Perhaps this time it may be right - taking a big chance

I wrote a while back how Shiva's measurements gave 0.29eV as the binding energies in our polymer/dye material (with an experimental uncertainty of 0.02 eV) which is responsible for forming domains that are at the heart of our theory of self-hearing .  I tried to figure out what interactions between molecules and polymer would give this energy and came up with a possibility.  But because I read the data tables incorrectly, I wrongly thought I had solved the problem.

When preparing my talk for SPIE a couple days ago, I drew the PMMA polymer chain with a molecule drawing program and added a few DO11 tautomer molecules to see where they would fit.  Miraculously, as a plopped the DO11 molecules on the page, I immediately saw that the NH from the DO11 tautomer cozies up to one oxygen in the PMMA polymer chain while the OH group naturally attaches itself to another oxygen in the chain, as shown above.  And he energy?  You got it; the sum of the two hydrogen bound energies is 0.30eV, a match.  The table below shows the energies of four types of hydrogen bonds.




There are always other possibilities that we have not yet considered, but this smells right.  Perhaps we are onto something.  Future experimentalists will allow us to test this hypothesis and zero in on what is going on when a molecule self heals.

This project has been one huge puzzle, were each new experiment presents to us a new piece.  It reminds me of how the discovers of the structure of DNA (Crick, Watson, and Wilson  ) pieced together cardboard cutouts of molecules to guess its molecular structure, and confirmed their results using x-ray scattering data from  Rosalind Franklin.  Incidentally, the story behind Franklin's contributions to the discovery of DNA and not being recognized  at the time makes for interesting reading.  I also recommend readers to check out Schrodinger's guess as the structure of DNA using simple physics principles.  The title of his very thin but fascinating book is

"What Is Life?: with 'Mind and Matter' and 'Autobiographical Sketches'"

I can imagine the thrill of discovery experienced by Crick, Wason, Wilson, and Farklin.  From little cardboard pieces and an "X" on a piece of film from an x-ray scattering experiment (shown above), they revolutionized our understanding of the workings of DNA.  Ironically, the forces that hold together the double helix reside in the hydrogen bond, the very forces that seem to be at work in our molecule/polymer system.

I am preparing my talks this morning, and plan to go on a limb proposing stating that the interaction between a DO11 molecule and a polymer chain  through hydrogen bonding underpins the phenomena of self healing.  I am not a chemist and have a naive view of the intricacies of how molecules interact.  But, I hope that my bold proposal will result in good feedback form my audience that will help us fine tune our models of the mechanisms of self healing.

I have been very excited in recent months by all of the discoveries that we are making.   Even if they end up being wrong, the process of the search for the truth is exhilarating.  Gotta run.  Too much to do.  And again, sorry for the typos!

A pendent necklace and a new insight about self-healing molecules

In a recent post on our research on self healing, I discussed our new theory, which is posted in the Physics Archives (see it here). The paper has been accepted for publication in the Journal of Chemical Physics and will appear soon.

We used lots of data as input to construct the model, which took years to complete. Data that seemed to support one model initially would later be contradicted by additional data. Over time, the model evolved into a coherent picture as more hypotheses were eliminated by experiments. Finally, we had a model that fit the data AND had as its cornerstone the formation of domains of molecules that together, would help a damaged molecule heal.

There is no direct evidence for domain formation, though the behavior of all the experiments to date are consistent with this model, and only this model. Remove the domains and the predicitve power of the theory is lost. The burning question pertains to the nature of the domains. What are they? Are they clumps of molecules or molecules that are somehow stuck to the same polymer chain? What is the nature of the force that keeps the domains together, and how is it that a domain of healthy molecules acts to promote healing in a damaged one?

We may be closer to an answer.

The lab is in a wonderful buzz of activity with lots of new measurements -- always an exciting time. There are bold new hypotheses based on initial data that generalize our model, followed by letdowns after new data or a more detailed calculation proves us wrong. The process is highly stimulating. I can just smell it; something new and wonderful is brewing.

