Friday, June 28, 2013

Tricking hard collisions into soft interactions(#AIP_JCP #justpublished)

One of the simplest ways to describe atoms or molecules is to pretend that they are balls with some effective diameter (roughly on the order of nanometers.) If you ignore the fact that they can collide, you recover the ideal gas law you might remember from college chemistry classes. On the other hand, because they occupy space, they must collide. These collisions can be "hard" if the balls are treated like billiard balls that hit each other without changing their shape. But actual molecules are more like tennis balls in that they deform during the collision and the nearest approach depends on their velocities. That is, molecular-scale particles undergo soft interactions. Unfortunately, it takes a lot more computational effort to simulate soft particles and we'd like to avoid the extra expense. The question my coworkers and I asked is whether we could mimic soft particles using a model in which the particles moved like hard particles some of the time and like ideal particles the rest of the time. It's a little tricky because the ideal gas particles don't occupy space so we had to calculate the effective density of a given system as a function of the degree to which the particles collided with each other as hard or soft. Meanwhile, the comparison between our model and corresponding soft particle systems with the same density gave us similar structure! We intend to use this model to understand more complicated reactions, and the degree to which we can understand the behavior of complex solvents that interact with the reacting system at comparable time scales.

The title of the article is "Stochastic dynamics of penetrable rods in one dimension: Occupied volume and spatial order" and the work was funded by the National Science Foundation. It was released just this week at J. Chem. Phys. 138, 244901 (2013). (doi:10.1063/1.4810807).

Wednesday, June 26, 2013

On a workshop on Dynamics in Complex Environments at #TellurideScience (TSRC)

In 2001, I co-organized my first TSRC Workshop on the Chemical Dynamics in Complex Environments (CHEM-DiCE). We've held this workshop biennially ever since, and the latest meeting of our group convened on June 25th! That's 7 workshops across 13 years with about 100 scientists. Not more than that because several of our participants (such as myself!) come back. Following the spirit of the TSRC workshops, we have always aimed to include participants in equal numbers whose research centers in theory or experiment. Meanwhile, computational science is well represented because simulations are invariably performed by both!

The term "complex environments" was relatively new back when we started, but is now much more prevalent. The idea behind the term was motivated by the need to create a contrast to systems—such as reacting molecules or folding proteins—that exhibit complex motions—dynamics—regardless of their surroundings. Meanwhile, large surroundings can do amazing things, such as crystallize or conduct, nearly independently of any given atom or molecule within it. So we wanted to put this together, and ask about small systems that are strongly interacting with their surroundings and vice versa. It turns out that such dynamics in complex environments occurs in many subfields of chemistry and physics. So our TSRC workshop brings in experts from three or four such subfields that usually don't overlap at typical meetings. The presentations focus on theoretical and computational techniques have helped a given subfield and what puzzles remain. Such techniques may be useful for the other subfields or may have analogues that hadn't been previously connected. It's common for a speaker to spend most of their allotted hour answering fundamental questions that allows the rest of the group to better understand what they are doing. Going that deeply into the concepts underlying someone else's science enables a cross-pollination of ideas that is difficult to do in other venues. (In financial speak, I would reiterate this statement by saying that collaborative culture spanning different market segments is an integral component of the value proposition for staging and attending TSRC's!)

Monday, June 24, 2013

Advancing Science Through Diversity #OXIDE #TellurideScience #TownTalk

This week, I'll be talking about diversity with the public in the town of Telluride. Is such social science, presented by a molecular scientist, appropriate as a Telluride Town Talk on Molecular Science? This is a venue in which scientists typically speak about their research or their scientific interests in a context accessible to a general audience. It could be human health or climate change. In 2000, I spoke about the analogies between proteins and glasses, and in 2009, I spoke about social, economic and chemical networks. These topics are complex in the sense that they involve many particles that interact strongly with each other. However, they all act rationally. As such, they are not nearly as complex as problems in the social sciences in which individual agents—that is, humans—often act rather irrationally. The Open Chemistry Collaborative in Diversiy Equity (OXIDE) lies at the intersection of these fields. Our perhaps daunting task is to transfer the knowledge gained from the social sciences into reframed professional practices within academic chemistry departments in which diversity inequities are entirely eliminated. Ultimately, we expect that this will lead to demographics within our profession that are comparable to those of our nation. Working with social scientists, we also aim to give back to their field by providing data and analysis of our field.

