Tag Archives: bionanotechnology

US Air Force takes baby steps toward shapeshifting materials

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When I see information about US military futuristic projects it’s usually from the US Army’s DARPA (Defense Advanced Research Projects Agency).  Consequently, I was surprised to notice that this shapeshifting project is being funded by the US Air Force Office of Scientific Research according to the July 11, 2012 news item on phys.org,

An international research team has received a $2.9 million grant from the Air Force Office of Scientific Research to design nanomaterials whose internal structure changes shape in response to stimuli such as heat or light.

Each of these novel materials will be constructed from three types of components: inorganic nanoparticles with desired optical or electrical properties; peptides that bond to these nanoparticles; and special molecules called spacers, which sit between the peptides and bend in the presence of heat, light or other triggers.

When stimulated, the spacers will cause the arrangement of nanoparticles within the material to morph — a process that can lead to interesting and useful effects.

Shape-shifting materials of the kind the researchers are planning to create could have use in applications including color-changing sensors and plasmonic circuits that divert light in two directions.

The news item originated from a July 11, 2012 news release from the State University of New York (SUNY) at Buffalo,

The project is being led by Paras Prasad, SUNY Distinguished Professor in the University at Buffalo’s departments of chemistry, physics, electrical engineering and medicine, and executive director of UB’s Institute for Lasers, Photonics and Biophotonics (ILPB). …

Prasad’s fellow investigators include Aidong Zhang, professor and chair of the Department of Computer Science and Engineering at UB; Mark T. Swihart, professor of chemical and biological engineering at UB and director of the UB 2020 Integrated Nanostructured Systems Strategic Strength; Tiffany R. Walsh, associate professor at the Institute for Frontier Materials at Deakin University in Australia; and Marc R. Knecht, associate professor of chemistry at the University of Miami.

The palette of parts the team will use to build the nanomaterials includes spacers of different sizes, along with seven types of nanoparticles — gold, silver, silica, iron-oxide, iron-platinum, cadmium-sulfide and zinc-sulfide.

To identify the combinations of components that will produce the most interesting materials, the scientists will use high-throughput experiments and data-mining techniques to screen and analyze the vast number of possible combinations of nanostructures, biomolecular linking elements (the peptides) and assembly conditions.

“One of our goals is to contribute to the fundamental understanding of how the spatial arrangement of nanoscale components in materials affects their optical, magnetic and plasmonic properties,” Prasad said. “The high-throughput techniques we are using were pioneered in the field of bioinformatics, but also have extraordinary promise in the exploration of advanced materials.”

Zhang said, “The computational capabilities offered by informatics and data mining will enable us to maximize the value of our data regarding the nanoassemblies, to generate and to construct new assemblies that span a wide range of inorganic and bimolecular components so as to achieve desired combinatorics-based properties.”

It’s not exactly the shapeshifting one sees in science fiction but this will be the real stuff (not to be confused with The Right Stuff, a 1983 movie about the US space travel programme of the late 1950s to 1960s).

Music, math, and spiderwebs

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I pricked up my ears when I saw the word ‘analogy’. As a writer, I tend to be quite interested in analogies and metaphors, especially as they relate to science. I certainly never expected to find an analogy established by mathematical rigour—it never occurred to the poet in my soul. Thankfully, mathematicians at MIT (Massachusetts Institute of Technology) were not constrained by my lack of imagination. From the Dec. 8, 2011 news item written by Denise Brehm on Nanowerk,

Using a new mathematical methodology, researchers at MIT have created a scientifically rigorous analogy that shows the similarities between the physical structure of spider silk and the sonic structure of a melody, proving that the structure of each relates to its function in an equivalent way.

The step-by-step comparison begins with the primary building blocks of each item — an amino acid and a sound wave — and moves up to the level of a beta sheet nanocomposite (the secondary structure of a protein consisting of repeated hierarchical patterns) and a musical riff (a repeated pattern of notes or chords). The study explains that structural patterns are directly related to the functional properties of lightweight strength in the spider silk and, in the riff, sonic tension that creates an emotional response in the listener.

