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!

Expertise is stagnation

A PhD degree in Physics represents a new contribution to the body of scientific knowledge; but, it is more than that. The power of new physics is not in the generation of new information, though that is one important side effect. It is the new or deeper understanding of the nature of how how things work that are its treasures. It is not a process in which a student goes through steps 1, 2, 3, 4, 5, and then is done, but a journey of exploration that often can come up empty handed. Putting in lots of time and effort is not enough. There needs to be a tangible result that adds to the corpus of Physics.

The dissertation documents the contribution a PhD student has made to science. The process of writing up ones work and results inevitably uncovers errors, weakness in logic, and oversights that need to be addressed. As such, the period of writing prior to submitting the dissertation to the examining committee is filled with stress. One never knows if the errors that are uncovered will be fatal to the thesis. Many students are unaware of the magnitude of the demands. In the end, it has to be right (internally self consistent and in accord with the rest of Physics) and the dissertation committee needs to be convinced that the work is significant enough to be worthy of a PhD.

I write this as Shiva is finishing up his dissertation and getting ready to defend. The work is excellent and I believe that it will be a major contribution to the body of Physics. We have proposed a novel model based on experimental observations that pass the test of simplicity - with only three parameters all of the data is explained over a huge range of conditions; and, it suggests new physics, namely, that a polymer mediates the interaction between molecules in a way that coerces them into healing after they are damaged by powerful laser pulses. This phenomena is new and its explanation is bound to be controversial; and it may end up being wrong...

In the process of writing his dissertation, Shiva had to make major changes to the analysis of the data, needed to take additional data, and had to take into account complications that had slipped by our attention. Each time he thought he was done, there always seemed to be one more thing to check, one more experiment to do or one more calculation to correct. I can imagine the ups and downs associated with the relief of being done followed by the anxiety over a potential error that could mean the downfall of the dissertation.

As I write this post, I believe that his dissertation is finally done, and I am comfortable with the scrutiny that is to come from the committee. There are certainly loose ends that will be addressed, but those can be completed prior to the oral or as minor revisions after the defense.

I have advised dozens of graduate students over the years. Many have vocalized the childhood question asked of parents during a long road trip, "are we there yet?" Others think about their progress quietly while some may assume that they will get a degree as a result of making an effort. In the end, only students who persevere after what appears to be endless failure and hardships will make it through to the end. The process includes hard work, independence, cleverness, deep thinking, and extreme grit. As a result, the future employer of a PhD physicist is not getting just an expert. If that is what they think, the employers miss the best part. They are getting an individual who is fearless in the face of new challenges that require a nonexistent expertise.

Expertise is stagnation. Dealing with the unknown is wrought with fear, insecurity, and doubt; but, there is an air of exhilaration from the possibility of successes. The PhD student builds problem-solving skills and the ability to think beyond his or her knowledge base and to thrive in a world of uncertainty. It is character not just expertise that the PhD represents.

The beauty of nature is that she is consistent and filled with rich and wondrous phenomena. On the downside, she holds the highest standards and is intolerant of contradiction. I am glad to have a job that allows me to be continually confused, insecure and humbled. Every new piece of knowledge or expertise gained drives me into a new unknown realm. I am simultaneously frustrated and ecstatic, perhaps a required blend of opposites that lead to fulfillment and happiness.

Having acquired a taste for this life, I wish the same for my students. As Shiva is finishing up, I look to the next generation of students coming up through the ranks in the hopes that they too will succeed.

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