Category: Technology

Tech Talk – Miscellaneous discussion of gadgets, industry, computer science, social media, AI

Open Access Abbreviated, Combined

Phys Math CentralJust when you thought that the publishers had ran out of combinations of shortened discipline names – PhysChemOrgPhys, ChemCommPhysChem, CommPhysOrgGeoAstroChem (You know who you are!), BioMedCentral(!) is yet to launch another – PhysMath Central. PMC, an open access publishing platform, goes live today with a call for papers for its first journal is officially accepting papers for publication in its first journal, PMC Physics A, B, and C.

My former colleague on ChemWeb(!) Chris Leonard who is now heading up PMC tells me about why this endeavour is so important to the scientific community and publishing in general. “Global access to peer-reviewed research is as essential in the physical sciences as it is in the life sciences,” he says, “The same benefits apply, namely; increased readership, increased citations, decreased access barriers and the retention of copyright by the author.” Leonard is on record as saying that his move from the world of traditional publishing to the OA end of the spectrum represented an epiphany. “I started off at ChemWeb.com and subsequently moved to Amsterdam to work for Elsevier,” he explains, “I have now seen the light and am very happy to be developing physics and mathematics journals for the Open Access publisher BioMed Central.”

BMC explains the rationale behind the launch as being aimed at meeting the increasing demand for open access journals from major research institutes (such as CERN, the European Organization for Nuclear Research) and other funding organizations and government bodies. PhysMath Central could make research in physics, mathematics and computer science more widely available and increase access to this research to all institutes and individuals, without the burden of subscription charges. “The demand for open access is growing constantly as all scientists from all disciplines become aware of the benefits of open access publishing,” adds Leonard. Success will hinge, as with any new journal launch, on whether or not the putative authors feel the return on investment of submitting to the new journal will pay off in terms of readership and impact factor.

If the existence of yet more journals in the literature is not enough, PMC is also launching a blog, be sure to add it to your blogroll to keep up with developments and impact factor evolution. Oh, and one more thing, for their British authors: they deliberately missed off the “s” from “maths”.

Five times faster than BitTorrent

Similarity Enhanced TransferAnyone who has dared to download, a large file using the Bit Torrent system in which chunks of the file are pulled from other BT users in a form of distributed file sharing will know how slow (and sometimes how fast) the method can be. Although much of the BT system is exploited to share pirated movies and music it has a serious, legitimate side that also allows scientists, engineers and programmers to share the burden of huge database and ISO image downloads. Now, thousands of US tax dollars (in the form of an NSF CAREER grant) have been spent on improving on the Bit Torrent system.

David Andersen and colleagues at Carnegie Mellon University spotted the fatal flaw in torrents that often leads to the file sharing system grinding to a halt if the number of users with the complete or almost complete file are offline.

In conventional BT downloads, the files being shared must match exactly across the distributed sharing network or else they are ignored for download purposes. Anderson realized that identifying relevant chunks of files that may not be identical but are similar to a desired file could speed up Bit Torrent downloads. Anderson and his colleagues have designed Similarity-Enhanced Transfer (SET) to exploit this concept.

Anderson claims SET could make some transfers five times faster. “This is a technique that I would like people to steal,” Andersen said. Though he and his colleagues hope to implement SET in a service for sharing software or academic papers, they have no intention of applying it themselves to movie- or music-sharing services. “But it would make P2P transfers faster and more efficient,” he added, “and developers should just take the idea and use it in their own systems.”

SET works in a similar way to BitTorrent. Once a download is started, the source file is broken down into unique chunks. These chunks are downloaded simultaneously from accessible sources on the sharing network and then reassembled on the user’s computer. While this is underway, the SET program continues to search for similar files using a process called handprinting. In this method, sampling of non-identical files is used to find chunks that match the required chunks. Relevant chunks can then be downloaded from the similar files identified by this method, making the overall process much faster.

Although the researchers hope to use the SET approach for legitimate academic file sharing, they tested it on more common music and movie downloads. They saw a more than 70% improvement in downloading an mp3 file. A larger 55 Mb movie trailer was 30% faster when it could pull chunks from movie trailers that were 47 percent similar.

The researchers hope that such efficiency improvements will make SET part of the next generation of high-speed online multimedia delivery. “We believe that handprinting strikes an attractive balance for multi-source transfers. It efficiently locates the sources of exploitable similarity that have the most chunks to contribute to a receiver, and it does so using only a small, constant number of lookups. For these reasons, we believe that this technique is an attractive one to use in any multi-source file transfer system,” say the researchers.

How to produce static electricity with water

Water powered batteryYesterday, we ran a video showing you a water powered battery that can generate a 15kV spark using nothing more than some simple hardware and a professor who looks a bit like Einstein. Some readers may have worried that it was a spoof given the date (April 1) but this is a genuine piece of science based on the principles of static electricity.

