First Week of Actual Work

      So it is Christmas Eve and I have now worked my first week at my new job. Things are falling into place. For starters I now know what I am exactly doing for my research. Basically it is a very natural evolution of the work that I did for my PhD. It's going mean I have to learn some new concepts with regard to Density Functional Theory, but the basic concept is really cool and might offer a route to doing the same sort of work but applied to the stuff I worked on at Warwick.
     I've almost settled into my new office. Getting music onto the computer there, setting it up how I like, getting back into using Linux (a good thing), have a play with LaTeX, Jabref, and I now need to convert my Endnote bibliograpy over to Jabref. I have also sorted out a few basics, like running the program I will be mainly using.
      On the subject of technology I have given up on keeping a paper lab book for ntoes and results, and have now started using Evernote a lot. Works perfectly, and for any written notes I take pictures of the sheet and store it there with the typed up notes.
      Also this week were are getting more used to shopping for food. There are a few shops we like shopping at, and really it is not any moe expensive that the UK. Just seems buying healthy is considered a bit weird over here. The assistants in the health food places are really nice though. I guess they are happy that we 'strange young people' want to shop there.
      We have also been to Essen, which is quite modern, and has a lot of shops there, including a Lush which Sam gets cosmetic and bathroom washes from. So we will be going back there for hopping in future.
      Also it looks like we now have two rpg groups. Or at least one and one in the making. One will be a semi frequent group playing Dresden Files (which is a pretty good system). But we will also soon be setting up a new WoD group. On that note Darker Days 32 is out where myself, Mark and Mike are joined by Vince, who with Mark, set up the podcast to begin with.
      This Xmas then is going to be spent watching Xmas films (Batman Returns, Gremlins, etc) and having our mate James stay over, as he has been in Germany for a month now and is working up in Hamburg.

First few days of the new job

So loving my new job. I know it has really been 2 days there but the thing is I can make more immediate contributions. Right now I just have to get familiar with the code, since the methods it is based upon I know inside out (shit I get asked to review papers on the subject as I am an "expert" on it). So instead the challenges are more related to the applications of the methods. It just feels like it will be less of an uphill battle.

Add to that I will be getting a decent wage for which my previous experience counts for a lot. So I being paid what I am worth. This means finally I can save money, while paying off the credit card, and in the next 10 months, finish paying off my loan to the bank.

This is weird. I have never been in such a scenario. Even better it looks like renting over here will actually give you good value (seriously our flat here is as big as our old one but we are paying less and bills are included).

Other plus', I feel like my work drive has been renewed, plus I like the atmosphere of living here. Not worked out what is different. Maybe it is the cheap, but excellent food.

Add to this I have a conference in Berlin at the end of March, and I can take my wife with me. So basically we just have to pay for her train ticket. :D

To finish off we now have almost everything ready for Venice for our 3 year anniversary. And well being married is great, and in Germany you get a tax break for it :D

My first week in Germany - Bochum, University and living in another Country

      So a week has gone by. And it has been my first week living in Germany. Where to begin?

      Well the week before the move was spent in Manchester with Sam's mum, and so we had a week with our cats. They are now justover a year old. Sam realised that the date that we got to Manchester to see them was a year to the day when we first got them. They have been living in Sam's old room, and seem very happy with that. They were unsure at first when we arrived, but then caught our scent and were back to their old selves, following us around and as a result, they were more brave and so ventured downstairs more often, with Yamato not bothered by the other two cats that are there. Yamato I think has got slimmer, but that is more than likely due to him being more powerful, as he seems to like running up and down stairs.

      That week we got the chance to catch up with family, such as Sam's aunts, my sister and her partner, Sam's brother and his partner, and also Kat and Dave from my year of chemistry at UMIST and PhD at Manchester. It was a hectic week, and flew by, and soon enough we were off to the airport for our flight to Dusseldorf.

    The weather that day was shit. We were able to get all our luggage on, with out paying for any excess weight. When we went to the gate to get on board we saw the air strip and well, it as crazy. The wind was blowing rain across the tarmac, and the plane we were flying on was a propeller driven thing. Needless to say it looked a little dodgy, but was in fact quite a good flight. However, take off was bad, with the plane having to wait as the rain and wind made zero visibility.

      Arrival at Dusseldorf was fine, and we got a taxi all the way to Bochum. The taxi as fine other than the driver taking the wrong way into the uni, and so this cost time getting the keys. Instead we went straight to the guest house and then I had to walk and get the keys. Not great when it was freezing.

      The apartment is pretty good. A nice big corner sofa, a fully kitted out kitchen area, a coffee filter machine (that made me happy), and a good bed (I've slept well on it, must be a firmer mattress). We should have the rest of our luggage arriving Friday, along with a new TV. We have internet and so we have been able to skype, but of course we have no new mobile number as it takes, and costs Orange, a lot to unlock my phone ust so I can use a different SIM card. Sigh.

     Anyway, Saturday we went to Dusseldorf, which was very busy and and found a nice tea shop there, and on the way back got stung on the train fare. We didn't get our tickets stamped properly. :( Oh well the money lost we have got back on our power bills from the old flat (we were in credit).

     Sunday of course was quiet. With everything shut we had little food in the flat. It's been a bit hard to know where to go shopping, more so when your phone is useless and has no access to google maps.

     Monday we went into the office, and from there were taken by one of my boss's students to register as living in Bochum, get our tax card started, get health care organised, and of course open a bank account. Fun day.

     So Tuesday was quiet as Sam has had a cold, which is a bit strange for her. We later went to the department Xmas party, where we met some of the others of the Theoretical Chemistry department,  and today I had my induction at the department. Looks like I need to learn how to use LaTeX and so forth. Fun!

    So tomorrow is the start of my new job.

    Other things to look forward to are joining a new RP group, and of course James is coming to stay over Xmas.

     Expect a few photos soon and more as I stumble through the German language.

5 days left

So in 5 days time I willbe flying over to Bochum, Germany, where I will be working for the next three years. Over the last month we have had a computer game cosplay themed leaving party, friends staying over, our friend James leaving for Hamburg to start his new games design job, and we have said farewell to a number of others.

Leaving our flat involved large amounts of books being packed and things being thrown away/given away. We got the flat nice and tidy in the end but of course there will be deductions from our deposit. Anything we get back will be a bonus.

Everything easily fitted into the moving van, and so we travelled up later on Thursday with the last few things, mainly laptops and electrical things.

Now we are at my mother-in-law's place, with boxes of our stuff everywhere. We will need to sort through it again so it can take up less space. We have also been reunited for a short period with our cats. They seem to have become even more friendly and are quite happy and get on OK with the two older cats that are already here.

Yesterday we had the chance to meet up with my wife's brother and his girlfriend. We had food at quite a hip pizza restaurant, with pizzas like brie and duck, or wasabi prawns. Today, later on, my sister and her boyfriend are turning up, and will be dropping off a suitcase for us to use, as we will be filling that one so that it can be sent so it arrives just after we get to Germany.

Overall it has been a bit draining the move. I will tired, mainly in my legs and back as muscles feel well and truely stretched. I'm also wheezing a little, but I think that is a combination of muscle tiredness, dust and also the fumes from the oven cleaning spray.

Tonight we will be going to Black Planet, a goth/industrial night. It is a special event in memory of a local DJ who passed away, but it will also then be a good chance to catch up with those we have not seen much of for the last 3 years.

Tuesday will also be a busy day as in the morning I will be popping into my old research lab and in the evening going to watch my wi'fe brother's band playing.

Right. I need to have breakfast and relax some more.

World of Darkness and the Science of Evil

World of Darkness and the Science of Evil

World of Darkness (WoD), both new and classic settings, has a primary focus on supernatural horror. Monsters are things from myths, from our past, Biblical or from our folklore. They are urban legends and ghosts of old, or quite simply men driven mad and have become something new.
But horror and terror are not just born from magic and the arcane arts and powers of forgotten gods. Horror can be born from science.

In classic WoD (CWoD) a war exists between science and magic, fought by the Technocracy and the Tradition mages. It is a war of belief and absolute truths and control. And so magic and science are different simply by definition and categorization. They come from the same source. The difference is the lens through which the truth is viewed. Spirits, ghosts, aliens, vampires etc, are just entities for which the science is not fully defined.
This view of science and the supernatural is also within new World of Darkness (NWoD), but the presentation is more fuzzy. There is no war between magic and science. Without that analogue in Mage the Awakening, science and magic bleed over into each other in many different ways. It is the interface between the two which can be exciting and lead to different horrors.

So what am I getting at?

The supernatural and scientific can blend together to give birth to new horrors. In CWoD  we saw this with the Hitmarks of the Technocracy. They are cyborgs powered and designed using hyperscience, Enlightened Science, which is simply magic manifesting as technology. In NWoD there similar concepts in Promethean the Created. Each Promethean lineage is aligned to an element (earth, air, fire, water, spirit). But the also present the concept of Prometheans born of nuclear energy and radiation. There are also those Promethean which are cybernetic. Essentially androids, but made human like by the Divine Fire. In Hunter the Vigil there are groups that turn to science to fight the supernatural, making use of advanced weapons to fight the things in the dark.

So can science give birth to things that in fact mimic or tap into supernatural powers, or can the reverse  happen? Why not. Can science modify the supernatural, and the reverse? Well yeah.

