Archive for November, 2009

Let’s sterilize things!

Monday, November 30th, 2009

I have been thinking what I wrote so far in my entries. To sum up, that was like a mix of theory and practice, with the more information about the first aspect of my research rather than the second thing. I guess what people like to know about new studies is how they can be applied. That seems to be reasonable as the scientific research are to find solutions to whole range of issues.

One could say.. we have had sterilization methods for years – steam sterilization, gamma and UV radiation, or different sterilizing agents. And those have many applications in varied industries and everyday life. However, researchers are going forward and new discoveries require another technologies.

As the sterilization with supercritical fluid carbon dioxide is considered to be very mild, and carbon dioxide is nontoxic and inert, that brings opportunity to implement it to the latest advanced technologies in the same fields. For example, current methods used in biomedical area have a lot of limitation for using them to thermally and hydrolytically sensitive polymers and instruments. As the more sophisticated and sensitive biomedical products are being developed, filling the gap for those limitations is needed. And here is an alternative method of supercritical fluid carbon dioxide sterilization might be used. And it does not attract only medical needs, but also food industry. That involves both containers for the food storage, as well as the food itself. Researchers have also informed on the sterilization of electronic devices – chips and pen drives are the first to be treated with supercritical fluid carbon oxide.

Be aware though right now, this is not limited to the things and industries I mentioned. The needs are growing, so are the technology advances. And everything to help us to live better.

The Aso Jinja

Monday, November 23rd, 2009
“Jinja” is a Japanese word for a Shinto shrine. Shinto is the indigenous religion of Japan, and comprises a collection of beliefs, rituals, and practices that center around getting along with the “kami,” or nature spirits, that dwell in Japan and have the power to make peoples lives good (or miserable). You won’t travel far in Japan without seeing rocks, waterfalls, trees, or other natural features that are draped with a “shimenawa,” a ceremonial rope that tells passers-by that the object is a natural shrine that houses a kami. Even whole mountains can house the kami. In fact, there used to be a shrine near the summit of Nakadake crater. The site, now known as the Furubochu archaeological site, is a ruined temple complex that was active during the middle ages. A few hundred monks and about 80 temples apparently existed in the area until about the 15th century, when volcanic activity (and possibly feudal wars) caused abandonment of the site.
Anyway, there is no question that the kami have been active in the Aso area since early times. Legend has it that the interior of the Aso caldera was a huge lake until the kami Takeiwatatsu-no-mikoto kicked a hole in the wall, allowing the water to drain out and making space inside the crater for people to live and work. The breach where Takeiwatatsu-no-mikoto kicked the wall is the spot where the Shirakawa (White River) currently flows out of the caldera on its way to the sea near Kumamoto.
Shaded relief map, courtesy of Google Maps. The arrow indicates the location of the Shirakawa gorge.

Shaded relief map, courtesy of Google Maps. The arrow indicates the location of the Shirakawa gorge.

Investigation of the crater has shown that the Aso caldera was, in fact, filled by a great lake, much as Crater Lake, Oregon, is currently filled with water. The sediments that were deposited in the lake, which is known as “Paleo-lake Shiobara,” contain many thousands of well-preserved plant fossils that imply the lake existed at least during the middle Pleistocene. To me, investigation of the plant fossils of paleo-lake Shiobara sounds like a job for University of Idaho paleontologist Peter Isaacson and paleobotanist Bill Rember!
Anyway, Takeiwatatsu-no-mikoto was later promoted to be the kami of Aso volcano and one of the major kami of Japan. The Aso Jinja is located in the northeastern part of the Aso caldera. Of course, those of you that know me know that, besides being a hydrogeologist, I have an interest in archaeology, history, and culture, so I wasn’t going to miss out on a trip to Aso Jinja!
One of the stone guardians of the Aso Shrine

One of the stone guardians of the Aso Shrine

The Aso Jinja is the principle shrine of the Higo area, and Takeiwatatsu-no-mikoto is the principle deity of Kyushu, which gives some indication of the importance of the Aso volcano to the entire Kyushu region. The Aso Jinja is one of four existing shrines in Kumamoto prefecture constructed in the Enki architectural style. Of these four Enki-style shrines, which date from around 972 A.D., three are located in Aso.
The main gate of the Aso Shrine

The main gate of the Aso Shrine

My understanding is that the Aso Jinja still has its original gate, which is unusual–most of the original gates have been lost to fire or earthquakes over the years. In any case, the gate is quite impressive, and I was pleased to have the chance to see it!

