Tools and technologies for researchers

The Library at Imperial run a course called Blogs, Twitter, wikis and other web-based tools. They asked me (and also Jon Tennant) to give a quick talk to the attendees yesterday on the things I use to do my work.

Rather than give a slide-based presentation I decided the best thing to do was give a demo. I quite like mind mapping to help me structure ideas so I made one for this. I’ve included links to web sites where appropriate. You can download a PDF of the mind map here (PDF).

It’s split into two halves: the tools that I do use, categorised into “inputs” (e.g. Twitter and RSS) and “outputs” (e.g. Google Drive), and those that I don’t with some short reasons why. If you’re interested in trying some of this out, give one or two a go and see if you find them useful. If you use something that I haven’t mentioned, let me know in the comments.

Light- and power-making things

Inspired by xkcd’s Up Goer Five comic Theo Sanderson created the Up Goer Five Text Editor. It challenges you to explain a hard idea using only the thousand ten hundred most commonly used words in the English language. Lots of scientists on Twitter have been using it to try and describe their work. It’s a lot harder than it sounds! Here’s my attempt:

Many years ago a few people were doing some work and, to their surprise, they managed to make light come out of something that had never had light come out of it before. People were very excited about it and now lots of groups of people spend their time trying to answer questions like “how does it work?” and “how can we make it work better?”. Everyone was interested because they thought it could be used to make new things like better TVs, very small computers and different kinds of lighting. But the perhaps the most important thing it could maybe do was give us all a new way to turn light from the sun into power for not very much money.

At the moment only a few people get to see them because they are hard to make. They are hard to make for lots of reasons, but perhaps the biggest reason is that the parts you need are themselves hard to make. Everyone struggles to make enough of them exactly as they need them to be. If the parts aren’t good enough, sometimes not very much light comes out, or for only a little while, or the ones that turn light from the sun into power don’t do it very well. No one wants any of those.

It doesn’t help that the normal ways of making the parts are often only good enough for making a little at a time. If you try to make more in the same way it stops working so well. I’m part of a group of people trying to make the parts in a new way that can make lots and lots and it still be good enough. In fact, our stuff is usually better than the best stuff you can buy.

I try lots of different ways to make things. I look in books to read how other people did things to get new ideas that no one else has had before. Sometimes they don’t work, but sometimes they do and when that happens it makes me very excited and happy. Sometimes we tell everyone but sometimes we only tell a few people. We can use my new way to make the light-making and power-making things work better and for less money than ever before so everyone can have them.

What do you think?

Microwave heating: still nothing special

For many years there has been debate over whether there is a specific microwave effect on chemical reactions or if it’s just a thermal effect. A couple of years ago I took lecture course on microwave and ultrasound chemistry. The course covered a few papers on the existence of a microwave effect and concluded that there isn’t anything special going on—microwaves just give very efficient and fast heating compared to normal convective heating in an oil bath or dry-syn block.

I found course particularly interesting, so whenever I see a paper on the subject I at least read the abstract to see if anything has changed. Angewandte Chemie have recently published a paper titled Microwave Effects in Organic Synthesis—Myth or Reality? (DOI: 10.1002/anie.201204103) by C. Oliver Kappe, Bartholomäus Pieber, and Doris Dallinger.

They looked at two recently published papers that allegedly found a specific microwave effect. Both claimed microwave irradiation significantly enhanced the reaction rate or yield in a way that couldn’t be replicated by regular heating to the same temperature.

Summarising a few pages: Kappe et al. couldn’t replicate the findings and argue that the problem lies in poor temperature management. To test the existence of a specific (non-thermal) microwave effect you need to run the same reaction twice at the same temperature, one with microwaves and the other normally (e.g. with an oil bath).