In the midst of all this activity, I found myself sitting at my computer writing my conference paper for SPIE, where I will give a couple of papers in August. I completed writing the introduction and then explained our new model. What next? I needed something new that did not detract from the presentations of my students. So, I drew the molecular structures of the polymer and the molecules, and started to play with them, rotating this one this way and that one here, etc.

In less than a few minutes, I realized again that a molecule could stick to a polymer through what is called hydrogen bond -- an attractive force between a hydrogen molecule and in this case, an oxygen, very much like the forces found between water molecules. This thought had crossed my mind in the past, and is indeed a motivation for a subset of projects. However, having all this jumbled data running around my head made me realize that Shiva, my coauthor on the theory paper, had already determined the three parameters of our model, one of which is the force that binds the molecule to a domain. If the molecules are sticking to the polymer chain through a hydrogen bond, the hydrogen bond energy should have the same value as the corresponding parameter in the model.

This is an excellent example of a model that we built to explain the data is now guiding us in figuring out what is going on.

I got on the internet and searched for hydrogen boding and found a table of numbers. The energy between a hydrogen and oxygen was one of the first values listed, at 0.3 eV. Then I nervously clicked through the directory tree on my computer to find its measured value. As I scrolled to the table with the results, my eyes focused on the value of the lambda parameter -- 0.29 eV with an uncertainty of 0.01. The two matched!

It is not often that things work out this easily, so I considered the next question, and that was how self-healing is mediated by molecules attached to a chain. A polymer with molecules connected by hydrogen bonding looks a lot like a necklace (polymer) with pendents (molecules) thrown on the night dresser as shown in the figure below.The hypothesis that I proposed is as follows. (a) When a molecule absorbs a photon, (b) it breaks into two fragments that are charged. There is evidence from earlier work that charged species are involved. One of the fragments is fixed in place by the polymer and (c-e) the other hops from molecule to molecule along the chain (f) until it finds its mate and recombines.

An alternative explanation is that the attached fragment attracts a small fragment from a neighboring molecule. The neighboring molecule then attracts a fragment from its neighbor, and so on, which propogates down chain like a wave of fans at a stadium until the original damaged piece combines with an adjacent fragment. The more molecules in the domain (i.e number of molecules attached to a polymer chain), the bigger the chance that there is a contiguous path for the fragment to find a mate.

This is indeed an exciting time. In addition to this work, there are other very exciting developments that I will post in the near future. Breakthroughs can be addictive. I can't wait for the next one!

My voice from the past

A while ago, David Bradly, a reporter from ScienceBase had contacted me about a paper from my group on self healing in a molecule called AF455. He wrote a short news piece on our work. After the piece was posted, he contacted me with additional questions. In response, I shot him an email, which he posted in its entirety. This was back in April of 2007, more than 4 years into my past.

Just 5 minutes ago, I was searching for articles related to our research and ran across my email. I tend to write emails from the top of my head, without much editing, so it was eerie to see myself in an unguarded moment. In effect, it was my own voice form the past, real and uncensored. When writing for the public, as I do in papers and proposals - and even in this blog, I choose my wording carefully, though often not with good results. While you may not notice the tone, reading this email rekindles in me the excitement of discovery that I was feeling at that time. It is better than any diary entry.

I am glad that David Bradley posted this email, which is truly a window into my past. It is reproduced below. As you may have guessed, he asked me about applications of our work.

Dear David,

The molecule AF455 is indeed complex, and that is what makes its irreversibility so puzzling. The DO11 dye, which we previously studied for reversibility is a relatively small molecule; and, the mechanisms for the recovery is the breaking up of dimers that form in the degradation process. This requires the molecules to be able to move around a bit. AF455 clearly can not move around easily, so another mechanism must be responsible.

Any device that operates at high intensity, such as lasers, displays, and all-optical switches and logic, suffer from photodegradation. Solid state lasers, for example, live longer than ion lasers and dye lasers; but, dye lasers have much more flexibility is the range of colors that are available. Polymer displays, on the other hand can be mechanically flexible and can be used to host all sorts of organic molecules. The general theme is that organic molecules have a much broader pallet of what they can do, but, they are not as stable.

