Chemistry World Podcast - February 2011

1:22 -Einstein in your engine

3:20 -Silk woven into transistors

5:30 -Joseph Jasinski from IBM on harnessing the power of your desktop PC to solve big scientific problems

13:08 -Using HIV against itself

16:39 -Microfluidic pinball 

19:50 -Joe Jones from Skyonic on turning CO2 from power plants into baking soda

26:15 -Urchins bare their teeth in materials research

28:33 -Measuring the strength of garlic 

31:20 -Who's your chemistry hero? To celebrate the international year of chemistry we want you to nominate your hero - join in on the chemistry world blog

  (Promo)

Brought to you by the Royal Society of Chemistry, this is the Chemistry World Podcast.

(End Promo)

Interviewer - Chris Smith 

Hello, welcome to the February 2011 edition of the Chemistry World podcast.   With me this month are Phil Broadwith, Mike Brown and Laura Howes and they're here to relate how relativity powers your car, the discovery of a new magic bullet for HIV- it's an antiviral but only activates in HIV infected cells and a new way to measure the amount of garlic in food, so you'll know better in future what not to eat before a hot date.   I'll also be talking to the man behind an initiative to harness for public good the power of the world's PCs.  

Interviewee -  Joseph Jasinski

Say, you're looking at drug screening, the actual computation you need to do only take a minute, but you've got to look at the million different combinations of molecules.   If you can only do that on one computer, it takes a million minutes.   On the other hand, if you have access to a million computers, it takes on the order of one minute to do the entire problem.

Interviewer - Chris Smith

Joseph Jasinski from IBM will be explaining the workings of the world's community grid later in the program.   I'm Chris Smith and this is the Chemistry World podcast.

(Promo)

The Chemistry World Podcast is brought to you by the Royal Society of Chemistry. Look us up online at chemistryworld dot org.

(End Promo)

(1:22 - Einstein in your engine)

Interviewer - Chris Smith 

And putting the key into the program's ignition force this month and please excuse the car-related introduction, it is relevant, Phil.

Interviewee - Phillip Broadwith 

Well Chris, the battery that actually starts your car is full of lead and sulphuric acid.   Lead is a very heavy element and a peculiar property of heavy elements is that because they've got very large nuclei, they accelerate the electrons around them extremely fast, so those electrons end up going up at a significant fraction of the speed of light and Einstein's Theory of Relativity says that that has some peculiar effects on their mass, which has very strange effects on the chemistry of these heavy elements.  

Interviewer - Chris Smith 

So faster something goes the heavier it gets, because it's got more energy.  

Interviewee - Phillip Broadwith 

Yes, that's exactly right Chris.   That phenomenon is the same one that makes gold a peculiar yellow colour rather than a sort of silvery colour in most of the metals.   It's also one of the reasons why mercury is a liquid rather than a solid.  

Interviewer - Chris Smith 

And this gives the car battery some of its peculiar electrical effects.  

Interviewee - Phillip Broadwith 

Well yes Chris.   What Rajeev Ahuja and Pekka Pyykk? at Uppsala University in Swedendid was in theoretical quantum mechanical calculations about how much of the voltage of a lead acid battery is down to these relativistic effects and it turns out to be quite a lot.   The voltage of a single cell of a lead acid battery is about 2.1 volts and the Swedish group's calculations say that 1.7 to 1.8 of those volts is down to these relativistic effects.  

Interviewer - Chris Smith 

So most of it. 

Interviewee - Phillip Broadwith 

Yeah pretty much, most of it.

Interviewer - Chris Smith 

How did they do that?

Interviewee - Phillip Broadwith 

The actual effect in terms of chemistry of what's going on with this relativity is it changes the energy levels of the different orbitals within the atoms and by doing quantum mechanical calculations of those energy levels and how they're affected in all of the chemical species present in the battery, they worked out what contribution that has to the potential.

Interviewer - Chris Smith 

Scary stuff.   Einstein was right and has even been driving my car today.   Thank you Phil.   Now Mike, sticking with the electric theme, but not quite car batteries, things you can wear, silk.   Now researchers are turning this into a transistor.

(3:20 - Silk woven into transistors)

Interviewee - Mike Brown 

Yes that's right.   So researchers in Sweden and Spain at the Link?ping University  and Biomedical Center in Sweden and the Center of Electrochemical Technologies in Spain have devised silk transistors that you can actually weave into clothing.  

Interviewer - Chris Smith 

So the wearable computer comes a step closer.  

