic energy (that is, temperature), they probably started to jiggle. They probably won't rotate much. Even if they do, it won't matter much because they collide with each other in the same way no matter what. So now take the balls and paint them with some pattern of red and blue paint, and suppose that there is a difference in the forces between the spheres depending on which colored surfaces are near each other. Now when they collide with each other, they have preferred relative orientation. The emergence of structure (or patterns in the positions and orientation) of the pool balls should presumably be very sensitive to how you painted them.

This is precisely the problem that Matthew Hagy and I have been studying over the past couple of years. Our pool balls are actually colloidal particles of a couple hundred nanometers in diameter. The paint corresponds to the charges encoded on the surface of the colloids. Opposite charges attract. Initially we studied Janus particles that literally have two faces, one hemisphere is positively charged and the other negative. (If interested, you can also check out my earlier blog post on the dynamics of Janus particles.) In the work that was just published in the Journal of Chemical Physics, we now consider the case in which the spheres are coated in stripes of alternating charge. This generalizes the surface pattern of the Janus particles to three, four, five, six, and more stripes. The funny thing is that very little happens to the packing of the particles because that property is so strongly dominated by the shape of the particles. But their motion, and the timescales in which they relax from a given deformation is highly sensitive to the number of stripes and perhaps also to how they are striped. In a sense, this says that if you want to maintain their behavior, you can fatten them up a little but you can't change their stripes.

The title of the article is "Dynamical simulation of electrostatic striped colloidal particles," and the work was funded by the NSF. It was released recently at J. Chem. Phys. 140, 034701 (2014), and featured on the cover!  Click on to access the article.

Friday, January 17, 2014

Power of analogies in science

If you know how a basketball spins on each of its axes, then it turns out that you also know how a classical methane molecule spins. Such analogical pairings are useful because they allow you to better understand the less familiar of the pair through what you know of the other. The trouble, of course, is that analogies are often imperfect. Not every property is directly connected between the pair. So you have to be careful to assign which are mappable. For example, you certainly won't be able to play basketball with methane despite the analogy with respect to rotations.

Meanwhile, mapping a problem to one that is even more difficult to solve sounds like a bad idea. But if the more difficult problem solves itself them you just might win out after all. Toshiyuki Nakagaki and his colleagues at Hokkaido University did just this, twice. First, they showed that they could map simple mazes onto a board in which mold could grow. It turns out that after a while, the mold grows best along the shortest path between the ends. It would be very difficult to simulate the mold growth, and yet the analogy allows the mold to solve a complicated optimization problem for us. It turns out that you can replace the maze with a real problem related to finding the best possible train network connecting some number of cities over a selected terrain. Now the mold can be used to find the optimal rail network. For each of these two analogies, Toshiyuki Nakagakii received ig Nobel awards. I mention him, in particular, because I got a chance to meet him while I was in Japan. And now, I wonder if I might be able to map the solution of a chemical reaction pathway to his mold growths?!

In detail, the dates and prizes of the teams recognized by ig Nobels for mold growths mentioned above are:

2008 ig nobel in Cognitive science: Toshiyuki Nakagaki, Hiroyasu Yamada, Ryo Kobayashi, Atsushi Tero, Akio Ishiguro, and Ágota Tóth, for discovering that slime molds can solve puzzles.

2010 ig nobel in Transportation Planning: Toshiyuki Nakagaki, Atsushi Tero, Seiji Takagi, Tetsu Saigusa, Kentaro Ito, Kenji Yumiki, Ryo Kobayashi of Japan, and Dan Bebber, Mark Fricker of the UK, for using slime mold to determine the optimal routes for railroad tracks.

Monday, January 6, 2014

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.