That all said, you may still be wondering whether the subject is appropriate for a Telluride Town Talk. This question is actually two-sided: Why should molecular scientists spend their time working on these issues rather than focusing on their molecular research? Why should the public care about how a professional discipline is addressing diversity inequities within their ranks?

The truth is that the professional practices of a discipline need to be changed from within, and that means that chemists must be the drivers to the change. The most obvious symptom of the diversity inequities present within the chemical sciences lies in the low numbers of women and under-represented minorities among the academic and professional ranks of chemists in comparison with the demographics of our nation. With the population of under-represented minorities increasing, the need for them to have access to chemistry careers becomes an economic necessity for our nation. Otherwise, our nation will be drawing its talent of future scientists from a shrinking pool. So chemistry departments must become attractive and accomodating destinations for students and faculty whose backgrounds are as diverse as that of our nation. Meanwhile we need the general public to be supportive of the molecular sciences as a viable career choice. Otherwise, students will choose other professions leaving the sciences without some of the best minds. Thus we need a partnership between chemists and the public to advance diversity in the molecular sciences. As for the public, they should care not just because this mission is important to the nation, but also because the diversity inequities that we are finding are relevant in to all professions and organizations.

Friday, June 21, 2013

Do you heart a scientist? (#TSRC and #PinheadInstitute)

In yet another sign that being a scientist is presently cool, here in Telluride, CO, you get 10% discounts at several area establishments just for being a scientist. Or more specifically, for being one of the attendees of a TSRC workshop. You might argue that this is actually an indication of the TSRC Director's prowess at marketing. It's true that she's good, and that the TSRC has a significant financial impact on the town. However, the Telluride folk are not wont to support something they don't believe in. So, if they are supporting this program, then it means that they are genuinely supporting science while seeing its value in facing the grand challenges that confront us in, for example, the environment and energy. Now all we need to do is to take the "we heart scientists" program nationwide! 

The motivation for this request is not so much about the money but the fact that it would bring science to kids' attention. It's hard for practicing research scientists to visit every school in the nation, but the Pinhead Scholars in the Schools program is doing its part in that direction. Back in October, I visited 7 classrooms in two days. The kids were kids. They needed to maintain their highly complicated social positions, and yet they opened up to me. They were that excited to learn about the underlying science of their everyday world! In each of those meetings, I spent an hour talking either about hard cooking an egg or about parachuting. Either way, we spoke about how you could rationalize the science of these processes, and how to use it to make predictions. They were evidently ready to heart science. They gave me hope that if we, today's scientists, engage more with them now, they will continue to do so throughout their lives.

Tuesday, June 18, 2013

Is Telluride on top of the world of science?

This week, I'm hanging out in Telluride at a workshop focusing on dynamics and kinetics in many dimensions. This is relevant to molecular reactions, protein folding and diffusion, metals and much more. It's brought together an eclectic set of chemical physicists, biophysicists, mathematicians and others from several countries around the world. But who would have thought that I would also run into specialists—and friends—in electronic structure or polymer physics who are attending other workshops? Evidently we're all attracted to the beautiful terrain of this box canyon at 8750 feet above sea level AND to the science we learn from each other in the small workshop format afforded by the TSRC.

In just the five workshops that are being run at the Telluride Science Research Center (TSRC) this week, there are several members of the National Academy, many more who have received national and international awards, and truly many of the leading scientists in their respective fields. After these workshops end, there will be another five workshops next week with another set of similarly highly esteemed researchers. This will continue to repeat weekly through early August. In all, well over 1000 scientists from around the world will have convened in Telluride by the end of the year. That's much more than you can find at any major university in the same span. All you need to do to run across nearly all the major researchers in the chemical sciences is spend your summer sitting at the main coffee bar in town! If all works according to plan, there will even be a permanent facility built for the TSRC by 2017. With that, there should be little doubt that the TSRC is the place to be to if you want to see the cutting edge of science and the landscape beyond it.