Water is a polar molecule – there is a small difference in electric charge from one end to the other – but pure (deionized) water is also a very good insulator. As the droplets of water fall through the bottomless metal cans, their polarity induces a charge in the cans (which are by the way heavily insulated from earth (or ground). A positive charge builds up on the cans as the water molecules falling into the buckets become negative. This results in a charge separation or a potential difference between the paint cans and the buckets of water (which are also heavily insulated from earth).

Eventually the potential difference reaches a threshold at which point the insulating properties of the air between the two balls breaks down and a spark leaps across the gap. This spark, which has a temperature of several thousand degrees Celsius carries a voltage of between 10 and 15 thousand Volts, far more than you need to power even the biggest set of plugin speakers for your mp3 player.

Several questions remain. Where does the energy come from to create this enormous potential difference and could this form of electricity be tapped by building some kind of power station at the top of a waterfall and using two enormous cans and buckets? Well to answer the first question just look at the vertical arrangement of the equipment. The energy comes from gravity, from the potential energy of the water, which is above the paint cans. The second question is a little more complicated to answer. It would be possible to build a bigger generator, although insulating the components from earth would be tougher and the dissolved salts in river water would make it far less efficient than a generator using deionized water, but those are probably not the main issues.

Think about it, to make electricity generation useful we need a current to flow. How might you “tap” off a current from this type of generator when its product is effectively small-scale lightning? A capacitor in the spark zone, you say? But then isn’t the air acting as a capacitor, still doesn’t solve the problem of tapping off a current. Find an efficient and safe way to tap the power of lightning and you could make a fortune and solve the world’s energy needs. But, please don’t try those kinds of experiment at home!

Instead of generating static electricity, however, it is possible to use gravity’s power to move water to produce a current, much more readily…think water wheel, dynamo-type generator…think hydroelectric dam.

By the way, this experimental setup was originally devised by Lord Kelvin in the nineteenth century and is known as Kelvin’s Thunderstorm, it featured in Bill Beaty’s amateur scientist column in 1995, you can find a more detailed explanation there.

Water-powered mp3 Player

UPDATE: 31st March 2011 In hard times, humour is often all we have to lift our spirits. Given the current situation in Japan regarding the state of their nuclear power stations following the tragic and devastating earthquake and tsunami, a twitter follower, Christophe Shiffert thought this electric sweet potato funny enough to tweet about it and to allude to the constantly unfolding tragedy that is humanity’s failure to address the problem of energy in more creative and sustainable ways.

In this week’s video, MIT’s Walter Lewin demonstrates how to produce 10 to 15000 volts of electricity using a couple of empty paint cans, a bucket of water, some wire, and two balls. The question is how does this work and could you use it like the potato powered mp3 player?


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I’ll look forward to seeing your suggestions in the comments and will post a more detailed explanation the the answers tomorrow.

Free software shows how drugs work

Partition coefficientIf you are already a user of free chemistry drawing package ACD/ChemSketch but need a little more physical information from your tools than simple structure drawing, then ACD/Labs’ latest freebie might be right up your street. They just released ACD/LogP, which can be used to extract a lipophilicity prediction from your structures with a few mouse clicks.

For those not in the know, logP, is the octanol-water partition coefficient and is a useful value assessing how a putative drug might partition between cell membranes and cellular fluids. It gives you an indication of potential oral availability in other words. This allows drug designers to find out early on whether they will need to do additional work to make a compound available by mouth.

logP isn’t only about drugs though, agrochemists can use it to help them predict how their experimental compounds might partition between different species. This allows them to see whether a compound might target particular pests in preference to beneficial insects, for example.

This property is also useful to flavour and fragrance scientists who can judge in silico how a new compound might behave when added to food or dabbed on the skin as perfume.

ACD’s physical chemisty products manager Greg Pearl explains that making logP available to the community for free will not only support research but will help students and educators get to grips with this important property. ‘Freeware is especially valuable to educators and students with limited resources,” he says. “For example, during a lecture, an educator can interactively demonstrate how subtle changes to a molecule changes it physical properties – much more compelling than discussing a table of numerical results. It also gives students a chance to use the types of tools they will encounter in the workplace.’

“Through this release of ACD/LogP freeware to scientists worldwide we continue our tradition of advancing chemical research by making critical physicochemical properties available to scientists in an open-access environment,” Pearl adds. “Users will benefit from over a decade of algorithm refinement resulting in accurate and reliable predictions.”

Just for the record, ACD/Labs hosts the Reactive Reports chemistry webzine. There’s more information about logP on their site here

Chemical pipe works

Chemical pipe worksMitch Garcia of UC Berkeley seems to be far more expert with the latest web 2.0 tool that lets you produce your own search algorithms than I, so I asked him to look into creating a Yahoo Pipe to allow anyone to search as many chemistry journals as possible that offer ASAP and in press papers online. And, much kudos to him, he has done just that. Here’s chemistry journals search pipe. He explains the process and the limitations in a little more detail on his own blog.

