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Saturday, August 20, 2011

Research in Biophotonics: Tools of the Trade

I love woodworking. Not saying that I’m great at it by any stretch, but I’ve found that in making cabinets, having the right tools makes all the difference in the world. It might be possible to find a table saw and router in the photonics center somewhere, but I haven’t seen any so far! More typically, high-level research calls for tools that are also highly technical, and which are based on science that’s not simple. To do their research, our group constructs microantennaes, like the ones shown in this image.

One thing that I found out is that the whole process involves a lot more chemistry than I would have thought. At every step, safety precautions are taken just like the ones we do at school, and more in a lot of cases. Here, they use organic solvents, and do everything under a fume hood, which is good because grad students care about their health too.

The first thing we did was to etch the pattern for our antennae using the electron beam machine. This was a lot like the process we used last year when we used photolithography to set up a design on a big silicon wafer. My friend John P. of Weymouth Physics fame did an awesome job explaining this process last year. And his blog is funny as all get out. Clean rooms will do that to people - it's gotta be the bunny suit.

After doing the first step with the e-beam machine, our chips had lots of tiny bowtie structures etched onto the surface of the wafer. The next step was to turn the outlines of bowties into things with holes in them, because the holes are key for getting light energy to go nuts in the structure.

The machine that does this is called the RIE, and it’s incredibly nasty – reactive ion etching would eat precise holes in your face if you climbed into the machine – wherever you didn’t have photoresistive material to protect you. Gas is introduced into the chamber, and it turned into a plasma by high-frequency radio waves. The plasma keeps eating silicon until you tell it to stop, so the timing of the operation is kind of a big deal.

After the RIE, we went to my favorite step – the one with the pellets of 99.999% pure gold as spray paint. Gold’s used a lot in nanotechnology for lots of reasons – it interacts really strongly with light and doesn’t react with anything in people to name two. We like it for the first reason, and to get this operation to work, we first mounted our chips upside down to the plate you can see in the picture.

Next, we put a pellet of our pretty pure gold int o a little crucible you see here. After closing down the hatch, the machine got to work creating a super-high vacuum. That took a while, but after that step, things heated up. A heating element (tungsten, I think) gradually raised the temperature to the point that the gold could vaporize.

Just like in the RIE machine, radio waves were used to excite the gold atoms, which helps them to vaporize into really tiny clusters.

At the end of the process, we had coated our bowties with gold, and they were ready for us to check out on the SEM.

In signing off for now, I would like to extend my heartfelt thanks to Serap, Ali and Prof. Altug. You were all so gracious in reaching out in the midst of your very busy schedules to teach, explain and sometimes, explain again. I know that I've gained so much understanding about what makes a research operation like this one tick - I'm sure my students and members of our school's sci-tech club will benefit. Thanks again for your support and commitment!

Monday, August 15, 2011

Research in Biophotonics: One bit at a time

When we left off, we were talking about the big picture in biophotonics, which has to do with getting the nitty-gritty information about what chemicals are doing what in disease processes. This is a tough trick because molecules are small, and because the ones we want to know about live inside of us, and not in test tubes. For the last reason particularly, Prof. Altug’s group has put a lot of effort into developing cheaper ways to build sensors that can be made cheaply, quickly and could be used not just in a lab, but also in actual living tissue.

I’ll explain a little bit about how Prof. Altug’s group is working to address these challenges, but I’d like to say two things. First, I would like to thank Serap Aksu, who always made herself available to lead the way and explain all of the many steps to the process we followed in making our sensors. Second, what I’m going to write about is research – some of this has already been published, but some if it hasn’t been yet, so I can explain in general what’s going on.

To begin with, here are a few pictures of the finished product. The bow-ties squeeze infra-red light energy into spaces that are much smaller than you could get normally. After doing some chemistry to the surface of the chip, antibodies that are designed to bond with a particular protein are added to it. Here, we’re looking at the antennae on the scanning electron microscope, which is an awesome tool by itself.

The SEM scans the surface of our finished product, gathering more scattered electrons from it when the SEM’s probe is closer to the work. In this way, the SEM can form images of very small items, and magnify things to an outrageous degree – like 500,000 X.

In the past few months, the group has created a couple of exciting developments – the first one is that they’ve perfected a system for making sensors more cheaply, and they’ve come up with ways to build sensors on soft materials, which is great, as it will enable sensors to be placed in a lot more places, like inside of us.