Friday, June 14, 2013

Drowning in Reviews, Part 2

Should we crowd source the review of research proposals as a way to solve the peer review system? This question may seem absurd. After all how does one even begin to implement such a scheme? The first problem involves the fact that releasing proposals to the commons would kill any protection for the ideas they contain and release them to your competitors. Even if you solve this problem, then you have to identify a mechanism through which the crowd would participate, perhaps motivated to learn about untested hypotheses. Likely what it would mean is that proposals would include even more ready-to-publish material than they do now. Regardless, these obstacles make it seem unlikely that granting agencies are headed down this path soon.

Or are they? Research grants are funded in part according to past accomplishment as measured, for example, by the level of publication of the investigator. Those principal investigators who publish in online journals are building capital through crowd sourcing. Moreover, through citation indexes and other network measures, weights to the impact of the work—whether published through traditional or open access mechanisms—are already being assigned and used by all sorts of parties interested in the so-called impact of their investments. Thus renewal proposals could, in principle, be awarded based on how the crowd has weighed in. Trouble is that the crowd is larger in some fields than others, and such a funding mechanism would tend to make large subfields more crowded. Therein lies the problem with crowdsourcing reviews: whether directly or indirectly, the sparsely populated research areas of today might not receive the attention necessary to remain alive to solve tomorrow's problems.

Wednesday, June 12, 2013

Drowning in Reviews, Part 1...

During the past few weeks, I've reviewed over twenty grant proposals for three different agencies and several journal articles. It's enough work that it reminds me of Yuan Lee's advice, "you can read articles or you can write them; it's your choice."  The problem is that we're not paid to review articles or grants, but the system of peer review falls if we don't. That is the social contract among scientists rests on all of us volunteering as reviewers. As a rough measure, we should review in proportion to what we submit. Since the reviewing task is not blind to the editors or the grant program officers, we build some kind of social capital that may affect the reviewing process of own submissions. However, the system is presumably "fair" because other reviewers aren't aware of our contributions to the reviewing process. So, as in the tragedy of the commons, not all scientists are motivated to contribute their fair share. This, in turn, has driven journals to create mechanisms of recognition for reviewers—like advisory board memberships or awards. But the scofflaws win because they spend more time writing and publishing.

One solution is to publish nearly everything, just like a blog, and let the crowd decide what's important. That's what the arXiv does. Trouble is that it creates an enormous volume that could lead to everyone drowning in articles all the more. Another solution being taken by many online journals like PLoS ONE is to review articles at a minimal standard such as that it be valid and novel. This still leads to article creep but perhaps not much more than what we are already seeing in standard journals. However, if the validation is crowd sourced without being manicured in some way, there is the danger that it will exacerbate fads, and obscure advances outside of them. So far I have published in traditional journals, and paid my dues by just keeping my nose above the waterline of reviews! But is the grass greener on the other side?

Monday, June 10, 2013

Flying with butter or margarine?

Traveling on transatlantic flights headed to Europe, I've discovered a surefire way to confirm the direction of my flight. Ever noticed that when you travel east across the Atlantic Ocean you're served margarine, but you get butter in the western direction? The plane's food is presumably prepared by the local purveyor at the originating airport, and that determines the nature of the food. As a consequence, there usually are slight differences in the meal linked to the regional cuisine. However, butter and margarine are direct counterparts, and you seemingly always get margarine going East from the States on Delta. It's reassuring, in some ways, that the world is not yet so flat that it still maintains some degree of regionalization.

Of course, the fat content and the chemistry of butter versus margarine is equally interesting. The distinction between them is not so simple because invariably most modern margarine spreads are a mixture of butter and "pure" margarine. In turn, the fat content varies considerably, and so does the taste. Other properties, such as melting temperature, viscosity and solubility presumably also vary affecting how you cook with them. This is all to say that the underlying chemistry of these products has employed many a chemist! My apologies that I've ignored the recent Mad Men debate over how to market margarine over butter, but that isn't about the chemistry at all...