Fountain for ritual washing

Fountain for ritual washing

One of the interesting things (to me) about the Aso Jinja is that it is located at the source of a culturally-important spring (a cold water spring, not a hot spring). As you approach the main gate there is a water-filled trough fed by the spring that is used for ritual washing. Usually, people rinse their hands and mouth before proceeding into the shrine as a sign of respect.
I visited the Aso Jinja on a Saturday morning, which happened to be a big time for bringing babies around to the Shinto priests for blessing. Of course, I wasn’t allowed inside the main building of the shrine. (I’ve probably been kicked out of more shrines and temples around the world than anyone I know–mostly for trying to climb down into old wells and things. Ask me about the main cathedral in Trondheim, Norway, the next time you see me.) But I did peer in from outside, watching the ceremonies and listening to the drums thumping and bells tingling.
A Shinto priest leaves the main shrine building after a "christening"

A Shinto priest leaves the main shrine building after a "christening"

My favorite of all the shrines that make up the main Aso Jinja was this shrine to the kami of a rock. In the photo below you can see the rock, draped in a shimenawa, under the awning. The red and white rope hanging down is a rope-pull for a bell, so the kami will notice you when you’re asking for favors.
The shrine of the kami of the rock at Aso Jinja

The shrine of the kami of the rock at Aso Jinja

I was interested to find that the water at the Aso Jinja is highly prized for its excellent flavor. Nearly everyone that visits the Aso Jinja brings along a gallon bottle (or larger) to fill with water for the coming week–except for me. What kind of hydrogeologist would visit the Aso Jinja without a sample bottle? But you can be sure I’ll bring one the next time I visit!
The spring at Aso Jinja

The spring at Aso Jinja

NOTE: Some of the geological and cultural information in the above blog entry was taken from the excellent field trip guide “Living with Aso-Kuju Volcanoes and Geothermal Fields” by S. Ikebe, M. Yoshikawa, and Y. Miyabuchi. Many thanks to them for a well-written and thoughtful field trip guide!

CAMBR at Cornell

Friday, November 20th, 2009

The Center for Advanced Microelectronics and Biomolecular Research - or CAMBR - is a University of Idaho research center located in Post Falls, about an hour-and-a-half north of Moscow. Over the past few years CAMBR has popped up in the news for various reasons, some for their outstanding research and some for personnel issues sparking major drama.

But despite anything you may have read, the facility is responsible for some pretty incredible science.

Besides churning out specialty processing chips for NASA satellite missions, CAMBR is also working on developing nano-sized biosensors capable of detecting deadly diseases far sooner than current methods allow. In particular, Wusi Maki is working to cut the detection time of the superbug MRSA down from days to hours.

Some of the center’s research was recently highlighted in the annual report from Cornell’s NanoScale Science and Technology Facility, one of the leading nano research centers in the world. Here’s what it had to say:

“Nanowire electronic sensing devices (nano-ESD) were fabricated with doped semiconductor nanowires (~50 nm) on silicon/silicon dioxide wafers using electron beam lithography, The two metal contact pads with these nanowires were 20-2000 nm apart, which serve as the basis for electronic bio-detection. The device characterizations, semiconducting properties and use in a robust and sensitive bio-molecular detection of these nano-ESD’s are in the testing phase. The device characteristics were demonstrated with varying gate and drain voltages.”

That makes complete sense, right?

Yeah, I have trouble understanding all of that too. But basically what it is saying is that CAMBR is running on a bunch of tests on biosensors that are just 50 nanometers thick spaced as little as 20 nanometers apart. As they run these tests, they are generating data that will help this project - and many others like it - successful.

(How big is a nanometer? Try this video on for size!)

For more information about the biosensor project, try reading a column I wrote for a nanotech site or this description from the University of Idaho’s web site.

Unfolding Acrobatic Proteins

Thursday, November 19th, 2009

If you think contortionists for Ringling Brothers fold themselves into a lot of different shapes, wait until you get a load of some of the proteins in your very own body.