However the researchers who report a microwave effect use external infrared temperature probes, which record a lower temperature than the bulk reaction mixture. Microwaves heat more efficiently than the normal heating, so the microwave reaction will give you a higher yield and both vessels are in fact not at the same temperature. Instead you must use fibre optic temperature probes placed inside the reaction vessels. Doing this eliminates any microwave specific effect. To quote:

Importantly, we firmly believe that the existence of genuine nonthermal microwave effects is a myth, as all our attempts to verify these often claimed “magical” microwave effects during the past decade have failed.

It’s a good read and, I think, a nice example of science at its best. I’m also glad I read it because a colleague and I had, for some reason, been looking at getting a microwave flow reactor—which would be completely pointless, as all the benefits of microwaves in batch chemistry (high pressures and homogeneous heating) can be readily achieved in flow using normal convective heating. If anyone could tell me why such an apparently pointless bit of kit exists, I’d like to know…

Reference: C.O. Kappe, B. Pieber and D. Dallinger, Microwave Effects in Organic Synthesis—Myth or Reality?, Angewandte Chemie International Edition, 2012. DOI:

Making semiconducting polymers in flow

Organic electronics has a problem with batch-to-batch variability in the quality of materials, particularly the active semiconducting layer. A fellow PhD student in my office described to me the trouble he often experiences. He made one batch of solar cells last week and measured an average efficiency of 5 %. This week, another batch had only 0.5 % efficiency, depsite having the same device structure and processing conditions. Further investigation revealed that the lab had recently switched to a new batch of polymer, even though they’re supposedly identical.

(This raises the question of how many positive literature reports describing organic electronic devices are “correct” and not anomalous? But here I want to focus on this problem in the context of large scale device production.)

Batch-to-batch variation is bad enough with the sub-gram quantities used for small area device fabrication. Printing optimised large area devices—measured in square metres/minute rather than square centimetres/day—would be next to impossible. You need to know that this week’s batch of polymer is the same as last week’s because different molecular weight size distributions, chemical defects and impurity levels have a big effect on the required processing conditions and final device performance.

It’s quite difficult to produce organic semiconductors on the large scale required for device printing because the polymerisation reactions scale up poorly from round bottom flasks to large batch reactors. You have to re-optimise at each scale, which costs time and money.

James Bannock, who is a PhD student in the same group as me at Imperial, has been working on the use of droplet flow reactors to make poly(3-hexylthiophene) and get around the problem of batch scale up. He’s recently published his work in Advanced Functional Materials (DOI: 10.1002/adfm.201203014) and it’s open access so you can read it yourself for free.

I encourage you to take advantage of the paper being open access and have a look. There’s lots of photographs and figures. Briefly, activated monomer solution is injected into a narrow plastic tube containing a flowing stream of immiscible carrier fluid dispersed with the catalyst. Microlitre-sized droplets form, like tiny individual reaction flasks, and travel through the tubing. Because the droplets are small the chemical environment is highly homogeneous and each droplet is essentially identical. The tubing is heated in an oil bath and the polymerisation reaction (a Grignard metathesis) happens as the droplets travel through the tubing.

You can produce more material by using longer tubing and a higher flow rate. Crucially, this can be done independently of droplet size. So unlike batch reactors, nothing happens to the chemical environment and you get exactly the same polymer, with a low polydispersity index and high regioregularity. The plan is to apply this method to other organic semiconducting polymers. It provides a way to produce device-grade polymer on large scale required for large area fabrication, with minimal batch-to-batch variation, and will hopefully drive the industrial production of organic electronic devices.

Reference: J. H. Bannock, S. H. Krishnadasan, A. M. Nightingale, C. P. Yau, K. Khaw, D. Burkitt, J. J. M. Halls, M. Heeney & J. C. de Mello, Continuous Synthesis of Device-Grade Semiconducting Polymers in Droplet-Based Microreactors, Advanced Functional Materials, 2012. DOI:


Chem Coach Carnival

Here’s my very late contribution to See Arr Oh’s Chem Coach Carnival. The hashtag is #ChemCoach on Twitter.

Your current job.

I’m a PhD student at the Centre for Plastic Electronics at Imperial College London. I make metal nanoparticles of various shapes and sizes using flow reactors. Other researchers want them for use in organic electronic devices.