So in our work, we are not so much interested in targeting specific applications. Rather, we want to understand the mechanisms for recovery since most materials degrade irreversibly. And here we have two very different molecules that behave the same way. There is one similarity. We discovered this property by accident!

If a material absorbs light strongly, it will damage when the absorbed optical power reaches the material's damage threshold. In applications where the material is transparent, light can be absorbed through a two-photon absorption process. Not as much light is absorbed in the process, but, over long-enough periods of time, cumulative effects cause the material to degrade.

Bright light can cause all sorts of things to happen in a material. If it induces a chemical reaction that causes a molecule to break apart into pieces, that process is irreversible. On the other hand, if the light causes the molecules to change shape into a form that no longer absorbs light or perhaps causes some charge to jump from one side of the molecule to the other, this change is reversible. The trick is to find materials that are not killed by the zap of laser, but that prefer to take a nap.

Another intriguing observation is that when such molecules wear out, rest, then recover many times, they seem to degrade more slowly and recover to a higher level of efficiency upon further cycling. It's like a weight lifter that gets stronger after each workout. So, it may be possible to make our molecules more buff by giving them a good workout. We observed this kind of response in the DO11 dye, but have not seen it in the AF455 dye.

So, while we see two-photon absorption (TPA) as a universal nuisance that destroys materials, and that's the motivation for our studies, there are many important applications. Two-photon absorption is strongest where the light intensity is the highest, and is ideal in applications where a chemical reaction in a material operates above a certain threshold power. The important consideration is that for absorption to occur, two photons must participate.

Cancer therapies are one such application. The patient drinks a cocktail of molecules that like to stick to a particular type of tumor cell. Also, these molecules are tailored to be strong two-photon absorbers to a color of light to which cells and flesh are transparent. Then, just aim a laser beam at the tumor right through the skin. In this way, only the tumor cells are zapped. Since the skin is not perfectly transparent, it will also absorb some of this light, causing a bit of damage. Ideally, you want to make the strength of two-photon absorption as high as possible so that the amount of damage to the tumor is as big as possible relative to the damage to healthy cells. You want the special molecules to live as long as possible so that they can be repeatedly zapped without the patient having to ingest more of the cocktail, which could have side effects.

Since TPA is a process where two photons are simultaneously absorbed, it can be used to drive chemical reactions at the intersection point of two beams of light. As an example, a liquid can be made to turn solid (i.e. polymerize) at the crossing points. In this way, a three-dimensional object can be made piece by piece inside the liquid, such as gears, shafts, and other nano-scale parts. So, it's like having the ultimate nanolab.

So, TPA is something that is simultaneously very useful in important applications; but, can be a nuisance in all applications that require the use of light. We are thinking more about ways to make a molecule snooze to help it recover rather than find more ways to put it to work. Happy dreams!

Mark

Confirmation Bias and the Scientific Method

Marc Hauser, a primate psychologist at Harvard and expert on the evolution of morality, was recently found guilty of eight counts of scientific misconduct. At issue was his interpretation of video tapes of rhesus monkeys performing tasks that test their ability to learn sound patterns. Hauser "saw" the behavior that supported his hypothesis and was convinced that he was right even when other members of his research group could not. Being an eminent scientist, his group members deferred to his authority, and his interpretation prevailed in the publications that followed.

Physicist Robert Park wrote in a web column that Hauser fudged the data, implying that it was premeditated and deliberate. Scott Lilienfeld, a psychologist, feels that this might be a simple case of confirmation bias, a psychological response of the brain to reinterpret the world by distorting the data to favor the believer's expectations - a phenomena that is commonly at play in strengthening religious faith.