Backed by a $360,000 grant from the National Institutes of Health, Marty Ytreberg, a computational biophysicist, will join an experimentalist from the University of South Florida in a project to understand the basic structures of proteins that change shape.

Because this class of proteins changes shape, they can perform many different functions in the body, making it extremely important to understand how they work.

However, gaining that understanding is easier said than done.

The class of proteins is called intrinsically unstructured proteins, or IUPs. Scientists believe that up to 30 percent of the proteins in the human body exist in this class that constantly change shape and perform multiple functions. But because they’re constantly undergoing origami, it is very difficult for researchers to determine the different structures they take on, which is essential for understanding their functions in human health.

Much of the current research on IUPs focuses on what the proteins do rather than on determining their structures. Scientists put the proteins in a wide array of situations and see how they react; very few are researching the actual structures and mechanisms because it is intrinsically difficult to do.

There are two primary ways that scientists can determine a protein’s structure: x-ray crystallography and nuclear magnetic resonance (NMR). The former requires the crystallization of the protein, which forces it to stay in one shape, defeating the purpose of the study on those that change shape, such as IUPs. The latter observes a changing protein over a period of time rather than at a single point in time, creating a mess of data.

But Ytreberg believes he may have found a way around this problem.

Over the next few months, Ytreberg will use computers to simulate millions – if not billions – of possible structures that the IUPs could take. His colleagues at the University of South Florida then will use NMR to collect data on the protein’s actual structure. Then the team will wade through it all to see which simulated structures fit best with the actual data.

“Basically, the idea is to take a simulated structure and suppose that it was the only structure the IUP could take,” says Ytreberg. “Then you see if that structure shows up at all in the experiment. If it does, you keep it. If it doesn’t, you throw it away. Then, you weigh it based on the strength of the match. In theory, the idea behind the project is pretty straight forward. But in practice, it’s going to be tricky.”

Rockin’ CO2

Wednesday, November 18th, 2009

Jerry Fairley might be exploring the geothermal properties of Japan at the moment, but he has his hand in many more projects back in Idaho. And you may not expect a geologist to be involved in fighting the rising emissions of carbon dioxide, but his research is a great example of just how interdisciplinary the issue has become.

The problem with CO2 isn’t that it is created, it’s that it gets sent up into the atmosphere where it eats away at the atmosphere and theoretically causes the Earth to heat up. So many scientists are asking the question, “Does the CO2 really have to go up into the atmosphere?”

The answer, in some cases, is no. It can be pumped underground.

But wait, won’t that just cause some sort of future, unforeseen problem? Won’t the gas just escape eventually and be released into the atmosphere anyway?

According to those scientists working with Fairley, the answer is not necessarily. The technique is known as Carbon Capture and Sequestration (CCS). The idea is to capture the CO2 and pump it into massive basalt formations thousands of feet underground. There, the gas will dissolve into the water, interact with natural metallic ions and produce carbonate minerals like calcium carbonate.

In short, the CO2 would be transformed into rock. And once that happens, good luck escaping back into the atmosphere, my globally warming friend.

Fairley’s involvement in the project deals with the flow of water and gas through faults, fissures and other cracks in the Earth’s crust. These formations play a large role in predicting how well the CO2 will stay where scientists want it. The project is part of a giant collaboration of energy experts at the Center for Advanced Energy Studies (CAES) located in Idaho Falls, Idaho.

I didn’t get the idea to post about this research project by Fairley’s recent posts from Japan, though. The research project was recently covered in length by an excellent article posted online in the Electronic Component News magazone written by Mike Wall, science writer and blogger for the Idaho National Laboratory. The article does a great job discussing the challenges and possibilites of CCS, how a company is already implimenting the technology in Norway and the projects currently underway to develop the technology.

But.. how does it work?

Sunday, November 15th, 2009

Continuing the subject of sterilization with supercritical carbon dioxide I took up in my last entry, here is the question how the mechanism of killing process works. So, let’s talk a little bit of hypothesis, as there is no known sure answer to that yet.

As the carbon dioxide is the major driving force of this kind of sterilization, the explanation to the question about its possible mechanism is very obvious to focus on the properties of supercritical fluid.