Interviewee - Mike Brown 

Yeah that's right.   So at the moment, transistors which are semiconductors that amplify or switch electronic signal are printed onto hard substrates, such as your mother board in your computer, but in our technological age, we want flexible transistors that, you know, may be can power your mobile phone or your iPod, while you're walking around.   So, the place to put them is in your clothes.

Interviewer - Chris Smith 

Okay, so what have they done and how they've done it?

Interviewee - Mike Brown 

So, the team have dipped silk fibres into a conducting polymer and then they've woven them together and at the place where the fibres meet, they put an electrolytes solution on which, which then hardens and that means the fibres actually talk to each other.   So, when you apply a potential to one of the fibres, you can actually then change the voltage and current in another fibre.   So it's acting like a transistor in the clothes.

Interviewer - Chris Smith

What about if you do this with swimming trunks?   Is there a danger they might short out.   I mean, if you go into the sea or may be even have an accident perhaps or just wash your clothes, what's the impact of water on this?

Interviewee - Mike Brown 

Well, at the moment, the research is mainly in the kind of weaving them into a fabric and then they are going to think about water and how that affects at a later date, but I'm not sure going swimming would be a very good idea.   The team also says that in the future they want to intricate the structures into biological tissue as well, so that's the next step on.

(5:30 - Joseph Jasinski from IBM on harnessing the power of your desktop PC to solve big scientific problems)

Interviewer - Chris Smith 

So no silk Speedos yet, you are all right for the time being, Mike.   In a moment, we'll hear about a potential new breakthrough in treating HIV, but before that here's a technology that's helping researchers all over the world to solve big scientific problems and that's by harnessing the power of the desktop PC.   It's called the world community grid.   It's been built by IBM and Joseph Jasinski  is one of the Directors on the project.  

Interviewee -  Joseph Jasinski

The idea is that there are lot of scientific problems in the world that if they're solved properly could benefit humanity in a general way that it benefits society, but they require a lot of computing power and frequently the researchers who were trying to solve these problem at universities and other not-for-profit research institutions don't have access to enough compute power.   So the idea behind the world community grid is to get ordinary citizens to volunteer time on their personal computers with no effect on the actual use of the computers.   What we do is we use the time, when you're not actually using your computer, and we assign problems from the projects that we're currently working on led by academic and not-for-profit researchers to your computer, over the internet.   So your computer gets a little bit of code -- it comes as a screen saver and when you're not using your computer because you got off to get a cup of coffee or cup of tea or something, your computer merrily sits around doing these calculations.   When it's finished its calculation, it sends its result back to what we call the head node or the machine that organizes the grid and asks for another problem.   The reasons it can be very powerful as we have about 1.6 billion machines on the grid currently and so think about this.   If you're a researcher and you need to do computation, it takes may be a minute on a personal computer, but you need to do a million different use cases, so say, you're looking at drug screening, the actual computation you need to do only takes a minute, but you've got to look at the million different combinations of molecules.   If you can only do that on one computer, it takes a million minutes, which is quite a long time actually.   On the other hand, if you have access to a million computers, it takes on the order of one minute to do the entire problem.   Now there's communications that has to be done and stuff that actually   just take one minute, but you could reduce the problem that will take years and years of computation on a single machine to may be a few hours or a few days on a grid of 1.5 million machines.

Interviewer - Chris Smith 

So its kind of similar, I suppose, to what you do when you type a search into something like Google and they're distributing the problem over many, many, many link computers and there's huge array of computers dramatically enhances the computing power.   We've seen similar with SETI@home and things like that, haven't we?   So how is your thing different, is it the first?

Interviewee -  Joseph Jasinski

No, so it's not the first.   The reason it's different and SETI@home  is an example of one of the first of these kind of cycle stealing or cycle borrowing grids, if you want to call them that;   things that work in the background on a computer that doesn't belong to the person who's using it.   So Google is a whole different; they have dedicated machines that are actually being used to search the internet full time.   This is kind of an idea of Citizen Science right where you're contributing time on your machine that you're not using, to solve some problem that is of interest to you but is being actually coordinated by some researcher.   So we are not the first.   What differentiates us from all other grids of this type that we're aware of is that what IBM has done is set up an organization which actually runs the grid, but we don't have a particular problem that we ourselves want to solve.   So we recruit members, we recruit principal investigators who want to solve problems.   We work with the principal investigators to first of all assess if their code can be run on the grid in an effective way.   We have an external Board of Scientific Advisors, who decide whether the project meets the requirements of our community, which is to produce some result that will benefit mankind and we have a technical committee which sort of assesses, you know, is this a good use of the grid and will the problem actually run on the grid.   And once we've done that, we work with the principal investigator to get the code up and running and essentially run the experiments for them and provide the data back.  