What you do in a standard “work day.”

Upon arriving at uni I immediately go for a shower because I cycle rather than take the tube. Riding my bike keeps me sane. Next thing: coffee.

After that I sit down and plan my day, most of which is spent in the lab. For my own research that involves analysing data, planning/doing reactions, ordering supplies/equipment, programming, building home-made equipment, doing electron microscopy, writing…

My work is very varied and I like it like that. I’m in a small group so everyone has to muck in and learn how to do lots of different things. Nothing is simply delegated to someone else. I think my work probably borders on chemical engineering/process chemistry.

I spent most of Friday running some preliminary tests on a new flow reactor. I also took delivery of a new optical microscope, then helped get rid of an old server rack because we’ve recently got a new optics table and need to make some space. After clearing up the mess I made in the lab I helped out our undergrad student with some MATLAB code.

I also spend one afternoon a week demonstrating for third year undergraduate physical chemistry labs. Teaching is fun, but sometimes very frustrating.

What kind of schooling/training/experience helped you get there?

I went to a comprehensive state school and sixth form before to Imperial for my undergraduate chemistry degree, where I’m now doing my PhD.

During my undergrad I did a summer placement with another group at Imperial, very generously funded by the supervisor. That confirmed for me that I wanted to do a PhD. I strongly recommend that students interested in a PhD do a summer placement.

I’ve also had a lot of non-chemistry part time jobs, mostly in bookshops. I’d like to think that’s given me a good try-anything, get-on-with-it attitude.

How does chemistry inform your work?

It doesn’t so much inform my work as form the core of it. It’s no good if I build the finest flow reactor in the world but my reaction doesn’t work.

I love running reactions, especially anything with a nice colour change. It’s so exciting when it works (and totally makes up for all the times it doesn’t). This Abstruse Goose comic sums up my feelings perfectly.

Finally, a unique, interesting, or funny anecdote about your career.

Not funny, but I’m fairly sure I’m the only person to have ever modified an Argos mini oven to make silver nanoparticles.

Conference talks: generally a bit rubbish?

Athene Donald recently wrote about what you don’t see at academic conferences. Academics may go to conferences in exotic places but they only see the inside of conference centres, hotels, airports and restaurants.

In the last year I’ve only been to two conferences. Unfortunately neither of them were in exotic places. The first was in York and I went with a few people from my group. As none of us are especially well-known in our field we unlike Athene had the freedom to explore York in the evenings. The second was held at Imperial and attendance was compulsory for DTC students. They were both small (no parallel talks) and lasted two days.

The speakers at both conferences, with the exception of one or two each day, were incredibly uninspiring and unenthusiastic. I remember trying to fall asleep one afternoon in York after nearly exhausting my iPhone battery reading papers. I was very disappointed as I had hoped to come back with fresh ideas but instead felt that it was a massive waste of time and money.

How can people talk so blandly about their own work? If the speaker isn’t excited by it then they most certainly can’t expect the audience to be interested. Many talks didn’t have any questions—the presentation equivalent of a death knell.

How have we ended up in this situation? I find it particularly baffling when I think about talks given by PhD students in my DTC. Recently we had a day with industry sponsors and visitors from other universities to listen to some third and final year PhD students present their work. The presentations were largely fantastic. Enthusiastic, confident, engaging, interesting… Really very good. Last month my cohort gave our MRes talks and the comments from markers were (nearly) all positive too. A world apart from the dreary, mind numbing talks I’ve sat through at my last two conferences.

Perhaps I’m overreacting, but I’ve really been put off going to anything other than something massive like the MRS conference where there will always be something related to my field and hence tolerable, even if the speaker is a bit tedious.