The very first assumption proposed is that acidification may caused inactivation of cells. Carbon dioxide dissolves in aqueous solution, forms carbonic acid, which then is dissociated into bicarbonate and hydrogen ions. And this is how pH is lowered. The other realistic hypothesis is based on the fact the cell membrane consists of double layer of phospholipids, which inner is lipophilic. In reference to that, it is hypothesized that maybe carbon dioxide penetrates this layer and somehow changes its fluidity leading to its different characteristics and at the same time to destroying results. However, this what was assumed taking the vegetative cells into consideration. What about spores? Those latent forms of life, produced by some of bacteria strains are ubiquitous and can survive harsh conditions: UV and gamma radiation, high temperature, desiccation, lack of nutrients and peroxide treatment. When they meet the “safe” conditions, they germinate to produce vegetative cells. But in order to survive, they characteristics are different; much less water inside, specific compounds and additional protective layers. Definitely, killing spores is not a piece of cake, although it does take place. However, it happens probably in a little bit different way. As the temperature helps them to germinate naturally, using a higher temperature in sterilization activates them, but later the story is different as they are treated with supercritical fluid carbon dioxide which brings sporicidal effect.

Possible answers are multiple, some of them more reasonable than others. However, there is still no clear explanation to that and more studies are needed, and this is why I am finishing this entry and going back to work.

The smell of freedom

Friday, November 13th, 2009
Komori-san on Mt. Hossho

Komori-san on Mt. Hossho

Crunch…crunch…crunch…

Gravel crunches under my feet as I make my way up the long, rocky slope. This used to be a road, but I only catch occasional glimpses of asphalt; it’s mostly buried under tons of rockfall. The early afternoon sun is burning down on me, and the sweat is rolling off, dripping in my eyes, making them sting. My hard-hat doesn’t offer any protection from the sun (I have to wear it, though–it’s the rules), and, although it’s not very heavy, my packboard is digging into my back. These packboards were made to haul geophysical equipment, and comfort obviously didn’t figure into the design. I look back over my shoulder, but I don’t see anyone behind me. I can’t help wondering if they sent me ahead because they figured I’d need extra time, or because they thought I might not make it at all, and nobody wanted to be around when I collapsed?

I’m high up on the eastern slope of Mt. Hossho, hauling equipment for an EDM (Electronic Distance Measurement) survey. Mt. Hossho is one of about 20 lava domes and cinder cones that make up the Kuju volcanic complex, an active volcano north and a little east of Aso that is part of the Aso/Kuju National Park– one of Japan’s oldest national parks. They’ve been doing these surveys ever since the eruptions of 1995. Immediately after the eruptions they surveyed it every month or so, but the last few times it’s only been once per year. Looking around, I get the feeling they might survey it even less frequently in the future…

When we left from the Aso Volcanological Laboratory early this morning we were all under the impression that we could drive to the survey stations, because a high-altitude road ran from the town to the old sulfur works where the stations are located. This naive idea began to tarnish as soon as we came to the first river crossing. The water in the stream was shallow enough, but moving the rocks out of the roadbed by hand was more work than anyone expected. Just after lunch we gave up trying to drive, put everything on the packboards, and started up the hill.

The "road" up Mt. Hossho.  What remains of the road is visible on the lower right-hand side of the photo.

The "road" up Mt. Hossho. What remains of the road is visible on the lower right-hand side of the photo.

Eventually, I turn the corner on the road and start up the valley that leads to the survey points. As I do, I catch my first glimpse of the fumarole area. At the sight of the white plumes of vapor streaming out in the wind, I forget all about the packboard, the sun, and my aching feet.

Fumaroles on the eastern slope of Mt. Hossho, Kuju complex.

Fumaroles on the eastern slope of Mt. Hossho, Kuju complex.

Kuju was dormant for hundreds of years until 11 October, 1995, when a phreatic eruption blew 20,000 cubic meters of ash into the air, and opened new lines of vents on the eastern slope of Mt. Hossho. Another eruption followed in December 1995, and many thousands of earthquakes under the Kuju volcanic complex have been recorded since. Most of the seismic activity is centered at a depth between 800 meters above sea level and 1000 meters below sea level. A strong high-frequency attenuation of the seismic waves indicates there is probably a zone of fluids (steam, water, and gas) underneath the volcanic complex. Those fluids are believed to be the reservoir that feeds the fumaroles on the eastern slopes of Mt. Hossho.

