Saturday, April 4, 2015

Balls of ice cream

When you go to your local ice cream shop, you likely ponder the question of how many scoops you wish to order. I, on the other hand, prefer to order balls of ice cream. The scoop corresponds to the void that is to be filled, but a ball corresponds to the filling. It seems to me that I'd rather order balls of ice cream rather than empty space. My wife suggests that this is just a matter of my literal mistranslation of "bolas de helado" rather than any deeper significance over the ontology of balls verses scoops. As an optimist, I certainly prefer for them to be more than half-filled, and hence naturally prefer balls of ice cream to voids, that is scoops.

This argument extends to the nanoscale. Are the properties of a particle driven by itself or by the space which it occupies? If the latter, then its properties are independent of the nanoparticle aside from its shape. As a chemist, this is a disappointing possibility because I would like to tailor the properties of the particles, such as how they assemble, by changing the atoms or molecules at the surface (and the interior). The good news is that such control can be exercised. That is why we have been studying so-called Janus particles and other patchy particles. In our rendering, they look like ice cream balls made of blueberry and strawberry ice cream halves or layers.  The blueberry faces like to face the strawberry faces (because they correspond to charges and opposites attract), and this gives rise to their interesting patterns and response to changes from the outside.

Check out our some of our recent papers on Janus and striped particles and stay tuned for the next ones!

M. C. Hagy and R. Hernandez, "Dynamical simulation of electrostatic striped colloidal particles," J. Chem. Phys. 140, 034701 (2014). (doi:10.1063/1.4859855)
M. C. Hagy and R. Hernandez, "Dynamical simulation of dipolar Janus colloids: Dynamical properties," J. Chem. Phys. 138, 184903 (2013). (doi:10.1063/1.4803864)
M. C. Hagy and R. Hernandez, "Dynamical Simulation of Dipolar Janus Colloids: Equilibrium Structure and Thermodynamics," J. Chem. Phys. 137, 044505 (2012). (doi:10.1063/1.4737432)

Tuesday, March 31, 2015

Controlling chemical reactions by kicking their environs

Chemists dream of controlling molecular reactions with ever finer precision. At the shortest chemical length scales, the stumbling block is that atoms don’t follow directions. Instead, we “control” chemical reactions by way of putting the right molecules together in a sequence of steps that ultimately produce the desired product. As this ultimate time scale must be sufficiently short that we will live to see the product, the rate of a chemical reaction is also important. If the atoms don’t quite move in the right directions quickly enough, then we are tempted to direct them in the right way through some external force, such as from a laser or electric field. But even this extra control might not be enough to overcome the fact that the atoms forget the external control because they are distracted by the many molecules around them.

In order to control chemical reactions at the atom scale, we are therefore working to determine the extent to which chemical reaction rates can be affected by driven periodic force. Building on our recent work using non-recrossing dividing surfaces within transition state theory, we succeeded in obtaining the rates of an albeit relative simple model reaction driven by a force that is periodic (but not single frequency!) in the presence of thermal noise. It is critical that the external force is changing the entire environment of the molecule through a classical (long-wavelength) mode and not a specific vibration of the molecule through a quantum mechanical interaction. The latter had earlier been seen to provide only subtle effects at best, but the former can be enough to dramatically affect the rate and pathway of the reaction as we saw in our recent work. Thus while our most recent work is limited by the simplicity of the chosen model, it holds promise for determining the degree of control of the rates in more complicated chemical reactions.

This work was performed by my recently graduated student, Dr. Galen Craven, in collaboration with Thomas Bartsch from Loughborough University. The tile of the article is "Chemical reactions induced by oscillating external fields in weak thermal environments."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 at J. Chem. Phys. 142, 074108 (2015).


Sunday, February 15, 2015

Blog Post #100 - Looking Back & Looking Forward

This is my 100th post. The first 99 posts have already received over 31,000 page views. The rather eclectic mix of my posts is visible in the top 5 viewed posts:

* 924 views:   Keep your outline to yourself! (A random walk through... (Jan 27, 2014)
* 634 views:   6. The blurring of physical chemistry and chemical... (Aug 14, 2013)
* 419 views:   Chemistry is Everywhere (My first post on Apr 27, 2013!)
* 412 views:   Advancing Science Through Diversity #OXIDE #Telluride... (Jun 24, 2013
* 356 views:   Soft materials made up of tricked-up hard particles... (Jun 18, 2014)


As traditional publishers have long known, how-to books and articles do well, and my post giving tips for delivering better scientific presentations is at the top. On the other hand, a historical view of physical chemistry and chemical physics also found an audience. A post reporting on our recent theoretical and computational research work has done well. Our discussion of diversity also found an audience. There is no telling how well such page views correlate with each other. For example, are readers of the diversity-related articles interested in my science publications or in my off-beat observations about the underlying science of a rock?

All of these analytics are catnip for scientists who crave hard data to support the impact and importance of our work. The h-index (named after Jorge Hirsch), for example, attempts to quantify the impact of a scientist’s oeuvre through a cumulative but tempered accounting of the citations that their work has received. It’s of practical use because it’s very hard to compare different scientists. On the other hand, the h-index is wrought with confounding factors… The larger the field, the more citations every paper within it receives; membership in groups of prolific scientists who happily follow each other’s work gives a happy boost to all; advances in “hot” areas will necessarily receive more attention; the Matthew effect; the longer the scientist's career, the higher the h-index; and the list goes on. Such factors, though seemingly giving some scientists advantages over others, are not necessarily positively uncorrelated with their impact. And the h-index has become a metric that nearly every scientist detracts, but simultaneously follows with equal interest.

So looking at the analytics of my posts, I am simultaneously humbled and dismayed. I never expected that there would be, on average, more than 300 page views per post. This number is likely more than what my scientific articles receive. The latter have been peer-reviewed and have advanced science, but have they directly touched nearly as many lives as my posts? On the other hand, 300 page views pales in comparison with some of the more established science bloggers, and is far surpassed by anything that LeBron James or Taylor Swift tweets by a factor of, like, infinity. So I’ll keep posting, if only because thankfully you, dear reader, are still reading, and hopefully I’m providing you with some outside-the-box perspectives not available elsewhere.




Monday, January 26, 2015

The Sight and Sound of Science

How do you process music? Do you let the music flow over you? Do you translate the sound to notes? Do you look at the fingering and movement of the player? The answers perhaps depends on your level of knowledge and talent in the instruments that generate the music. The beauty of music is that you can enjoy it at any or all of these levels. I would argue that it is the same for science. Whether the details are in the equations or in the instrumental apparatus, you can still enjoy the phenomenon. 

When you look at the sky during the day or at sunset what do you see? It’s likely you’ve noticed that the sky is blue, and sunsets are red. I see that too, but I also think about the jumble of collisions between photons and the particles in the sky. The red photons are less likely to be back scattered than the blue ones… So in the end, the red ones get jumbled less, and reach my eye directly as the sun is setting. The blue photons scatter more and spread across the sky. Each of those trajectories involves equations describing the motion of the photons and one could try to follow them too. But actually, there are so many that no one can really follow them all. Instead, it is their emergent behavior that can be tracked in some collective way. You might think that that emergent dance of photons is all of the beauty in and of itself. You, like me, might find all the fun in determining the governing equations and finding their solution. Or you might remain steadfast that the beauty lies in a visually arresting sunset as if it were a painting. Regardless, the beauty comes out from science! 

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!