Next: Tools of the Trade

Friday, August 5, 2011

Research in Biophotonics: Big Picture

During the first several weeks of my RET program, I had the privilege of working on materials for the summer challenge program with our group’s research leader, Prof. Altug. This is always a great learning experience for me, and the chance to get to see her perception of developments within the field of photonics is invaluable – it’s really like being on safari with an expert guide. In the latter half of my time there, I got to be involved with the research end of the business, and was able to get to know a couple of graduate student members of her team as I participated in their research. Here, Alp checks out the result of some work he's done on his chips, while Serap waits to check on hers.

If you’ve followed the last entry about beating the diffraction problem, then you know that one of the keys to ultrasensitive detection of molecules is to focus light right where it needs to be. To do this, members of the Altug group, like Alp and Serap, have tried out many different designs for tiny antennae that can work this particular magic. Participating in this process was really educational on a couple of levels. Most importantly, everyone that I spent time with works incredibly hard at understanding each step of what they’re doing. Building and testing these tiny devices takes a few days at least, and everything is done along each step of the way to verify what’s been done. What I saw first-hand was a great example of how science really works - anyone who would ever doubt the honesty or ability of the people that I worked with just hasn’t seen these folks work up close.

So here’s the big picture: right now, screening for diseases like Alzheimer’s, Parkinson’s and many cancers is a hit and miss kind of deal. For example, breast cancer screens may miss what’s going on as much as 10% of the time. While there are some amazing new medicines out there right now that can work if the diseases are caught early, the tests that will tell you if you have the disease are still expensive and don’t work that well. The trick then, is to find which molecules will definitely mean that a particular disease is present or isn’t present.

Here’s a brand new one that seems to work: Alzheimer’s disease seems to be closely tied with a particular protein. In order to understand how the disease is working, what researchers would like to do would be to get sensing equipment actually inside of people who are developing the disease. That way, we’ll be able to really peel apart how the disease is operating, and know for certain if the biomarker is a clear indicator. And that’s another big aspect of Prof. Altug’s research – building better sensors so that researchers can speed up and improve their quest to exactly pinpoint the chemicals that are doing the dirty work in some of the nastiest diseases human beings can get.

Next: One little slice of the pie.

Monday, August 1, 2011

Summer Challenge!

Summer Challenge!

Providing clean water, ample food, high-quality medical care and education to people around the world are a few of the challenges facing the global community today. We know that when these things are in place, many other crucial social benefits like stable birthrates, can be achieved. Sustainability is at the heart of many of the grand engineering challenges, which I linked to in my first post this summer. One of the things that’s really significant to me about this list is that nanotechnology is going to play a significant role in achieving many of these goals. When biomedical testing can be made cheap enough that doctors can deliver the same high quality care in Boston as they can in Ghana, we will have really changed the world for the better.

Sharing this excitement was part of our challenge this summer as twenty high school students came to live at BU for two weeks, check out New England, and participate in a range of two-week mini classes. Toward the end of July, we met with our group of twenty students from San Francisco, China, Japan, New York, Texas, New Jersey, Virginia and Massachusetts to explore the basic science and new technology that is behind the developments at the Photonics Center. If you’ve followed some of my past blog posts, you have seen a lot of basic science – that light is made of small waves that bend around small things in a process called diffraction. This phenomenon is an example of super-important basic science. Here, Howard and Briana are talking through the math that explains that pattern of light on the white board, while Malika, our super undergrad engineering student looks on.

Why is it so important to understand how light and matter connect with each other? Because it’s the basis for an incredible array of new technologies – that’s why.

Take computers for an instance. As you may already know, one of the co-founders of Intel, Gordon Moore, published an observation in 1965 that became known as Moore’s Law. In that paper, Moore noticed that computer chips were becoming exponentially better, while at the same time becoming exponentially cheaper. It’s what’s behind every smart phone, every digital camera, and every other place chips find a hope, which is in almost everything we use today. However, as you might expect, there is a big problem with the idea of never-ending improvement. Today’s computer chips are smaller and faster than ever, but two things are happening.

  1. is that they keep getting hotter. Like inside a nuclear reactor hot, or even hotter.
  2. is that you can only make chips so small. Today’s transistors are around 25 nm. When designers get below 10 nm, Moore and others expect that electrons simply won’t behave themselves, and chips at that size will be useless.
Boom, done, end of high-tech industry as we know it.

