Monday, May 25, 2015

Stretching proteins and myself into open access (OA)

I'm not sure where to side on the Open Access (OA) publishing business. On the one hand, paying for an article to be published is a regression to the days of page charges albeit without the double-bind that readers are also required to pay. On the other hand, it does flatten access to the article, and often panders to enlightened self-interest by way of increased exposure and citations. Indeed, a strong argument in favor of OA for articles, data and code was just published in the Journal of Chemical Physics by my friend, Dan Gezelter. (Fortunately his Viewpoint is OA and readily available.) Regardless, publishers need to cover their costs, and here lies the challenge to the scientific community. The various agencies supporting science do not appear to be increasing funding to subsidize the fees even while they are making policy decisions to require OA. Libraries love OA because it might potentially lower their skyrocketing journal costs, though no substantial lowering appears to have yet occurred. Long story short, my group is now doing the experiment: We recently submitted and just published our work in PLoS (Public Library of Science.) Props to them for being consistent as they also required us to deposit our data in a public site. I was also impressed by the reviewing process which did not appear to be lowered in any way by the presumed conflict-of-interest that a publisher might have to accept papers (and associated cash) from all submissions. The experiment continues as I'll watch to see how our OA article fares compared to our earlier articles on ASMD in more traditional journals.

Meanwhile, we are excited about the work itself. My students, led by outstanding graduate student, Hailey Bureau, validated our staged approach (called adaptive steered molecular dynamics, ASMD) to characterize the energies for pulling a protein apart. The extra wrinkle lies in the fact that the protein is sitting in a pool of water. That increases the size of the calculation significantly as you have to include the thousands (or more) of extra atoms in the pool. The first piece of good news—that we had also seen earlier—is that ASMD can be run for this system using a reasonable amount of computer time. Even better, we found that we could use a simple (mean-field) model for the water molecules to obtain nearly the same energies and pathways. This was a happy surprise because, for the most part, the atoms (particularly the hydrogens) on the protein appear to orient towards the effective solvent as if the water molecules were actually there.

Fortunately, because of OA, you can easily read the details online. The full reference to the article is: H. R. Bureau, D. Merz Jr., E. Hershkovits, S. Quirk and Rigoberto Hernandez, "Constrained unfolding of a helical peptide: Implicit versus Explicit Solvents," PLoS ONE 10, e0127034 (2015). (doi:10.1371/journal.pone.0127034) I'm also happy to say that It was supported by the National Science Foundation.

Wednesday, May 6, 2015

Using dice, fuzzy or not, to move molecules

We just published what might seem as yet another paper describing the properties of our model for (coarse-grained) large-scale macromolecules. A critical part of the model is that we roll dice every time these particles collide so as to decide whether they bounce or go through each other. They can go through each other because at long enough length scales, they don't behave like rocks even if they are corpuscular unlike fluids. Despite our simple (and dicey) model, in our earlier papers, we showed that our particles give rise to the same structure as the corresponding particles that would interact through typical (so-called soft) interactions. But Einstein's famous quote about God not playing dice with the universe (albeit in a different context) serves as a warning that our particles might not move in analogous ways to those driven by Newton's deterministic laws. In our most recent paper, we confirmed that our particles (if they live in one dimension) do recover deterministic dynamics at sufficiently long (that is, coarse-grained) length scales. That's a baby step towards using our model in human-scale (three) dimensions. So there are more papers to come!

The work was performed (and the paper was written) with my recent Ph.D. graduate, Dr. Galen Craven, and a Research Scientist, Dr. Alex Popov. It's basic research and I'm happy to say that It was supported by the National Science Foundation. The title of the article is "Stochastic dynamics of penetrable rods in one dimension: Entangled dynamics and transport properties," and it was recently published at J. Chem. Phys. 142, 154906 (2015).

Monday, May 4, 2015

Monthly Status Reports (A random walk through how I run my lab, Item 4)

In the business world, or in "Office Space," everyone has seemingly heard of the TPS that must be submitted to your boss at arbitrary (but far too often) frequency. More annoyingly, the TPS often appears to remain unread serving only to occupy one's time with busy work. So it is with ironic amusement that I rediscovered this tool so as to improve the efficiency of my lab. After all, theorists are out-of-the-box thinkers who don't want to be constrained by the mundane, right? And yet this monthly task is exactly the extra structure my students needed to maximize their progress, liberating them to not even see the "box."

For nearly two years, I have asked my students to submit a Monthly Status Report (MSR). It includes only four components: accomplishments, accountability, goals, and pain-points. The goals include not just what is to be done in the next month, but also their overarching plans. In accountability, they summarize what was performed with regards to the previous month's goals. If they succeeded with all of their goals, then that serves to calibrate a more ambitious plan for the following month! The pain-points provide a quick summary of which items I might need to help them with or which I am overdue on. (Yes, I also need help keeping all the balls in the air!) The MSR needs to include items regarding their educational plan, and not just their research projects. To this end, I ask them to include a running clock of the time spent as a graduate student or postdoc. The clock increments by one month each time, of course. The total number, though, reminds us to track professional development activities appropriate to the student's educational timeline. The key to insuring that this is not a totally pointless exercise is that the MSR is followed by a 1:1 thirty-minute meeting discussing progress and charting out meetings and tasks for both student and me to follow up on. I've found that this "meta" meeting is critical to ensuring that both the student AND her or his projects succeed. When I had a smaller group, the MSR wasn't necessary, but now it's critical. I have found it to be more effective than the annual Individual Development Plan (IDP), if the latter is done exclusively, because the IDP is yearly and that feedback isn't often enough. Indeed, the MSR makes the IDP easy for students to complete and increases the effectiveness of the IDP.

Again, the MSR is a simple tool from business school 101, but don't scoff it if you want to help your students increase their productivity and maximize what they learn in graduate school. The key is to use it as a vehicle to hold a frequent and periodic conversation between you and every one of your students!


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!