The Dec. 8, 2011 news release at MIT goes on to explain,

While likening spider silk to musical composition may appear to be more novelty than breakthrough, the methodology behind it represents a new approach to comparing research findings from disparate scientific fields. Such analogies could help engineers develop materials that make use of the repeating patterns of simple building blocks found in many biological materials that, like spider silk, are lightweight yet extremely failure-resistant. The work also suggests that engineers may be able to gain new insights into biological systems through the study of the structure-function relationships found in music and other art forms.

The MIT researchers — David Spivak, a postdoc in the Department of Mathematics, Associate Professor Markus Buehler of the Department of Civil and Environmental Engineering (CEE) and CEE graduate student Tristan Giesa — published their findings in the December issue of BioNanoScience.

Here’s part of how they developed the analogy between spider silk and music using mathematics (from the MIT news release),

They created the analogy using ontology logs, or “ologs,” a concept introduced about a year ago by Spivak, who specializes in a branch of mathematics called category theory. Ologs provide an abstract means for categorizing the general properties of a system — be it a material, mathematical concept or phenomenon — and showing inherent relationships between function and structure.

To build the ologs, the researchers used information from Buehler’s previous studies of the nanostructure of spider silk and other biological materials.

“There is mounting evidence that similar patterns of material features at the nanoscale, such as clusters of hydrogen bonds or hierarchical structures, govern the behavior of materials in the natural environment, yet we couldn’t mathematically show the analogy between different materials,” Buehler says. “The olog lets us compile information about how materials function in a mathematically rigorous way and identify those patterns that are universal to a very broad class of materials. Its potential for engineering the built environment — in the design of new materials, structures or infrastructure — is immense.”

“This work is very exciting because it brings forth an approach founded on category theory to bridge music (and potentially other aspects of the fine arts) to a new field of materiomics,” says Associate Professor of Biomedical Engineering Joyce Wong of Boston University, a biomaterials scientist and engineer, as well as a musician. “This approach is particularly appropriate for the hierarchical design of proteins, as they show in the silk example. What is particularly exciting is the opportunity to reveal new relationships between seemingly disparate fields with the aim of improving materials engineering and design.”

I always like to have a visual,

Graphic: Christine Daniloff

You can get more details from either the Nanowerk website or the MIT website.

Since it’s a Friday I thought I’d include a video of a song about spiderwebs and found this on YouTube,

Happy Friday!

Aptamers and Maria DeRosa

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Today’s (Oct. 25, 2011) next interview is with Maria DeRosa of the DeRosa Lab at Carleton University (Ottawa, Canada) where she and her colleagues work on bionanotechnology projects. (The Highlighting the 2011 Dance Your Ph.D. contest posting featured a Ph.D student from her lab who is one of this year’s contest finalists.)

Before proceeding to the interview, here’s a little bit about the DeRosa Lab (from the website homepage),

The first step in the rational design of novel bionanotechnology is to find the right molecular components for the task. Our group seeks to investigate the use of chemically-modified nucleic acid aptamers, single stranded DNA or RNA sequences that specifically bind to a diverse variety of targets, in biosensing and catalysis.

Here’s some information about Dr. DeRosa,

Dr. Maria DeRosa’s research examines a type of nucleic acid called ‘aptamers’ that can fold into 3D nanoscale shapes capable of binding tightly to a specific molecular target.  Her group is focused on developing a better understanding of how these systems and using this information to design useful nanotechnology, like biosensors or “smart” delivery devices.  Dr. DeRosa received her Ph.D in Chemistry from Carleton University in 2003 and was presented with a University Senate Medal. She was awarded an NSERC Postdoctoral Fellowship to do research at the California Institute of Technology from 2004-2005 with Prof. Jackie Barton, a world-leader in DNA sensor research. In 2005, she returned to Carleton as a faculty member in the Chemistry Department. Her research group has received funding from the Natural Sciences and Engineering Research Council (NSERC), the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), the Canada Foundation for Innovation (CFI) and Alberta Innovates Biosolutions.  DeRosa was a recipient of the John Charles Polanyi Research Award for new researchers in 2006 and an Ontario Early Researcher Award in 2010.

Here’s the interview,

*   Are you one of those people who always wanted to be a scientist or was this something you discovered later?

I was never one of those people who knew what they wanted to do from an early age.  I thought about being a doctor, pharmacist, plumber, engineer, bank teller…  In high school, I had many great math and science teachers that inspired me to go into science when I started at Carleton University.  Then, in my third year I got a summer job working in Dr. Bob Crutchley’s research lab.  He was a great mentor and it was then that I started seriously thinking about a career as a scientist.  I loved the idea of research, that I was working on a problem and no one knew what the answer would be.  I wanted the answers!

*   How did you get interested in aptamers (and could you briefly describe what they are)?

Aptamers are synthetic pieces of DNA that can recognize and stick to a molecular target.  The targets can vary from things that are very small, like a drug molecule to something much larger, like bacteria or viruses.  Because they can recognize and stick to other molecules, people are interested in using them as receptors for sensors.  I had never even heard of them until about 2005.

After my Ph.D., I went to Caltech to do something called a postdoctoral fellowship.  It was a research position in the lab of Dr. Jackie Barton, one of the world’s top DNA researchers (she just won a National Medal of Science a couple days ago).  She wasn’t working with aptamers but she opened me up to the idea of using DNA in an “unnatural” way.  Most of us, when we are thinking of DNA, we think of our genes and that it is the blueprint for life.  But from a chemistry point of view, DNA is just another material that has certain chemical properties that can be useful for other applications.  In Jackie’s lab, I learned how to make synthetic DNA and I started reading about aptamers.  I found the whole field fascinating and I knew that I wanted to be a part of it.

*   What applications are there for your work? (I noticed that you discussed fertilizers in your TEDxCarleton talk. Is agriculture an area of particular interest?)

Applications for aptamers mostly stem from their ability to bind tightly and selectively to other molecules.  So, they are typically used in technology such as biosensors where they can serve to detect low levels of something, like a toxin or a virus for example, in another matrix.  We’re developing aptamers for the detection of mycotoxins (toxins that come from moulds) in crops and food.  We’re also working on aptamers for norovirus (the virus that causes Norwalk, that awful stomach bug) so that we can catch it if it is in meat and other foods before they get sent off to stores.

We are also trying to use aptamers for triggered delivery of drugs and/or nutrients.  In many cases with drugs, we want them to act on certain cells or tissues and not on others.  So, we need to be able to control where the drug is released in the body.  There is a similar problem in agriculture.  We want to give crops certain nutrients from fertilizers but if we deliver them at the wrong time, they will be washed away and not taken up by the crop.  This leads to major economic losses for the farmer and problems for the environment.  With our work, the idea is that we use the aptamer to control the release of whatever we are delivering.  We incorporate the aptamer into a coating that covers the drug or nutrient.  The aptamer is there to recognize a stimulus that we want to use to release the contents.  For drug delivery, that stimulus might be a cancer cell or a disease biomarker.  For fertilizers, that stimulus might a be a plant signal that corresponds to the plant’s need for nutrients.  (We are working with Dr.Carlos Monreal from Agriculture and Agrifood Canada on the fertilizer project, and he is an expert in these plant signals and ‘smart fertilizers’.)  In the absence of that signal, the coating does not allow the release of the drug or nutrient.  But, once the aptamer recognizes that key signal, the aptamer distorts or destroys the coating and it allows the nutrient to be released.

*   According to the information on your lab website, you are the recipient of Canada Foundation for Innovation (CFI) Leaders Opportunity Fund (LOF) monies. Are these funds being applied to a particular project in your lab or are they used to support your general area of research?

CFI funds helped us to build our facility called the LADDER (Laboratory for Aptamer Discovery and Development of Emerging Research applications).  That funding allowed us to get the state-of-the-art equipment we need to support all of our research projects.  Without CFI funding, our work would not be possible!

*   Given your TEDxCarleton talk and your involvement in the 2011 Canadian Science Writers conference (researchers’ speed dating [I couldn’t confirm it but I’m pretty sure I saw your name listed for this event]), I gather you’re quite interested in public outreach. Why do you think it’s important?

Yes, I was at that ‘speed dating’ event and I am very committed to science outreach.  The public helps to support my research through funding like NSERC and CFI, so I think it is critical that I can explain to them what it is that I do, why it is important, and why their money is well-spent.  The general public may not know what an aptamer is, but they all realize the importance of keeping our food free of toxins or the need to make drugs that are better able to target disease.

*   I noticed that one of your students is a finalist in the Dance your Ph.D 2011 contest. And it’s not the first time. Do you find a lot of scientists with ‘dance’ tendencies are attracted to your lab? Are you one of those scientists?