EDM (or GPS) surveys on active volcanos are a common activity. The reason is that volcanos often swell up before they erupt. No, I’m not kidding. As magma and volatiles (like water, steam, and carbon dioxide) flow into the shallower reaches of a volcano preparatory to an eruption the ground actually begins to inflate; individual points can gain on the order of a meter (3 feet) of elevation. Often, this deformation can be detected by a distance or GPS survey.

Unfortunately, no one thought to do an EDM survey on Kuju BEFORE the eruption. To be fair, the thing had been dormant for hundreds of years! But now that it’s given a little burp, someone decided maybe they’d better keep an eye on it. The last ten years of surveys have all shown the same thing: a decreasing trend in volume. Most likely this is because the mountain has been venting gas through the fumaroles; like slowly letting the air out of a balloon, Kuju is deflating.

inowai_san

Inoue-san setting up the EDM

By the time everyone catches up with me I’m already at the first base station for the survey. They don’t really need me, other than to get the gear up here; after all, I’m a hydrogeologist, not a geophysicist. So, while they’re setting up, I decide to take a walk over to the fumarolic area.

The old sulfur works on Mt. Hossho. Some fumarole activity is visible at the upper right.

The abandoned sulfur works on Mt. Hossho. Some fumarole activity is visible at the upper right.

This used to be a sulfur mine, but it’s been abandoned since the eruption. I wander around below the fumaroles, unwilling to go up into the cloud of vapor without a gas mask. The air is thick with fumes, in spite of the breeze. There are chunks of native sulfur scattered around everywhere; I pick one up and put it in my pocket “for luck.”
A native sulfur sample. This sample came from Mt. Hossho, Kuju complex.

A native sulfur sample. This sample came from Mt. Hossho, Kuju complex. (Scale about 25mm/1 inch.)

Volcanologists used to think that volcanos swelled before an eruption because magma was being injected into the magma chamber, and lots of modeling was done to estimate the magma volumes on the basis of how much swelling was observed. Recently, however, it has come to people’s attention that some percentage of the swelling is not due to magma at all, but to the volatile components that come with the magma. So now we have to re-think all those calculations of magma volumes. I say, “good!” More work for hydrogeologists.
By the time I get back from the fumaroles everyone is ready to move to another base station, and an hour or two later the EDM survey is finished. As we pack up to head back to the car, someone mentions how strong the smell of sulfur is. It’s true. The air reeks of it, and I know the odor will cling to us for the rest of the day. “Smell of freedom” I say. Everyone stops packing and looks at me.
“Well, when I’m with my students at hot springs they sometimes complain about the rotten egg smell. I always say ‘it’s the smell of freedom,’ because, you know, instead of being in an office or a classroom or somewhere, we’re outside in the middle of all this…” I wave my hand around vaguely at the scenery.
Everyone smiles and shrugs. I can’t tell if they know what I’m talking about or not, so I just slip on my packboard and pick up an extra tripod that’s laying on the ground near my feet. It’s all downhill to the car, there’s a cool breeze blowing, and I’m up on a volcano in Japan. Suddenly, I don’t care anymore about the sun, or the rock slide across the road, or the packboard digging into my back–I’m just happy. After all, this is one of the reasons I wanted to be a geologist in the first place.
The author, on Mt. Hossho.

The author, a very happy man, on Mt. Hossho. Photo by S. Komori.

Collaboration is the Key

Friday, November 13th, 2009

If you’ve ever tried to get a document - or any sort of program/data - from a PC to a MAC, then you know sharing information between computers can be a maddening experience. So imagine for a second how many different computer languages are used to write programs and software for research purposes. Not only do you have to deal with the common ones, there are plenty of talented individuals out there who will write their own language to get a program to do exactly what they want it to.

This is all well and good until scientists try to collaborate and exchange information. One person’s data set might not run with another’s program. And we’re not talking about a few Excel spreadsheets here. We’re talking about terabites of information.