Monday, June 3, 2013

Collaboration in Art and Science

This past weekend, I visited the Dalí exhibition at the Museum of the Reina Sofía in Madrid. Dalí was much more prolific than I had realized (thus my walk through the galleries took twice as long as I had anticipated) and he was a (very disturbed) genius. But the real surprise was how much his trajectory had crossed other great artists in his and in distant fields. For example, he worked with Hitchcock on Spellbound. He worked with Luis Buñuel on a number of his movies, and with Disney on a pair of animated shorts. He is also well known for his ups and downs with his fellow surrealists and his willingness to monetize his craft through so-called Avida Dollars. It's amazing that art which appears to be so individualized is evidently quite collaborative.

In similar fashion, the progress of science is extremely collaborative. One often thinks of the great physicists acting alone while laying down the foundation for quantum mechanics, but it was the Copenhagen interpretation (born from collaboration) and presented at Solvay in 1927 that truly cemented the foundation. In today's world, scientists, great and small, necessarily collaborate. That's why I'm here in Madrid in the first place. I'm working with complex dynamicists at the Politéchnica, a mathematical chemist at the Autónoma, and a mathematical physicist at Loughborough. Together, we're trying to make sense of the structure of the multi-dimensional surface that separates reactants from products. It turns out that this is, by now, fairly well understood when the number of atoms can be counted on one hand regardless of how many fingers you actually have. The trouble is that when you put molecules in a liquid (or some other complex media), it's a bit more difficult to keep track of all of them. So that's where working in a group of people with different talents and expertise comes in useful. And, like Dalí, we need to eat, so we'll take any dollars (or euros) that will allow us to advance our science!

Saturday, June 1, 2013

Jet Set Life of Chemists…

The WSJ recently ran a story titled "To Avoid Jet Lag This Summer, Travel Like a Scientist." When I first saw the headline, I feared that it was going to talk about how one needs to make sure to bring datapads and a laser pointer while on travel. (No more pocket protectors for us!). Or perhaps it would discuss the stamina required to endure the long days we spend when we visit a university to present a seminar on our latest research findings, starting with breakfast and ending after dinner just in time to spend a few more hours working on the datapad. The schedule is usually so full that you have to ask someone permission to take a bio break as such activities take away from the precious time that a given host has been scheduled to meet with you. Of course, invariably the schedule runs late, making everything all the more harried. Immutable entries on the schedule, such as meals and the scheduled seminar time, are the only saving grace for keeping some semblance of order during a visit.  But alas, I was wrong. The story, instead attempts to discuss recent findings on the types of actions one can take to mitigate jet lag during trips travelling across multiple time zones. Even then, the article disappoints because it tends to offer conflicting advice with much of it based on hearsay in the absence of sufficient hard data for a foolproof action that works well for everyone.

The title nevertheless caught my eye because I believe that the advice is actually correct. Namely, a traveller should first set up a control by essentially doing what is natural during the process of a given trip. Well, not quite nothing. She should take good notes of what she did and how her body behaved during the process. If all goes well, then she will have proven to herself that the null strategy is effective for herself. As she repeats the experiment in subsequent flights, presumably with positive results, she will simply be verifying it to the degree that it becomes statistically accurate. If, on the other hand, the outcome is not positive in the first case or repeatable in subsequent cases, then she has reason to try alternative strategies. Based on her knowledge of her behavior in other scenarios, she should then approach the introduction of new strategies (preferably one at a time) that are most likely to mitigate her jet lag, and then observe the outcomes. (The WSJ article does provide many such strategies for you to choose from either individually or as a cocktail.) Through successive iteration, she can optimize the protocol for herself. (WARNING: Don't share the protocol with others because it will be different for different people.) One difficulty here is that your statistics are poor because you have a sample size of one, yourself. On the other hand, different people respond differently to timezone hopping, and hence you need the strategy personalized to just yourself. So it falls on you to do the series of experiments to optimize your own strategy. Doing so means that you're truly travelling like a scientist. Now that advice you can share with others.