Does anyone else find most talks bad too? Are good talks unfortunately the exception? On the positive side, at least I’m at the beginning of my career so I can follow Athene’s advice, especially for my next trip to Italy in April:

Early career researchers, don’t kid yourself your professors enjoy themselves on such trips by seeing all the sights of the world you’ve always wanted to see yourself. Chances are, if you get to visit some far-flung place for a conference, you will enjoy your trip much more than your seniors because you live your life at a more leisurely pace. Make the most of it!

Open Access: Going for Gold?

Tonight the Science Communication Forum at Imperial College held a debate called Open Access: Going for Gold? with Stephen Curry (Imperial) and Mark Thorley (NERC, RCUK). The debate was chaired by Richard Van Noorden (Nature News).

Update 2 (28th September): you can listen to the debate on Figshare and here’s a useful link to RCUK’s open access policy (PDF).

Lots of things were discussed but a couple things in particular stuck in my mind writing this on the way home.

RCUK require for CC-BY for gold, but only CC-BY-NC for green

Under the new RCUK policy researchers must either pay a fee to publish in a gold open access journal or alternatively publish in a closed access journal and then deposit the article in a repository within 6 months [1].

Gold articles must be published with a CC-BY licence. This is good as it means anyone can do what they want with the work as long as the original authors are attributed. However, green articles deposited in a repository after the embargo period are only required to have a CC-BY-NC licence, meaning that you cannot use the work for commercial purposes.

This is very disappointing. Sadly it wasn’t discussed in the debate. CC-BY-NC is, as tweeted during the debate, a licence of fear. All it says is that the authors couldn’t think of a way to make money out of the work, so they’ll be damned if anyone else does. The work might as well have never happened.

Thorley talked about open access benefiting “UK PLC”, but CC-BY-NC is at complete odds with this. CC-BY-NC stifles innovation and progress. Furthermore, if the state funded the research, then the state and the rest of society should benefit from it. Under CC-BY-NC, no one benefits.

Green is of poorer quality than gold?

A couple of people doubted the quality of papers published straight to repositories like arXiv. I’m not so convinced. Firstly, they assume the reader is stupid and can’t work out for themselves if a paper is a load of nonsense. Secondly, it assumes that peer review weeds out all the bad papers. It doesn’t. Someone suggested a kitemark to say that a particular paper in a repository is trustworthy. I hope I don’t have to explain why that’s an awful idea.

Thorley did at one point say something about gold papers being better for the lay person. Curry looked quite suprised. This is a completely different debate. Just because a paper is literally accessible to the public doesn’t mean the information contained within it is intelligible to the public. But if someone is interested enough to be reading papers I don’t think gold/green will really make that much of a difference to them—not enough to justify an APC. I wonder what percentage of papers even undergo any major revisions between submission and publication.

Concluding thoughts

CC-BY-NC for green is a real disaster. I sincerely hope RCUK revise their policy so that it’s the same as gold.

I still can’t make up my mind about green versus gold. On the one hand, I think everything should go straight into repositories like arXiv. Forget journals and use the money we save to help fund and develop repositories, (although I know this is really very unlikely to ever happen). But on the other, if we are going to pay journals to publish work, we should expect more in return. Not just PDFs, but high quality (interactive?) documents including data and code in reuseable formats and tools to help us do things like text mining. I can’t help but think there’s very little innovation in publishing, especially considering the size of their profit margins.

It’s clear a lot more will happen in the open access debate. As Thorley said, this isn’t an event, it’s a journey. Hopefully it won’t be too arduous.

Update: gold—a free market for innovation?

Having slept it on it I can see where RCUK are coming from with their preference for gold, but I think they’re overestimating what publishers actually offer at the moment. Do most journals currently add enough value for it to be worth the APC? I’m not sure. I get the feeling people tend to think that every journal produces papers as beautiful as NPG. Authors will be paying the journal to publish, therefore we should expect more in return—especially considering the tidy profit margins. At present, I don’t think gold is that much better than green in that respect.

If, as Curry said, scientists end their addiction to impact factors (increasingly likely as HEFCE will be enforcing their ban on them), gold might lead to a more free market-like situation. Scientists will look around for journals that offer the best value for money. This could really drive innovation in scientific publishing as publishers are going to be competing in terms of what they can offer scientists rather than what the journal can do for an author’s career.

(Updated on 09:02 on 27th September 2012 with additional section.)

[1]: Thorley said that the embargo periods vary in length from publisher to publisher. He was pretty clear about 6 months and said 12 months was “a joke”. Personally I think 6 months is still far too long. It also raises the question: do publishers only add such little value that its only worth 6 months? Why bother with it in the first place?

The way-it-should-be-ness

The BBC have published an audio slideshow called Chair Champions on Charles and Ray Eames, designers best known for their furniture. The Eames Lounge Chair is probably their most famous work.

I like well-designed things. Not in the sense that they look a particular way, but that they fulfil a specific function extremely well. The couple designed objects that were both functional and stylish. The following from the end of the slideshow has stuck in my mind:

“Charles and Ray had this idea that good designs had ‘way-it-should-be-ness’. If something was really well-designed, then the idea of it being designed shouldn’t come up at all.”

I love this idea of ‘the way-it-should-be-ness’. In my own work, I try to find solutions to problems that are elegant. I want my solutions to have ‘way-it-should-be-ness’. Writing my MRes report led me to reflect on the last year and I’ve noticed that this desire to get the perfect solution has actually been a bit of hindrance.

I spent far too long sat at my desk searching the literature for the best solution. When I finally settled on a plan, it was a bit of a long shot. If it worked, it really would have been awesome. But it didn’t. The paper that I based my idea on was almost certainly suspect.

Around the time I was working on the dodgy reaction I read Tim Harford’s Adapt: Why Success Always Starts with Failure. It’s quite good. He’s like a better Malcolm Gladwell. Harford summarises the way Russian engineer Peter Palchinsky, who ended up being executed by the Soviet government for criticising them, solved problems as three ‘Palchinksy principles’:

  1. Seek out new ideas.

  2. When trying something new, do it on a scale where failure is survivable.

  3. Seek out feedback and learn from your mistakes as you go along.

I like them. I do the first, but my problem lies with the other two. Over the last year everything depended on this one reaction—a risky, naive strategy. There was little feedback and refinement. I ended up rushing another reaction towards the end so that my report on ended on a high note. After all, no one likes a sad thesis.

I bet Charles and Ray Eames didn’t come up with their objects overnight. There must have been hundreds of drawings and prototypes of the Eames Lounge Chair, but it’s easy to forget them as you only think of the final product. They probably worked in a similar way to Palchinksy.

Now I’m making an effort to work more iteratively. I still think of rather grand ideas, but instead of going for it in one enormous optimistic leap, I’m working towards them bit by bit, in a process of steady refinement.

I’ve already had some success last week working in this way. It gives much more positive mindset of working too. Hopefully I’ll soon have my own chemistry equivalent of the ELC and after refining it down I’ll look at it and think “yep, that’s the way it should be.”

Forget the scotch tape: how to make loads of graphene

Earlier this year I was writing a review about transparent conducting materials for organic electronic applications. As part of it, I wrote a fair bit about graphene. One of the key problems is that it’s difficult to scale the desirable properties of small pieces of graphene to large areas without resorting to quite challenging techniques.

In 2004, when Geim and Novoselov managed to isolate single-layer and few-layer graphene, they did it using Scotch tape to “mechanically exfoliate” graphite—basically using Scotch tape to peel off a layer of graphene from the graphite [1].

This technique gives very high quality crystals of up to 10 micrometres in size, but it’s limited to laboratory scale production—you’re not going to use this in a factory to make components for electronic devices. When I was writing the review, I wanted to write something along the lines of “…mechanical exfoliation, whilst producing very high quality graphene, is impossible to scale up…” but my supervisor told me to change it to something less definite, hinting these things have a habit of a coming back to prove you wrong.

To my surprise, someone has managed to scale it up. Chen and co-workers recently published a paper describing mechanical exfoliation of graphite using a three–roll mill [2]. Here’s a pen and paper sketch of their set up.