Give it a try and let us know what you think. What makes this tool totally tubular is that once you’ve run a search using a pipe, the results are their own RSS feed, which means you can subscribe to the results with your news reader (My Yahoo, Bloglines, Google Reader etc). Even more intriguing is the idea that you could presumably then use that feed as the basis for creating an even more sophisticated Pipe of your own.

For instance, this feed displays the results from Mitch’s Pipe searching all those chemistry journals for the word greenhouse. It’s quite unlikely that there will be any gardening papers in the ACS, RSC or Wiley chemistry journals, so you can be fairly sure that this feed will bring you the latest papers on greenhouse gases and their effects. Combine that with a feed for global warming, and one for climate change, and you should have the niche covered.

Orders of magnitude

Strangely, the phrase “orders of magnitude” featured in a visitor’s search efforts while browsing the sciencebase site. Unfortunately, other than using the phrase myself in the context of, for instance: “the amount of greenhouse gases emitted by human activities is several orders of magnitude smaller than those emitted by natural processes”. I did not actually have a definition of orders of magnitude on the site. Until now. So here goes:

The order of magnitude is the scale of any given amount where each class contains values of a fixed ratio to the class preceding it. The ratio most commonly used is 10. For example, a kilogram is three orders of magnitude bigger than a gram.

In the greenhouse gas instance cited above, the phrase “orders of magnitude” is simply being used colloquially and can apply in many situations, such as the volume of water in the Pacific Ocean is many orders of magnitude greater than that contained in Lake Michigan. To give a more solid example, one might say “An order of magnitude difference between two values is a factor of 10. For example, the mass of the planet Saturn is almost 100 times that of Earth, so Saturn is two orders of magnitude more massive than Earth.

Orders of magnitude are not always on the decimal scale. For instance, the difference in size between a megabyte and a gigabyte is three orders of magnitude, but the multiplier is 1024 rather than 1000. Please correct me if I’m wrong on that, I guess you could define a single order of magnitude her as being based on 1024 rather than “10”.

More on order of magnitude here.

Intelligent materials protect sports lovers

An intelligent plastic that is so flexible when left to its own devices while flow like a very slow moving liquid, but hit it with a hammer and the intelligent molecules form which it is made stiffen up instantaneously and absorb the energy of the blow. Such a polymer has been incorporated into textiles and clothing to create lightweight and flexible body armour for high-impact sports and other activities to save users from serious impact injuries. The polymer and textile-embedded material was the brainchild of UK company d3o, which has recently worked with a sports clothing manufacturer to develop a range of protective gear.

There was a video that demonstrated how to protect a falling egg using this material. This would make an excellent science fair project: compare different packaging materials for protecting eggs – cardboard, polycarbonate, d30 intelligent material. Unfortunately, the vid is no longer available.

The smart material is made up of a matrix of polymers with tiny pockets filled with a fluid. In normal wear, the material moves freely with your body movements but if you take a dive, the intelligent molecules in the fluid stiffen in less than a thousandth of a second, which makes them absorb the energy of the impact It works because under normal conditions, the polymer molecules move and slide across each other, but when they are put under rapid shear stress in an impact, for instance, the polymer molecules immediately form cross-links with one another and the material stiffens to take the brunt of the impact. Once the force is removed, the polymer cross-links are disengaged by further low force movements and the material reverts to its flexible state.

Chemical Wedding Gifts

FullereneMost people are well aware of the traditional materials offered to married couples to celebrate their wedding anniversary. You know the kinds of thing I mean – ruby for instance is the gem of choice for a 40th anniversary, although why a chunk of chromium infested aluminium oxide should have been chosen for this year in particular I don’t know. The noble elements silver and gold are 25th and 50th respectively, while the hardest allotrope of carbon, represents the 60th celebration (diamond, that is). If you want the complete list check out our traditional wedding anniversary gifts page, but if you want something a little different, a reference for Kevlar, zeolites, buckyballs, or PVC say, take a look at our chymical wedding round-up.

A semantic chemist – fixed

RSC ProspectI recently interviewed Robert Parker, the new Managing Director of RSC Publishing, you can read his interview in the February issue of chemistry news magazine Reactive Reports in which he discusses a new approach to the publication of scientific papers, RSC Prospect, and how it will benefit readers and the scientific community at large. It would be interesting to know what users think to the RSC’s new approach to meta data and a semantic chemical web.

“We needed a meaningful way of identifying compounds uniquely and one that’s machine readable – InChI fits the bill. Similarly, CML offers us a way of structuring lots of the science within a paper to both preserve the original science and do interesting things with it, and by demonstrating some of these applications, we hope to encourage wider adoption,” Parker told me, among other things. Check out the interview for his take on Web 2.0 for chemists, blogs and wikis, and more.

Also, featuring in Issue 62 of Reactive Reports: