Chemistry Blog

Sep 26

The Minecraft Chemistry Challenge


Minecraft is an truly awesome game. Think of it as digital lego set in a infinitely explorable world. But its real draw is that is encourages creativity on so many level. Players can build what they like, but also the code is open source, allowing creative coders to fiddle with rules and resources in the game. The result is a multitude of modifications (or mods in Minecraft parlance).

L5mDx

There are mods for every taste, including those who favour a spot of virtual  chemistry, in the form of Minechem. It allows for some surprisingly sophisticated chemistry. With a range of devises and tools everything in the world can be broken down into elements, and then reacted together to yield an incredible array of compounds.

As fun as Minechem is, my favourite mod of the moment is Printcraft. This allows the player to output anything they have built to a file that can be read by a 3D printer. And given that I have just assembled one of these wonderful contraptions (or ‘plastic tat generators’ as my better half prefers to call it), combined with my son’s Minecraft addiction means that my house is now slowly being invaded by virtual buildings turned real.

So I think I need something more meaningful to do with it. And so over to you. Build me something! Build me something original that’s related to the chemical sciences, be it useful, interesting or just plain cool. And I’ll 3D print (and send the designer) the best ones.

So here are the rules:

1) Construct something related to the chemical sciences in Minecraft, using the official printcraft server (use Minecraft 1.7.8)

Alternatively you can download the sever and run it locally or use the one I’ve set up (connect to IP 54.68.24.135:25565 using Minecraft 1.6.4)

2) Upload the STL file ,that printcraft spits out, to Thingiverse and tag it with 3DMineChem.

3) Add a link to your Thingiverse file in the comments below.

Lets see what we can come up with shall we?

P.S My ulterior motive is that I’m trying to come up with an Minecraft/chemistry workshop for school children and I need some inspiration and some beta-testers of my server.

Sep 23

First Friday: Ask a Scientist


Soon after moving to Tallahassee my wife (Debbie) and I were encouraged to check out First Friday, an eclectic, once-a-month gathering of local musicians, artists, food trucks, and performers. Located in a lumber yard-turned-art park known as Railroad Square, First Friday is a wonderful opportunity to see locals celebrating their hobbies and personal interests. Following this spirit, Debbie and I, along with my colleague Greg Dudley, decided to contribute as well – and our Ask a Scientist (AaS) booth was born. We gather 4-5 scientists–predominantly FSU faculty—from across disciplines like chemistry, physics, engineering, psychology, medicine and biology and stand by a tent with a sign proclaiming Ask a Scientist. What follows is ~3 hours each month spent drinking beer and talking science with people passing by.

Below is a time-lapse of our August AaS event. The evening featured the following scientists: David Meckes (virology and biomedical sciences), Brian Miller (biochemistry), Tom Albrecht-Schmitt (nuclear chemistry), and myself (Ken Hanson, energy/material chemistry). We try to rotate a new batch of scientists every month.

There are four types of common interactions/questions:

1) Most people are genuinely excited to ask questions, many which are prompted by current events. Our virologist was asked about Ebola in August and our paleontologist was asked about the colossal dinosaur in September. Other examples of general questions include: How are memories formed? How accurate is the chemistry in Breaking Bad? And my personal favorite as a photophysical chemist: Why is the sky blue?

2) Some people interpret our “Ask a Scientist” prompt as, “Stump a Scientist.” At best these questions come from fellow scientists who good-naturedly know what is difficult to answer (like how do you cure x?). At worst, these questions come with sarcasm or a prepared (dare I say egotistical) lecture on what our answer missed.

3) The third type of question is political: How do you feel about fracking? Is global warming real? These questions usually lead to long conversations.

4) The final type of question seeks to understand who we are and why we created the booth: Who is coordinating this event?” Who is sponsoring this? When we share that we’re unsponsored and just having fun the response is usually something along the lines of, “This is very cool” or “Keep up the good work.”

So, if you happen to be in Tallahassee during the first Friday of any month, please stop by Railroad Square and our AaS booth. We’re always happy to say ‘hello’ and talk science. We also try to post ‘example questions’ each month to help prompt participation. So I welcome any accessible, general science questions you’ve heard as well.

Sep 16

Hack your inkjet printer and turn it into a lab robot


If you stop and think about it for a moment, you will realise what an astonishing feat of precision engineering your colour printer is. It can take the primary colours – cyan, yellow, magenta and black – and mix them together carefully enough to achieve more than a million different hues and shades. Not only that but the drops of colour are mere nanolitres (billionths of a litre) in volume, each of which is then placed on the paper – assuming its not jammed in the feeder tray – with better than pinpoint accuracy.