Sketch of the three roll mill set up used by Chen et al. to mechanically exfoliate graphene.
Sketch of the three roll mill set up used by Chen et al. to mechanically exfoliate graphene.

First they prepared an adhesive (polyvinylchloride (PVC) in dioctyl phthalate) which was poured between the feed and centre rolls. They then started rolls rotating then spread the graphite powder onto the adhesive. The adhesive runs in an S shape around the rolls. The graphene is continuously exfoliated to give graphene, unlike the scotch tape method where you exfoliate once with each application and removal of the scotch tape. After 12 hours of operation, you collect the material, wash it and then burn off the PVC to get the graphene. There’s a video (direct link) in the supplementary information showing the mill in operation.

I’m not entirely sure why anyone would want that much graphene in this form. For transparent conducting applications (where you want to maximise transparency and minimise electrical resistance) it’s likely you would still have high electrical resistances between flakes of graphene and poor performance. But it’s still a clever way of scaling up what, to me, looked like a completely unscalable process. I won’t be so certain when writing in the future.

[1]: K. S. Novoselov, A. K. Geim, S. V. Morozov, D. Jiang, Y. Zhang, S. V. Dubonos, I. V. Grigorieva, A. A. Firsov, Science, 2004, 306 (5696), 666-669. DOI: 10.1126/science.1102896.

[2]: J. Chen, M. Duan, G. Chen, J. Mater. Chem., 2012, 22, 19625-19628. DOI: 10.1039/c2jm33740a.

Sentences were written

Yesterday I was dicussing a draft of my MRes thesis with my supervisor and one of my questions was whether, in a few particular cases, I should write in the active or passive voice, and if I do use the active should I use the pronoun we or I?

Active or passive?

The sentence I had written was (key bit emphasised):

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, I found that the growth precursor formed a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

To begin with please ignore whether you think that’s a good sentence or not (I’ve read it so many times I’m beginning to think the word order is completely wrong).

It’s written in the active voice: I (the subject) found (the verb) that something was the case. I chose to use the active because I want to make it clear that I found that the precursor was unstable, in disagreement with what some other researchers found. I also tend to choose the active voice because it’s more direct; the passive can feel rather viscous and verbose. I’m often told to make it easy for the reader.

I could take out I:

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, the growth precursor formed a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

It’s readable, but I don’t like it because it’s slightly ambiguous.

In the passive voice (I think—this just sounds incredibly weird to me so I could be wrong):

Despite Bloggs et al.’s description of the growth precursor as “extraordinarily stable”, the growth precursor was found to form a fine red-brown precipitate within approximately 30 min of being loaded into a syringe, blocking the syringe outlet.

Both ambiguous and horrible. Hence I chose the first option: active and I.

I, we—no one?

But the problem now is the dreaded I. It does sound a bit schoolboyish. We is used in scientific writing all the time, but I—shudder—never, because science isn’t conducted by individuals, but by groups. In fact, no, not even groups, but by the whole scientific establishment. No one does science, science does itself! Hmm… But ignoring that, I does make me cringe a bit.

Putting we in place of I is significantly less cringeworthy but completely nonsensical. It always amazes me to see a single author paper start with “We [verb]…”. Is I really that repulsive? Is it meant to give an illusion of absolute truth? Perhaps it’s meant to say “this is not my opinion , it’s scientific fact”, but there’s always a personal element in science and to pretend it isn’t there is ludicrous and delusional.

So I’ve got to decide whether to stick with I or not. It’s only my MRes thesis not my PhD thesis, but I still care about the details. I’m definitely not writing we. My supervisor was told by his supervisor to do a find on “we” and replace with “I”. I’m leaning towards I because it’s concise and unambiguous about was my work (apparently it’s good to show in an MRes that you’ve done a good amount of work) and, whilst it may be a bit cringeworthy, it is definitely the easiest to read. Hopefully the mysterious anonymous marker will agree.