This is where photonics comes in. What electronics was to the 1960’s, photonics is now: an evolving field that aims to do with light what Gordon Moore and others did with electrons back then. Right now, we use fiber optics to carry information around the world, but the insides of our computers are basically 1960’s type machines. Really tuned-up, but still things that run on electrons. Today, companies like Infinera and IBM, and research universities around the country are building the technology that will enable light to carry and process information through every part of the computer. This will create computers hundreds or thousands of times faster, while using much less energy than current ones do. The Infinera link takes you to a video that demonstrates a networking chip they’ve built. It’s not a whole computer yet, but it is a big improvement on that part of the system, and the technology is a step forward. This is part of what our students learned in summer challenge, and it’s a good backdrop for the research that I did on ultrasensitive biosensing. More on that soon!

Thursday, July 28, 2011

Smart Lighting vs. Dumb Politics

[Warning: the following blog post contains opinions that may be objectionable to politically sensitive readers. Please, if you care for Bunnies at all, read on.]

The picture currently is that RPI and BU are leaders in a $20 Million dollar research effort designed to give U.S. companies a leg up in a field that will become known as Smart Lighting. The whole idea goes beyond saving energy, although that’s definitely part of it. As U.S. energy secretary put it recently, this type of energy savings is the “low hanging fruit” in building a sustainable energy economy - one that does not rely on burning vast amounts of imported oil. Here are the facts:

  • 19% of electricity worldwide is used for lighting.
  • There are over 30 billion light bulbs in use around the world, with most of them being traditional incandescent style.
  • It’s estimated that all of these bulbs could be changed over by 2025, that the world would save 1 Billion Barrels of Oil each year – the equivalent of 250 nuclear power plants.Current lighting systems are beyond dumb – they’re just relics from a time when indoor lighting without having to burn kerosene or gas was a miracle of sorts by itself. What Smart Lighting entails is the use of LED lights (the type that are now used in that next fancy big-screen TV you want to get) to do several things:

  • Save lots of money
  • Last for a long, long time
  • Provide light that is sensitive to the amount of natural lighting available, so that your home or office is never too bright or too dim for comfort
  • Mimic the shifting color spectrum of light throughout the day, which works in support of our circadian rhythms. Yes, research says that current lighting in offices is not great for us, and that some folks react badly to it. This lighting will be natural.
  • Provide the bandwidth needed to send GHz of data wirelessly, using pulsed visible light. This would be especially useful on airplanes and other places where heavy copper wire networks are bad for lots of reasons.
  • And in a totally different setting, allow cars to communicate with each other and with traffic signals wirelessly, increasing safety

During George W. Bush’s presidency, members of both parties worked to develop legislation calling for higher standards for light bulbs. They ended up setting standards so that by 2012, light bulbs would have to be at least as efficient as the halogen bulbs you can buy today. Only the oldest style bulbs for sale today don’t make this standard, and they’re currently being re-worked by Phillips and other companies so that they’ll make it.

So who in the world would be against this kind of development? Well, Reps in Texas and South Carolina have written a law creating separate, worse standards for their states. The argument usually runs something like this:

“You can’t tell me what to do.”

I’ve gotta be honest – I cannot imagine a more backward-looking way to behave than this. With American kids fighting around the world in part to maintain our free access to oil, the people behind this kind of legislation aren’t just clinging onto the past – I really think they’re kicking away the future - in lives and money, while keeping us from moving in the direction of sustainability, which we simple must do.

The research money that our government is spending is designed to create a database of intelligence to help U.S. companies create a leadership position for our businesses in this area, which makes the sort of knee-jerk reaction to any type of standards just so frustrating to me. Being against U.S. energy independence is bad enough, but to be against the kinds of good quality jobs that are created by establishing U.S. leadership in an area is just not being a smart American. It's just an example of dumb politics.

Thursday, July 21, 2011

Engineering the Future

Planning for this summer began a long time ago, back in August of last year. I felt very fortunate to have been able to be part of the goings on at the BU Photonics center in 2010, and spoke with Prof. Altug, my cooperating professor from BU about the possibility of coming back for a second visit. There were really two reasons for doing this – the first one was that we collaborated really well together and helped design some teaching materials that people seemed to like. The second was that seven weeks is waaayyyyy too short of a time to digest even a small percentage of what’s going on at a professional research facility, and I hoped to be able to learn more to bring back for my students. During the year, a few students at SJP and I

made some strides at helping bring more of an understanding of research science to the school, visited a couple of research sites and did some experimenting with lasers. Nanomaterials and Photonics are such hot topics in the world of research right now that both of the AAPT conferences I attended had it as their main topic, and I got to hear from many angles how the world of nano-research is shaping the future of engineering. Along the way in May, we heard back from NSF that our grant proposal for me to come back for another summer was approved – Psych!!

When June of this year rolled around, I got a surprise email from Prof. Altug asking me to go out to RPI for a conference. That turned out to be a fantastic experience – I love visiting schools to see what people do there, and I’d never been to RPI before. My awesome wife took a day off from work to come with me, and we made it into a road trip. What I saw was actually something like an audit – scientists and others from the National Science Foundation were conducting a public hearing of sorts where members of the RPI community described what they had been doing with the millions

in Federal grant money they’d gotten. I’m certainly no expert, but it seemed to me that NSF representatives asked a lot of tough questions, and challenged researchers not only to show progress, but also to prove that they were being responsible with their grant money. My little bit in the thing was to chat with people and explain to them what we had done during my summer RET experience, which turned out to be awesome.

I met with Prof. Ken Connor from RPI, and with professors from several other colleges in the research program, and we sat down together to share teaching strategies. Educational outreach is a huge part of work that professors do these days, and it’s a thread that will work its way through all of the blog posts that I do this summer. There has been a lot of talk centered on the need of U.S. schools to educate more engineers, and to educate citizens about what job opportunities exist in the future. In many ways, developing enough people with technical skills is a fundamental challenge that every society faces in the world today. The group’s work in Ghana centered around making

low-cost education in electrical engineering available through the mobile studio, a piece of hardware developed at RPI. The wealth of our countries is very different, but the challenge is the same – how to present students with a sense of the exciting challenges the future holds, while giving them the tools they need to tackle those challenges.

Monday, November 1, 2010


This weekend was a lot of fun! Twice a year, the local AAPT (American Association of Physics Teachers) group hosts a conference somewhere in the area. This year, it was at Brown University, and the topic was nanobiotechnology. That was awesome, because it was such a great fit with the research work that I was involved with this summer. The conference kicked off Friday afternoon, and went through Saturday afternoon, so there was a lot going on.

There were five or six talks where people presented their research, and it was pretty technical even though everyone tried to keep the math to a minimum. Consequently, I lived the weekend somewhere between "that's awesome!" and "uh-oh..what are they saying now?" The photo here is of Mark Reed from Yale University. Like a lot of research groups in nanophotonics, Mark's group is into a lot of different things all at the same time. Mainly, Mark spoke about his work with biosensors. He's doing his stuff in a different way from Hatice's research group, using computer chips to sense the presence of biological agents, but he's also gotten some really good results.

When researchers say that they can now sense 10^-15 moles of a
chemical, it kind of puts it into perspective when Mark compares that to putting a single grain of salt into an Olympic sized swimming pool! That really goes to a lot of the reasons why this new sensing technology is so cool. There are new meds for diseases like Alzheimer's and Parkinson's available, but they work the best when the disease is caught early. So for researchers like Hatice and Mark, the challenge is in trying to develop a practical way of sensing a small amount of a certain marker, like CA15.3, which is a marker molecule for breast cancer and many others. The way that his system works is that he builds nanowires from a single crystal of semiconductor. Then, they "functionalize" it by attaching a molecule that will bind with the disease molecule they're testing for. Because Mark's device is so sensitive to changes in the landscape around itself, they can tell very easily if they've got a hit in their blood sample or not. I talked with Mark after the conference, and his feeling was that human trials using his
type of technology are probably 1-2 years away, and that the plumbing of his device remains the big challenge.

That comment struck me, because I knew that our research group got itself on the cover of one of the big nanotech journals for coming up with one solution to that problem. I'll have to ask
Hatice or Ali next time I see them to see if their solution is one that he should be using or what the deal is there. One thing that I thought was funny was that he said "everyone always makes it sound so easy in their publications, but there's stuff they're leaving out!" That sounds like good old-fashioned gamesmanship to me!

There were a couple of other talks that were just awesome. I want to use them with my club's sci-tech club - totally inspiring and amazing! For a hint, google Naomi Halas and Peter Nordlander - they're a wife and husband team at Rice University, and had some really exciting stuff to share. More later!