Now a group of enterprising chemists from Tsinghua University are exploiting that precision engineering, which normally results in high-resolution colour prints, to screen millions of different chemical reactions. Their results have been published in the journal Chemical Communications.

Yifei Zhang and colleagues have been trying to understand reaction pathways in living things. Every chemical process that goes on in living organisms is controlled by a cascade of reactions. The steps in a cascade are mediated by protein molecules called enzymes. Each enzyme makes a small chemical alteration, like workers on a production line, to a molecule before passing its product onto the next enzyme. In this way, for example, plants build sugars from carbon dioxide and your food gets broken down and then reconstructed into other useful chemicals for your body.

The problem is that to understand these complicated processes by reconstructing them outside of a living cell is difficult. The concentrations of an enzyme relative to the next in the line is key. Get this wrong and bottle necks are formed in the production line, as one enzyme works faster than the next.

To figure out what are the right conditions to replicate a living cell’s workings, chemists must set up and monitor a vast number of reactions. Screening large numbers of reactions like this is often done using “96-well plates”, which are 96 tiny containers with a unique combination of chemicals in each. These reactions might be set up manually or, if the lab is well-funded, by an expensive robot. But even with the best robots available it can still be a slow process.

Colour printers are a lot cheaper than robots. And if the inks are replaced by solutions of enzymes then suddenly you have a device that has the potential to dispense more than a million different reaction mixtures.

That is just want Yifei and colleagues have done. Their printers were loaded with a series of enzymes that, when they work together in the correct ratios, produce coloured reaction products. These were printed directly onto paper where it was immediately obvious, from the intensity of a coloured dot, which reaction mixtures worked best.

In the test cases reactions were deliberately chosen that resulted in colour changes. This made for a nice quick visual indication of whether the system worked well. So for example one test started with glucose and a chemical called ABTS in the magenta cartridge, then the enzymes glucose oxidase (GOx) and horse-radish peroxidase (HRP) in the yellow and cyan cartridges. When they are mixed together the GOx removes a hydrogen from the glucose and adds it to oxygen, producing hydrogen peroxide. Next the HRP reacts this with the ABTS, which results in a green chemical.

The potential applications for these printer-based mixtures extend beyond curiosity-driven research on biological pathways. Yifei and colleagues have already shown that by loading the printer cartridges with the right enzymes they can use the set up to indicate the presence of glucose in a sample. Glucose in urine is a indication of diabetes, so their printer-based chemistry already has the potential to diagnose diabetes.

The result then could be a future where a trip to the doctors results in a printout of, quite literally, your urine and some enzymes alongside, after 30 seconds or so, a diagnosis and the prescription.

The Conversation

Mark Lorch does not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article, and has no relevant affiliations.

This article was originally published on The Conversation.
Read the original article.

Sep 12

Major fire destroys Nottingham University’s new GSK labs


Nottingham University, last night, lost its new chemistry building in what has been described as a ‘major fire‘. The building which has been part fund GSK was still under construction, so thankfully no-one injured.

Pictures posted on twitter show the building engulfed with flames. However firefighters have brought the blaze under control, and no other buildings were affected

Here at chemistry-blog we are saddened to hear of the news which sees the lose of major investment in chemistry.

More coverage of the story can be found here and here.

Sep 09

Aspiring Graduate Students: You have questions, FSU Graduate Recruiting & Admissions Committee has answers!


Last December, Mike Shatruk, chair of Florida State University’s chemistry graduate recruiting & admissions committee, hosted an AMA (ask me anything) on reddit.com/r/chemistry. The post generated considerable interest with 191 upvotes and 178 comments. The questions ranged from job prospects to metrics for grad school acceptance.

This year we have decided to give it another try and this time a little earlier in the application timeline. Mike will also be joined by me, Ken Hanson, one of the newest members of the graduate recruiting & admissions committee.

So if you have any questions about graduate school or the admissions process please swing by reddit.com/r/chemistry/ on Tuesday September 16th beginning at 10:00 am (EDT). If you’re unable to join us on Sept. 16th, please feel free to share your questions below and I will make sure they make it on the AMA.

 

Update: Here is a link to the AMA.

Jul 18

A Year in the Life of a New Research Lab…in Less than One Minute


The Hanson Research Group’s first experiment—initiated my second day on the job—involved two strategically placed Brinno TLC200 time-lapse cameras programmed to take one photo per day. The video from our first camera that covered our less-trafficked support space was posted in March. Below is the video from our second camera, which was placed in the main lab and focused on one of our fume hoods.



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