Interviewer - Chris Smith 

And what sorts of problems are you solving because people will probably find it easier to understand if you can give some tangible examples of the kinds of things you're grappling with using this, what sounds like a very powerful tool.

Interviewee -  Joseph Jasinski

Yeah so as an example, we have a project called Five Dates at Home which is a project where a group of University of California, San Diego is trying to find new antiretroviral therapy, so new anti-AIDS drugs by doing a computation that is called a docking computation, so they have a model of what the protein is in the AIDS virus that they're trying to effect.   They have what's called a library, so a vast compilation of potential compounds that might have a beneficial effect on stopping the AIDS virus from doing what it does and they essentially need to find out which of those compounds are more like to stick to this protein compared to other compounds.   So it's very simple, what's called a docking calculation.   It can be run very well on single PC; you just need to screen millions and millions of pairs of proteins and molecules.   Another example has to do with analyzing results of gene sequencing experiments.   So we've worked on a project called Nutritious Rice for the World, where the gene sequence of different strains of rice have been determined and if we can now do simple computations to understand the function of the different genes in the rice genome, you can do what's called a marker assisted hybridization, which means that you can pick genes that impart beneficial properties like resistance to certain kinds of disease or tolerance for being overly water-logged and you can hybridize using normal hybridization methods that agriculturalists have used for years - new strains of rice with high probability of getting something that has improved yield or improved resistance to disease.

Interviewer - Chris Smith 

Well, it sounds absolutely terrific.   But what hurdles did you have to overcome in actually setting it up in the first place because it sounds the way you   tell it, terrifically simple, but I'm sure it hasn't been so.

Interviewee -  Joseph Jasinski

So the technology is not that challenging, we actually have used a number of different kinds of grid agents.   We currently run on Blank, which is a well known open source grid technology.   The real challenge is in getting a community together because obviously this thing doesn't work unless people volunteered on machines. So if you want to participate in the world community grid as a member, you go to a web site called worldcommunitygrid.org, all one word and you essentially register yourself, so we know who you are and you can join a team if you want, you can form a team and you download a screen saver and then you tell us if you want to work on a specific problem, we can assign your machine only to that problem, if you're generally open to working on any of our problems, we'll assign whichever problems we need more compute power on a given time to a machine.   It's very easy, you get some really pretty screen savers that you can show off and show people how your computer is saving the world.   So, it's really fun if you're interested in science.   The other thing I should mention is that each principal investigator produces a web page about their project that's written in plain English so that you can understand what kind of problem you're solving and what progress is being made and we send out regular news letters about, you know, what problems have been finished and what projects we're starting and updates when the results are made public as to where you can find those.

Interviewer - Chris Smith 

IBM's Joe Jasinski.   And the address again if you'd like to contribute some computing power to the project is worldcommunitygrid.org.

End jingle

Interviewer - Chris Smith 

You're listening to the Chemistry World podcast with me, Chris Smith.   Still to come, how to cheaply turn waste CO2 into salts and how sea urchins can keep their teeth sharp.   We'll look at the hardest hitting stories here, but first a new way to selectively hit AIDS infected cells, Laura.

(13:08 - Using HIV against itself)

Interviewee -  Laura Howes

HIV is obviously a major health problem and one of the things the Bill and Melinda Gates Foundation have been doing is a lot of grand challenges about HIV and how people can solve it.   Craig Crews and his group at Yale University in the US have taken all that money and have been looking to make a smart drug that will kill the cells that HIV is in without harming the rest of the body.

 Interviewer - Chris Smith 

Because obviously one of the big problems with AIDS drugs is that yes, this antiretroviral therapy involving a combination of drugs is very effective, but the side effects from some of these drugs are terrible - aren't they? And you also get resistance all the time, so always looking for new ways to come up with new drugs.

Interviewee -  Laura Howes

Sure. Sure.   So what Crews is actually looking at is instead of fighting the virus, he's looking to try and kill the cells that the virus lives in, the reservoir that it is in inside the body and actually trying to get rid of the illness   that way.  

Interviewer - Chris Smith 

How are they doing that?

Interviewee -  Laura Howes

Well, so they've got this drug, it's got a protease inhibitor and protease inhibitors work and kill cells, they're cytotoxic and lot of people have been using these for cancer therapies including Crews himself.   What they've done is modified one of their cancer killing, cell-killing molecules, so that it's only activated by the HIV virus itself.

