VRML for MEMS

I first wrote about MEMS – microelectromechanical systems – some time in the early 1990s. There was a promise at the time of scalable, modular reaction units that would eventually preclude the need for chemical plants to have multi-gallon reaction vessels and enormous distillation towers. Last time I looked, most chemical plants still had those vessels and towers but MEMS technology has nevertheless moved on apace. It has made enormous, or should I say tiny, inroads into the analytical arena in chemistry and life sciences.

One obstacle that stands in the way of the widespread adoption and further rapid development of MEMS technology is the fact that these devices are becoming increasingly sophisticated and so harder and more expensive to prototype.

Some MEMS designs are as complex as microelectronics circuits. But, whereas conventional chip designers can simulate their systems with software relatively easily, MEMS designers need something more solid to carry out simulations of the microscopic movements of fluids and energy in a MEMS device.

Now, Liao Ningbo and Yang Ping of the Laboratory of Advanced Design and Manufacturing at Jiang Su University, in Zhenjiang, and Yi Huijun of the Department of Mechanical Engineering, at Nanjing Institute of Chemical Technology, China, think they have the answer. They have turned to the collaborative and interactive design framework made possible by the concept of web-manufacturing.

In their approach, technologies used in dynamic web Java Server Pages (JSP) and computer graphics Virtual Reality Modelling Language (VRML) are integrated to allow them to model a MEMS device. “VRML, is a scene description language that can be used to describe 3D models of objects and scenes with the capabilities of interactive operations on them,” the researchers explain, “These models can be viewed using a web browser with a free plug-in for VRML2.0.” they add that several tools exist to convert almost any computer-aid design (CAD) format to VRML, which enables geometric models to be easily imported from pre-existing formats without having to redraw them. “VRML can be used to simulate fluid flow, of cause, with the description of fluid equations,” Nigbo told Chemspy.

SOURCE: International Journal of Materials and Product Technology, 2008, 31, 259

Doing Science

An interesting item on doing science from Chad Orzel represents more than a nod and a wink to the late, great Carl Sagan, although I didn’t see his name mentioned for whatever reason. Anyway, Prof Orzel distils the scientific process down to the following and has triggered an interesting debate nevertheless:

Science is a Process, Not a Collection of Facts The essence of science, broadly defined, is that it is a systematic approach to figuring out how the world works:

  1. look at the world around you
  2. come up with an idea for why it might work that way
  3. test your idea against reality
  4. tell everybody you know the results of the test

Put those steps together, over and over, and you have the best method ever devised for increasing our store of reliable knowledge.

That’s basically it. Not too scary is it? So, why do we seem to have such a vast gulf in understanding between those who eschew science and its proponents?

Curing Pubmedophobia

Scienceroll’s Bertalan Meskó has come up with a solution for PubMed fatigue. It’s a debilitating condition that leads to feelings of inadequacy, but it’s not the patient who feels inadequate it’s the PubMed bot itself. “For a site that is as vital to scientific progress as PubMed is, their search engine is shamefully bad. It’s embarrassingly, frustratingly, painfully bad,” says Anna Kushnir on her nature networks blog.

So, Meskó has been connecting up some pipes on the interwebs to come up with the Scienceroll Search. Basically, a personalized medical search engine powered by Polymeta.com. “You can choose which databases to search in and which one to exclude from your list,” he explains, “It works with well-known medical search engines and databases and we’re totally open to add new ones or remove those you don’t really like.” I almost have a feeling it is something that might have been done with a personalized Google search, but I doubt it could be taken to this logical extreme in Google. So give it a try and leave feedback on Meskó’s site.

Pricing Petrochemical Know-how

An informatics approach to pricing petrochemical products has been devised by scientists at the Market Research Department of the Research Institute of Petroleum Industry (RIPI) in Tehran, Iran. Their model puts a price on “know-how”, which is the most complicated activity of the commercialization stage.

Writing in the International Journal of Technology, Policy and Management, (2008, 8, 279-297), Reza Bandarian, Ahmad Mousaei, Abbasali Ghadirian and Maham Tabatabaei explain their approach. “The RIPI has a mission to bring ideas to market in terms of developing new technologies and new products,” they say, “Commercialization is one of the critical stages in this process.” Their model examines three pricing scenarios – optimistic, pessimistic and actual – for selling technology and was validate against historical data of various RIPI petrochemical products.

There are increasing demands on companies, not just in the petrochemicals sector but across the commercial spectrum. The marketplace needs better, faster and cheaper technology and products, while intellectual property, once simply seen as an expense has become an important source of revenue. Indeed, many of the problems seen in modern business hinge purely on IP rather than solid, hands-on extracted or manufactured resources. IP provides a critical competitive advantage for the firms that hold it but a serious disadvantage for those that do not.

Bandarian and colleagues point out that companies can no longer rely on the incremental innovation, i.e., improving on what has already been done, to compete and survive. Today it seems that “radical innovation” and “breakthrough products” are essential to long-term commercial sustenance. Even governments are beginning to recognize this in their wealth creation programs. The US National Science Foundation (NSF), which funds a huge amount of academic research in the USA not only demands that research projects are interesting, good quality and important scientifically, but that they also demonstrate the solution to a societal need or goal, which might be in constant flux.

The bottom line is that: “What customers want today, they will not want tomorrow, says the team. They point out that almost half the major corporations that existed in 1975 no longer trade. This is probably best explained by the fact that those corporations failing to grasp this simple tenet.

“One of the explanations for this dismal record is that companies are still trying to link emerging technologies with existing markets when they should be linking emerging technologies with emerging markets.”

In Iran and other countries of the Middle East, the researchers explain electronics, medicines and chemicals are major imports, while Iran’s national income comes essentially from oil production. Unfortunately, this resource has been used for wealth creation rather than technology creation. “Traditionally, the oil industry has improved in engineering maintenance while based on technology limitation; we have been kept behind that of developed countries, and the gap has increased.

This is perhaps the most important reason why Iran is the market leader in basic petrochemical products, but in high-value products, we have lost the market against developed countries,” the researchers add. They present a model that could allow innovation to seep, if not surge, through, by using know-how to evaluate and price innovative products, it is based on the low-cost and speed of current pricing models -experiential and mathematical – and side-steps their disadvantages of being untimely, requiring too much pre-market testing, and being highly skills dependent.

The researchers incorporate various factors into their model – the life cycle of know-how, annual market size, raw material and total production cost, selling price, net profit, earned income during investment, risk-free rate of return, know-how investment required, know-how return in its life cycle, know-how annual return in its life cycle, present value of know-how return in its life cycle.

Other factors can be fed into the model depending on the specific characteristics of the product in question. Indeed, “Our comprehensive framework of the commercialization of new technologies in the petroleum industry that can be used with some modification for other industries,” the researchers say. They tested their model retrospectively against RIPI product data and demonstrated an accuracy of around 97%.

Drinking Softened Water

A Chemspy reader sent me an email asking about the best way to fix their water softener.

Hi, I have a water softener. I met a local repair service, not affiliated with the manufacturer in any way, who can rebuild my broken unit with better quality after-market parts. Sounds like a good plan to me.

So far so good…the reader goes on…

The repair guy proposes to add some good quality resin to the tank to “top it up” if needed, and to add charcoal to the resin tank as well, as a filter enhancement. He claims the charcoal will get cleaned when the resin goes through the water softener’s normal recharge.

Again, sounds reasonable to me, although I suspect that the efficiency of a unit will depend on the quality of the components and presumably the actual fault and how that has been repaired. But, it was the final sentence of the email that made my heart skip a beat.

I only know charcoal filters as something you put inline, and replace before it poisons the drinker with its collected contaminants. Could the charcoal really be recharged and have the same useful lifetime the resin has?

Can you spot the potentially fatal flaw in what this Chemspy reader is doing with his water softener? I can and I’ve emailed him to tell him to cease and desist with immediate effect or suffer the consequences…your thoughts in the comments below would be appreciated.

Copyright and CAS Numbers

There’s discussion all over the chemical blogosphere at the moment about copyright and CAS numbers Chemspider’s Tony Williams first broached the subject in his blog and has followed up here. Cameron neylon has touched on the issue here as too have PeterMR and Kurt Wegner. If I’ve missed any links, please leave a reference to your post in the comments.

Anyway, here’s a thought…

Thumbnails (i.e. reduced size) versions of photos, images, and other visual creative works were recently the subject of a court case in the US, I believe. The judge suggested that displaying a thumbnail of an image was not a breach of copyright.

CAS registry numbers, InChIs, DOI’s and other such “creative works” might, in some sense, be considered an analog of an image thumbnail, and therefore may fall outside of a copyright claim similarly. Has anyone got the legal prowess to test such a case.

However, in writing this comment it occurred to me that there may be a more fundamental factor that would preclude CAS numbers being copyrighted. Aren’t they generated sequentially and automatically? If so, then perhaps they don’t fall under the description of “creative works” and therefore may not be copyrightable at all.

Chemical MSDS Sheets

Material safety data sheets (MSDS) is a perennial search favourite on the Chemspy site. The site has its own MSDS section and a javascript widget you can even add to your own site to allow your visitors to search for chemical MSDS sheets (yes, I know it’s a tautology on two counts, chemical material safety data sheets sheets, but like PIN number and “ATM machine”, the phrase is in common parlance.

Anyway, follow the link to search for MSDS on ChemSpy and here if you’d like to add the MSDS search toolbox (feel free to edit the script once you’ve saved it to your server to fit your site’s requirements).

Meanwhile, an offsite resource that looks promising for Chemical MSDS sheets is the obviously named MSDS Search, which duplicates some of the ChemSpy resources but adds a few new ones too.