My students won the competition last year and then they were finalists again this year!  I’m not sure if dancers are attracted to my lab or if my students are just as committed to outreach as I am!  My students are very excited to talk about their research with anyone who will listen.  This contest is a fun way to explain their work to everyday people.  Friends and family, after watching these dances online, have told me that they finally understand what is going on in my lab.  Maybe I should dance more!  (I’m not a dancer and you will not find me in either video…I support them from the sidelines!)

*   Is there anything you would like to add?

Thanks for profiling me and it has been fun!

Maria, thank you for this intriguing peek into your research, the field of DNA nanotechnology, and your (and shared by your students) commitment to public science outreach. I’m very happy you managed to cram the time to answer these questions into your schedule.

Science policy, innovation and more on the Canadian 2010 federal budget; free access in the true north; no nano for Van Gogh’s The Bedroom; frogs, foam and biofuels

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There are more comments about Canada’s 2010 federal budget on the Canadian Science Policy Centre website along with listings of relevant news articles which they update regularly. There’s also a federal budget topic in the forums section but it doesn’t seem have attracted much commentary yet.

The folks at The Black Hole blog offer some pointed commentary with regard to the budget’s treatment of post doctorate graduates. If I understand the comments correctly, the budget has clarified the matter of taxation, i. e., post doctoral grants are taxable income, which means that people who were getting a break on taxes are now losing part of their income. The government has also created a new class of $70,000 post doctoral grants but this will account for only 140 fellowships. With some 6000 post doctoral fellows this means only 2% of the current pool of applicants will receive these awards. Do read The Black Hole post as they clarify what this means in very practical terms.

There’s been another discussion outcome from the 2010 budget, a renewed interest in innovation. I’m kicking off my ‘innovation curation efforts’ with this from an editorial piece by Carol Goar in the Toronto Star,

Five Canadian finance ministers have tried to crack the productivity puzzle. All failed. Now Jim Flaherty is taking a stab at it.

Here is the conundrum: We don’t use our brainpower to create new wealth. We have a highly educated population, generous tax incentives for research and development and lower corporate tax rates than any leading economic power. Yet our businesses remain reluctant to invest in new products and technologies (with a few honourable exceptions such as Research in Motion, Bombardier and Magna). They don’t even capitalize on the exciting discoveries made in our universities and government laboratories.

…

Economists are starting to ask what’s wrong. Canada ranked 14th in business spending on research and development – behind all the world’s leading industrial powers and even smaller nations such as Belgium and Ireland – in the latest statistical roundup by the Organization for Economic Cooperation and Development.

I believe she’s referring to the 2009 OECD scorecard in that last bit (you can find the Canada highlights here).

There are many parts to this puzzle about why Canadians and their companies are not innovative.  Getting back to Goar’s piece,

Kevin Lynch, who served as Stephen Harper’s top adviser from 2006 to 2009 [and is now the vice-chair of the Bank of Montreal Financial Group], has just written an article in Policy Options, an influential magazine, laying the blame squarely on corporate Canada. He argues that, unless business leaders do their part, it makes little sense to go on spending billions of dollars on research and development. “In an era of fiscal constraint, there has to be a compelling narrative to justify new public investments when other areas are being constrained,” he says.

Here’s a possible puzzle piece, in yesterday’s (March 15, 2010) posting I noted a study by academic, Mary J. Benner, where she pointed out that securities analysts do not reward/encourage established US companies such as Polaroid (now defunct) and Kodak to adopt new technologies. I would imagine that the same situation exists here in Canada.

For another puzzle piece: I’ve made mention of the mentality that a lot of entrepreneurs (especially in Canadian high tech) have and see confirmation  in a Globe and Mail article by Simon Avery about the continuing impact of the 2000 dot com meltdown where he investigates some of the issues with venture capital and investment as well as this,

“It’s a little bit about getting into the culture of winning, like the Olympics we just had,” says Ungad Chadda, senior vice-president of the Toronto Stock Exchange. “I don’t think the technology entrepreneurs around here are encouraged and supported to think beyond the $250-million cheque that a U.S. company can give them.”