Interviewer - Chris Smith 

Oh cunning! How?

Interviewee -  Laura Howes

To get the protease-inhibitor to work, it needs to get inside a small room and essentially pull a trigger.   What they've done is added a large stearic group onto their drug that can only be removed by a protein and an enzyme that the HIV excretes itself.   So it's a bit like if you're trying to get into a room with your umbrella, you end up dropping it, if you drop the umbrella, and you can get in much quicker.  

Interviewer - Chris Smith 

And it's the HIV's presence, the protease in HIV that effectively removes that umbrella and the drug goes in.

Interviewee -  Laura Howes

Yeah.   So the umbrella is how we link with a specific few amino acids that is specific for the HIV protease1 enzyme.

Interviewer - Chris Smith 

Sounds good, but the promise thereof a number of constraints with these, one of them being of course it won't get the virus which is resident in the genome because HIV goes into the genome and lurks there as a provirus doesn't it?    It periodically comes out from there.   So it won't get to that.

Interviewee -  Laura Howes

Sure. So one of the things that Cruz is talking about it having to actually activate the virus, so the word is it's sitting there hiding there in your genome.   You'd have to actually slightly activate it, start its working, start it producing the enzymes and the proteins that it would do naturally and once it does that your drug can be activated and kill the cells that it's resident in.  

Interviewer - Chris Smith 

What about, I mean, two important questions will they need sort of new drug or anything, one is safety - do these agents work in the body, are they biocompatible first and foremost.

Interviewee -  Laura Howes

These agents are biocompatible.   The actual drug that they've modified is already in phase III clinical trials for cancer research.   So there shouldn't be too much of a problem with it interacting badly in the body and indeed it shouldn't sort of kill cells that aren't containing HIV.

Interviewer - Chris Smith 

My next question was going to be what's the timeline because normally when a drug is in trial you're looking at 10-15 years.   But if it's already in trials and they're in an advanced stage IV albeit another disease that should speed things up.

Interviewee -  Laura Howes

Hopefully, hopefully, if they can prove that their concept works which they have and that that's not a problem the fact that's its already in phase III clinical trials could mean that its going to be developed a lot quicker.

Interviewer - Chris Smith 

Okay, Laura thank you.   We're keen on that because obviously HIV is very big problem with millions of people every year catching it, 7000 deaths a day and 7000 new infections with HIV everyday.   So anything that can be done to mitigate that is very important.   Now Philips, sticking with a very small but not quite as small as a virus, microfluidic pinball is on the agenda, tell us about this one.

(16:39 - Microfluidic pinball)

Interviewee - Phillip Broadwith 

Lots of us have fond memories of pinball machines, little balls being bounced around on the table.   But what Dieter Trau at the National University of Singapore is doing is using that kind of pinball idea to develop a way of making layers on the outside of oil droplets using polymers, so that they could be used to deliver drugs or do various other kinds of things.  

Interviewer - Chris Smith 

So this is a bit like if you got a sweet, these sweets that you get in which you've got multiple layers around the outside and you want to put those layers on this.    This is doing that at a tiny scale for droplets that could be drug molecules.

Interviewee - Phillip Broadwith 

Yeah Chris. It's a bit like a gobstopper as you say, so what these guys have done is take a sort of channel which has three parallel streams of liquid running through it in very straight streams in a kind of laminar flow.   Two of those on the edges, the polymers that they want to use to coat the droplet and the third one in the middle is a kind of washing solution that removes any residues of polymer that haven't stuck.   The pinball part comes in because in diagonal lines throughout the channel they have tiny little pillars. So,   when you push an oil droplet into the stream, it gets pushed along by the streams of polymers flowing but the pillars divert it across between the different streams so it goes through one polymer stream, picks up a coating of the polymer, goes through the middle wash and gets rid of any sort of excess and cures off the polymer then it goes to the other, the second polymer on the other side drops down on to the next set of pillars and goes back across.   So, for every diagonal line of pillars you get another layer of each polymer so you can build up as many layers as you want all continuously have a continuous stream of droplets.

Interviewer - Chris Smith 

And you could use this to make say, smaller drugs then, so these will be drugs with all these different layers on which will un-coat at a certain rate so they're delivered to certain bits of the intestine or they stay in circulation for certain amount of time before they activate that kind of thing.

Interviewee - Phillip Broadwith 

Yeah, one of the biggest problems with drug delivery is that drug molecules are often very fat soluble rather than being water soluble, it's one of the big problems in medicinal chemistry, you can find a drug that's fantastically active but it doesn't dissolve in water, so you have real problems getting it into the body in the first place.