What’s more, the age of independent research is over. Sure, Edison could invent the light bulb by himself back in the day. Bell could figure out how to make telephones work. But no single scientist is going to solve global warming or the draining aquifer systems of the west on his or her own.

Luckily, the National Science Foundation recognizes this.

Recently, the states of Nevada, New Mexico and Idaho submitted EPSCoR proposals to study similar issues of climate change and its affect on the west’s dwindling water supply. EPSCoR is a program supported by the National Science Foundation aimed towards building the research capacities of states that don’t usually get many research grants. After each of the grants were approved, NSF realized that the three projects were similar, and suggested the three states write a joint proposal to get further funding.

So they did. And they got it.

Now the three states will be researching issues of climate change and water supplies together. As part of the grant, there will be people assigned to ensure any data collected or any programs written can all work together. I think this is genius.

Oh, and the grant also provides millions of dollars to improve the internet connections of research stations out in the middle of nowhere.

For more information, read the recent Idaho press release, or the story from the Idaho Statesman.

The Bayview Experience

Wednesday, November 11th, 2009
The ISMS is a net of acoustic sensors big enough to fit the Kibbie Dome inside!

The ISMS is a net of acoustic sensors big enough to fit the Kibbie Dome inside!

When you think about Idaho - a giant, mountainous, land-locked state in the inland Northwest - I’ll bet the first thing that comes to mind is “experimental Naval research center.”

Right? Right???

Hmm… probably not. But that’s exactly what you’ll find on the southern edge of Lake Pend Oreille, located about 2.5 hours north of Moscow and a mere 2 hours south of the Canadian border.

The Office of Naval Research’s Naval Surface Warfare Division collaborates with the University of Idaho to run the facility dedicated to making submarines invisible to the most sensitive of instruments. There are several reasons why the pair decided to begin the research station about 15 years ago.

One, the lake is the 5th deepest in the country coming in at 1150 feet. Second, the unique structure of the bay makes that entire depth isothermal, meaning it is a constant temperature from the top to the bottom and it does not change throughout the year. These facts allow the bay to have a background noise level less than that of the open ocean on most days.

So since it’s so quiet, if acoustic sensors can’t pick up a scaled-down submarine there, then nobody will be able to detect it in the open sea.

One of the things the center tests for is the sound of the water running over the surface of the hull. To do this, the Navy has set up a complex system of acoustic sensors and buoys that form a giant circular net all the way from the bottom of the lake to the top. It is called the Intermediate Scale Measurement System (ISMS). The outer edge of this is so big that it could fit the Kibbie Dome inside of it!

Scientists then take a scale model of the latest hull design and drag it to the bottom of the lake. Then they release the model, which floats to the top nose first. It takes roughly 30 seconds for the mini sub to reach the surface, during which time the net of acoustic sensors tries to detect it.

But the most fascinating part of this story is the fact that they usually do this at night so as to not hit any surface boats. But you can imagine the sighting of a test submarine suddenly surfacing in the hours around dawn has sparked some pretty interesting local legends!

Dual nature of carbon dioxide

Monday, November 9th, 2009

I thought that it would great to start with introduction what my project is about.
Carbon dioxide is a simple compound that has fallen into disgrace as a greenhouse gas. However, it is a natural gas, with chemical and physical properties extremely worth noticing. It is interesting that this gas at a particular combination of critical temperature and pressure becomes a supercritical fluid (SCF). It sounds like an extreme and somehow it is. Imagine a state that has both gas-like and liquid-like properties; that the density is shared between those two. What should be added is that it is nonflammable, nontoxic, chemically inert and noncorrosive. This mix of characteristics has already widely been used. Chromatography, a method of separation and the extraction of natural substances, take advantage of those dual properties, as a supercritical fluid carbon dioxide dissolves many compounds.
Love having a cup of coffee, but caffeine is no longer good for your health? Manufacturers used the properties of supercritical carbon dioxide to remove caffeine from the beans. That is one of the practical application and here is maybe another coming soon – sterilization. There is still a need for a gentle alternative of it and as the inactivation of bioburden with supercritical fluid carbon dioxide has been explored, there is a promising chance.
So I am continuing the project on finding out the optimal conditions for this method of sterilization. I am also trying to figure out what the mechanism of this process is and I will share more details about it in the next entry.