One last comment from  Kevin Lynch (mentioned in the second of the Goar excerpts) about innovation and Canada from his recent opinion piece in the Globe and Mail,

A broader public dialogue is essential. We need to make the question “What would it take for Canada to be an innovative economy for the 21st century?” part of our public narrative – partly because our innovation deficit is a threat to our competitiveness and living standards, and partly because we can be a world leader in innovation. We should aspire to be a nation of innovators. We should rebrand Canada as technologically savvy, entrepreneurial and creative.

Yes, Mr. Lynch a broader dialogue would be delightful but there does seem to be an extraordinary indifference to the notion from many quarters. Do I seem jaundiced? Well, maybe that’s because I’ve been trying to get some interest in having a Canadian science policy debate and not getting very far with it. In principle, people call for more dialogue but that requires some effort to organize and a willingness to actually participate.

(As for “rebranding”, is anyone else tired of hearing that word or its cousin branding?)

On a completely other note, the University of Ottawa has announced that it is supporting open access to its faculty’s papers with institutional funding. From the news release,

According to Leslie Weir, U of Ottawa’s chief librarian, the program encompasses several elements, including a new Open Access (or OA) repository for peer-reviewed papers and other “learning objects”; an “author fund” for U of Ottawa researchers to help them cover open-access fees charged by journal publishers; a $50,000-a-year budget to digitize course materials and make them available to anyone through the repository; and support for the University of Ottawa Press’s OA journals.

…

But the university stopped short of requiring faculty members to deposit their papers with the new repository. “We all agreed that incentives and encouragement was the best way to go,” said Ms. Weir, who worked on the program with an internal group of backers, including Michael Geist, professor of intellectual property law, and Claire Kendall, a professor in the faculty of medicine who has been active in OA medical journals.

There is some criticism of the decision to make the programme voluntary. Having noticed the lack of success that voluntary reporting of nanomaterials has had, I’m inclined to agree with the critics. (Thanks to Pasco Phronesis for pointing me to the item.)

If you’ve ever been interested in art restoration (how do they clean and return the colours of an old painting to its original hues?, then the Van Gogh blog is for you. A member of the restoration team is blogging each step of The Bedroom’s (a famous Van Gogh painting) restoration. I was a little surprised that they don’t seem to be using any of the new nano-enabled techniques for examining the painting or doing the restoration work.

Given the name for this website, I have to mention the work done with frogs in pursuit of developing new biofuels by scientists at the University of Cincinnati. From the news item on Nanotechnology Now,

In natural photosynthesis, plants take in solar energy and carbon dioxide and then convert it to oxygen and sugars. The oxygen is released to the air and the sugars are dispersed throughout the plant — like that sweet corn we look for in the summer. Unfortunately, the allocation of light energy into products we use is not as efficient as we would like. Now engineering researchers at the University of Cincinnati are doing something about that.

The researchers are finding ways to take energy from the sun and carbon from the air to create new forms of biofuels, thanks to a semi-tropical frog species [Tungara frog].

…

Their work focused on making a new artificial photosynthetic material which uses plant, bacterial, frog and fungal enzymes, trapped within a foam housing, to produce sugars from sunlight and carbon dioxide.

Here’s an illustration of the frog by Megan Gundrum, 5th year DAAP student (I tried find out what DAAP stands for but was unsuccessful, ETA: Mar.31.10, it is the Design, art, and architecture program at the University of Cincinnati),

illustration by Megan Gundrum, 5th year DAAP student

Thank you to the University of Cincinnati for making the image available.

India-Canada Confab in Edmonton

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Just got a notice from Nanotech BC that there’s going to be a Canada-India Nanotechnology Bionanotechnology workshop Aug. 10-11, 2008 in Edmonton at the National Institute of Nanotechnology. 10 scientists from India will be there and Nanotech BC is leading a delegation from BC attendees. If you want to collaborate with scientists in India, you can join the BC delegation by contacting:

  • Darren Frew, Executive Director, BC Nanotech Alliance at 604.602.5260 or darren.frew@nanotech.bc.ca

I can’t find this info. on the Nanotech BC website (which is here if you’re curious) or on the National Institute of Nanotechnoloy website here in their newsroom.

This comes in the wake of a new Canada-India Science and Technology agreement which launched 10 initiatives totalling $17M and was announced in June 2008.  Details here.