I just returned from a trip to Wright Patterson Air Force Base, where I gave a seminar about our work on self-healing materials and fundamental limits. My visits to the materials lab are always gratifying because the interdisciplinary team of researchers there understand our work from a broad range of angles. There are chemists who understand structural subtleties of chromophores and how they aggregate as well as the role of the host polymer on the properties of the embedded chromphores. The physicists and quantum chemists, on the other hand appreciate the beauty and utility of our models of light-matter interactions. Each individual brings a unique perspective that enriches my understanding of materials and potential mechanisms of a variety of interesting phenomena that we can apply to interpreting our data.

The initial response of people who have just learned about our observations of self healing conclude that diffusion is responsible. Some of the air force scientists shared this concern. The idea is simple; the laser heats the molecules in the polymer, and the added kinetic energy causes them to move away from the laser. When the laser is turned off, the random walk associated with thermal jiggling causes the molecules to return. Thus, rather than the molecule burning (i.e. breaking into pieces) and then recovering (i.e. resembling), they simply move away and return.

When we first observed this phenomena, diffusion was the first hypothesis that we tested using optical absorption spectroscopy. All molecules absorb light at a set of discrete characteristic wavelengths. The DO11 molecule, our model system, has a big absorption peak centered in the middle of the visible part of the electromagnetic spectrum. If molecules move away from the beam, then the height of the peak will drop, but the shape will remain unchanged. If the molecular structure changes, as should happen in the photo-decomposition process, then a new peak forms that is characteristic of the "burnt" molecule. One can show that as one set of molecules is being converted into another set, then the spectrum evolves in a way where all the spectra cross at one point. This point is called an isobestic point.

When I am asked if self healing might be due to diffusion, I can confidently respond that we see an isobestic point in the linear spectrum. Everyone in the audience then usually thoughtfully shake their heads and acknowledge that this is strong evidence against the diffusion hypothesis.

However, upon reading the article about the Hauser case, I began wondering if I am not being deluded by confirmation bias. While we do see an isobestic point, the process of aligning the probe light (used to measure the spectrum) with the pump is difficult, so the measured absorption changes are not always clean. So, I started wondering if we were not being fooled by subconsciously dismissing data that does not meet our expectations. Upon my return, I met with my students and suggested that they try all sorts of other experiments that differentiate between the two mechanisms. I regret this extra burden that I place on my graduate students, but I would hate to be wrong.

On the computational front, we are also seeing weird results that may render some of our ideas invalid. In particular, we normally observe that when a quantum system is at the fundamental limit, only two excited states contribute to the nonlinear response. We call this the three-level ansatz. In recent Monte Carlo calculations, we are seeing rare outliers where more states contribute. Even more disturbing is that in these rare cases, the limit appears to be broken by a tad.

There are two interpretations to these results. First, there may be a flaw in the fundamental limit calculations. In our work using variational approaches of potential energy functions and vector potentials, we never see a system with a nonlinear response larger than 0.709 times the fundamental limit. In these cases, the three-level ansatz seems to always hold. That gives me some degree of confidence that the calculated limits are correct. The resolution to the problem might lie in the fact that the Monte Carlo work uses truncated sum rules. However, such truncated sum rules are also used to calculate the limits. Are we dismissing the effects of truncation when it suits our purposes?

It is likely that there are many subtle issues that we will need to consider to resolve our new observations. I fear that my brain may be driven by confirmation bias into believing in the fundamental limits and to blame counterexamples on the problem of truncation. We must consider the possibility that the limit calculation may be flawed, in which case it needs to be fixed. In the end, getting to the truth should be our top priority.

I learned about the quirky Monte Carlo results just before my trip to Dayton, Ohio. In addition to my preoccupation with my possible affliction with confirmation bias, I am overwhelmed with all sorts of other work, such as doing the annual reviews of our faculty, refereeing papers, reading dissertations, writing letters of recommendation, and writing new papers, as well as struggling to keep up with my lectures and homework solutions - all while fighting a nasty cold.

I look forward to weekends as a time to catch up with my work. Given my workload, I cannot realistically climb out of this hole; but, I take pleasure in my expectations that in the process of preparing for class and pondering our problems, I will learn new physics. Perhaps these activities will lead to the next new breakthrough on our understanding of the universe. I'll keep you posted.