Interviewer - Chris Smith 

I do not quite get it, because I can see that you've got three parallel trains of fluid there, and you've got these pillars running across them, so why do the little things that you're introducing to get coated, why do they transfer between the different fluid channels but the fluids themselves don't get perturbed into each other or mix up?

Interviewee - Phillip Broadwith 

I think that's partly to do with the way that the channel is designed; you have to have a very straight channel but also to do with the difference in viscosity and different surface properties of the polymers and the washing stuff.   If you get the properties of those right then they don't mix when they come into contact with each other.   But you can push the droplets through the interface and that way you get the coating.

Interviewer - Chris Smith 

Thanks Phil. Capturing carbon now and here's a man who's come up with the concept called Skymine which involves electrolyzing brime to make sodium hydroxide and using that to capture the CO2 in a flue stream.

(19:50 - Joe Jones from Skyonic on turning CO2 from power plants into baking soda)

Interviewee - Joe Jones

My name is Joe Jones, two-year-old president founder and inventor of the Skymine process that we use here at Skyonic Corporation to capture carbon dioxide from large stationary emitters like power plants and the biggest emitters and the biggest problem in the industry.   The process begins with taking very ordinary salt water, placing the salt water on one side of the membrane and then electrolyzing it. Hydrogen gas forms on one side of the membrane, chlorine gas forms on the other side and on that same chlorine side it forms caustic soda which pours off the bottom, one can then take the caustic soda and it's similar to drain cleaning products around the world, you take that hard lye and combine it in a spray tower with the carbon dioxide flue gas escaping a power plant or cement plant and it first forms washing soda in one column and then we use a secondary column where it is mixed again with carbon dioxide under right conditions and it forms baking soda.   The hydrogen and chlorine gases then go off and displace other means of making hydrogen from natural gas and we're making the chlorine at such low energies that we are able to displace higher larger carbon footprint means of making chlorine. At the same time this process accomplishes a full strobe of the acid gases sulphur dioxides and nitrous oxides both acid rain gases that people read about and eliminates the spread of mercury, lead, arsenic and terminate all the bad things that are otherwise in flue gas.

Interviewer - Chris Smith 

So what can you actually work with, can a power plant literally just send you what's coming out of the furnace or do you need something which is relatively clean already?

Interviewee - Joe Jones

Other techniques that use amine-based chemicals to capture CO2 and then re-release it and properly ground, they actually require a pre-scrubber but our process has its own scrubber.

Interviewer - Chris Smith 

What's the actual business model here, you would take the chlorine and hydrogen as you said, you offset some of the cost of selling it, the bicarb that you make is pharmaceutical grade, very high purity but there's only so much chlorine, so much baking soda and so on that people around the world need, what's the actual business case here for doing this?

Interviewee - Joe Jones

We performed studies in our work for the Department of Energy grants that we've achieved that show that we can proliferate up to 25 plants in the US and maybe four times around the world on the very first intermediate products which are baking soda and hydrochloric acid.   After that you can continue to make other products from those intermediates that's sodium carbonate and various grades of calcium carbonates, aragonite is a form that is used as a very low iron limestone that's used in the manufacture of plate glass. Then there's precipitated calcium carbonate which makes up about 40% of all the white paper that we use and then you start getting into the lower grades, so your point is well taken and eventually you run out of market but the business model is in turn upon using those profits to go use the invisible hand of economics to drive the marginal cost of CO2 capture to its lowest point but thereafter when we're doing it beyond the extended markets in capturing carbon, you are doing so at the least marginal cost for a ton captured.

Interviewer - Chris Smith 

That's the business model though but what about the energy model if I am running a power plant, I roughly know how much energy I am going to extract from my fossil fuel, if I staple on your technology, what's the energy cost to me doing this?

Interviewee - Joe Jones

Well the main thermodynamic laws can be translated as you cannot do anything without having any energy penalty and in this case when you convert a gas CO into mineral, carbonate or bicarbonate material, yes there is always an energy penalty.   The question then becomes well how bad is the energy penalty compared to other techniques? Amine and part of the ground technologies which are the current world standard for that will claim 25% energy penalties against coal and then the critics will state that those run up into the mid 40%.   We have been able to demonstrate in the field 27% like numbers and in laboratory with other techniques beyond what we are currently deploying commercially we are saying things that get down into the low 20% quite well.

 

Interviewer - Chris Smith 

So if I pass my flue gas through your process an