YACJ – Nature Chemistry

April 2009 sees the launch of yet another chemistry journal, this one coming from Nature Publishing Group. It will, apparently, “provide a unique forum for the publication of high-quality research in all areas of chemistry.” Well, they would say that, they’re hardly going to tell us it’s a run-of-the-mill publication offering tedious and dead-end research, are they?

The launch site usefully reminds us that, “Chemistry is concerned with the study of matter on all levels, including its composition, structure, properties and how it can be transformed in chemical reactions.” Again, they’re not wrong there. But, speaking of definitions of chemistry, I thought Walt’s definition in Breaking Bad was pretty good.

If you don’t know about Breaking Bad (It’s not on UK TV yet, for instance), the plot involves a stressed-out, 50y old, high school chemistry teacher, who’s moonlighting at a carwash to make ends meet when he discovers his wife is pregnant and he’s dying of lung cancer. In desperation he hooks up with a crystal meth pusher and starts cooking up some highly pure and enormous crystals in the back of an RV. Needless to say the local dealers don’t like him muscling in on their patch, and he attempts to murder them (in the back of the RV) by pouring powdered red phosphorus on to a pan of boiling methanol. A quick lesson in the incredible corrosive properties of hydrofluoric acid – it burns through metal, rock, ceramic, but not polythene – all adds to the fun and games.

Anyway, Breaking Bad, with its periodic table credits, is a lot more entertaining than yet another chemistry journal. Although I am sure the Nature effort will turn out not to be YAFCJ at all but instead a major success, nudging JACS, Chem Comm, and Angewandte a little further along the virtual shelving.

Meanwhile, thanks for Chemistry Lab Notebook for the tip-off.

Drug Design on the Playstation

Serious drug design researchers are apparently hacking their PS3 machines to turn them into drug discovery workhorses. At least that’s according to my alma mater New Scientist magazine. It’s the kind of catchy subject they cover and is a classic from Mike Nagle.

The PS3 console uses a Cell chip, made by IBM, Sony and Toshiba, which is composed of a CPU and eight slave processors that run on Linux. According to NS, this chip is prized by chemists and physicists alike because the same kind of calculations it uses to produce the stunning, high-quality PS3 graphics for gaming are just about the same those needed to simulate reactions between particles, ranging from the molecular to the astronomical (apparently, you can do black holes with it too).

But, when we say they’re hacking the PS3, it’s not like these scientists are just plugging in a data cable and running their lab. According to NS, University of Massachusetts astrophysicist Gaurav Khanna has actually strung together 16 PS consoles to simulate the gravity waves that to occur when two black holes collide. While University of Illinois chemist Todd Martinez is running particle simulations on a Playstation, with 1000 atoms (a small protein in other words) that can be done 130 times faster than on an ordinary PC.

It’s all quite twee really, what with the surgeons cannibalizing their Wii consoles to do virtual operations and chemists latching on to the power of virtual world Second Life too. One can almost imagine the response of the peer review panels as the grant applications start to roll in with instrumentation inventories listing costs for 32 PS3 consoles, 20 Wii controllers, a couple of PSPs, and a dozen iPhones. The real test will come though if they can get away with tacking on a few copies of World of Warcraft and Nintendogs Labrador Retriever & Friends.

PaperID – An Open Source Identifier for Research Papers

As a journalist, I receive a lot of press releases that cite “forthcoming” papers. Depending on the publisher one can usually find the paper in a pre-press state on their website. However, it’s often the case that the DOI does not go live at the same time as the embargo expires on the press release, and so I might legitimately publish an article about the research I cannot use the DOI as the reference and must use the direct URL for the paper. Unfortunately, some publishers then move the paper when the paper publishes, so the link I used ends up broken.

Moreover, this cannot be useful for authors themselves in that a paper that does not make the grade at the International Journal of Good Stuff and ends up being resubmitted to the Parochial Bulletin of Not So Good Stuff will gain a different identification code along the way.

Will Griffiths on ChemSpider was recently discussing the possibility of an OpenURL system. I think we could go one step further.

A simple standardized way of generating a unique identifier for each and every paper that would be transportable between different phases of the publication process from submission to acceptance and publication, or rejection and resubmission elsewhere, would be a much better way of registering papers. The identifier would be created at the point when the final draft is ready to be mailed to the first editorial office in the chain, perhaps based on timestamp, lead author initials, and standard institution abbreviation. It could be the scientific literary equivalent of an InChIkey for each research paper.

There would have to be a standardized validation system, so that authors were sure to be using the right system, but that could be established relatively painlessly through the big institutions, be networked and have cross-checking to avoid duplicates. And, of course, be open source, open access.

The possibilities are endless, PaperID would create an electronic paper trail from author through preprint, in press, to online, and final publication. It might even be back-extended into the area of Open Notebook Science and equally usefully into archival, review, and cross-referencing.

DOI is useful most of the time OpenURL sounds intriguing, but PaperID could be revolutionary.