Some of may favourite story seeds look at things like this. For example, in the Chicago book for NWoD, they talk about Bell Laboratories and the particle accelerator there. Because of the cutting edge science being used the suggest the idea that such machines tear open the skin of reality and allow in strange energies, material and entities. These entities could easily fit the definitions of spirits, or even aliens, or the Fae. In Night Horrors: Wolfsbane, this idea is further expanded upon when detailing the Idigam. These banished spirits consumed the powers of spirits that rode to the moon from other worlds. This along with the book Summoners for Mage the Awakening, and of course the concepts in Changeling the Lost, allow you to play on the question, ‘Just what are spirits?’ Are some spirits really just inter dimensional beings? Can you clone from them? What about demons and angels? Are they just other forms of aliens? Are those were creatures just some sort of cryptid? Perhaps just a mutation? We know there are ghosts, but what about ghosts from alien worlds brought to earth on a comet? What does vampirism mean in light of blood research and stem cell science?

So my advice for games? If you want to through your gaming group a curve ball add a bit of science. There are things in the world that science has yet to explain but can be used to fight. But there are things not understood that science has created.

So some random story seeds to use:

•  
  • An organ transplant from a werewolf leads to something strange and murderous.
  • Cloning of a changeling leads to something more like a fetch.
  • Quantum teleportation allows for a exponential spread of a spirit.
  • From the depth of space comes a signal that follows Atlantean magic, but sent by a race from another world.
  • A supernova sends energy, in the form of flux, to earth, and awakens Pandorans.

Posted via email from Etheric Labs at http://doctorether.posterous.com

Packing for Germany - 1 month to go. #germany #moving #life #chungkuo #davidwingrove #rpg

So there are now about 5 boxes of books. 1 of them is just RPG books. It weighs a freaking ton. I've basically downsized what I am taking with me to Germany to a few books while the rest goes into storage at the mother-in-laws, so if I really need something she can post it out to me (or we can ship whole boxes even). So I plan to take with me;

NWoD Core
Vampire the Requiem
Mage the Awakening
Cthulhu Tech
Geist the Sin-Eaters.

The last two I can ditch if I need more space/weight.

Thank god I have a lot of books in pdf format.

I'm doing the same with clothes as well. Plus we have unboxed 99% of all DVDs and put them into 5 big wallets (and I mean big) so that we have stuff to watch. But again we might have to downsize some and get the rest posted out or even ripped to a hard drive.

Moving sucks, but then it does me we are getting rid of a lot of crap (which we did when we moved from Manchester), which means welcome to an even more minimalist life style. Thank fuck for digital I say.

Oh, reading wise, the first of the prequels to the original Chung Kuo series by David Wingrove is great, but makes the world we live in look quite fragile.

Cat based story

Around the Interwebs: Clever Kitteh Leads RSPCA Rescuer to Her Kittens - http://pulse.me/s/246jx

Big Wide World: Post-doc: Career uncertainty is wearing us down

Lewis Dartnell, astrobiology post-doc

The most common feeling I experience during my working day is being uncomfortable. I feel stupid. Unfortunately, this is elicited by the very nature of the scientific beast; in research, you are constantly testing different approaches, perfecting new techniques, trying to get your head around some puzzling results, and writing papers that will be critically torn-apart by the best minds in the field. You are constantly trying to reassure yourself that what you're attempting is sensible and worthwhile as you stumble through the unknown. To a certain extent feeling stupid is a necessary part of the process.

Every now and then, this background uneasiness is ruptured by peaks of elation. You finally get a fiddly experiment to work or a paper is accepted by a journal for publication. These moments of success keep you hooked on science. Late last night was a case in point: I finally finished debugging some data analysis code, replotted the key graphs, and submitted the paper I've been working on for the past few weeks to an appropriate journal. I woke up this morning feeling pretty good about things.

Finishing my paper means that I've finally got some spare time to devote to that other constant concern for young scientists: securing the next pay packet. As a post-doctoral scientist you are only ever employed on short fixed-term contracts: two or three year positions within a particular research group. This means that you end up spending a lot of your time simply applying for every job you see to try to continue supporting yourself for the next two years.

You are also expected to regularly change institutions, moving up and down the country, or the continent, settling in one place for only a few years at a time. Permanent positions - university lectureships - are exceedingly rare (acutely so at the moment with the faltering economy and academic cut-backs), and so you can easily get stuck in the uncertain rut of post-doc'ing well into your thirties. This makes buying a house and settling down to raise a family very difficult.

The reality is that the life of an early career scientist is erratic and unsettled, more so, I think, than most other professions. Science must remain a competitive pursuit, but it needs to offer greater career stability and more permanent positions if it is going to remain an attractive prospect for young students.

To this end, I have been helping run a lobby group called Science is Vital. Over the last few months, we have been gathering scientists' views on the state of science. We polled people from all over of the country, from different research fields, and at different levels in their career (from students to fellows of the Royal Society).

Yesterday we delivered the report to David Willetts, the Minister for Universities and Science, detailing the results from nearly 700 respondents. We summarised the widespread dissatisfaction our respondents reported feeling at the pattern of successive fixed-term contracts and the shortage of permanent posts. We also pointed out the risk to the stability of the UK research base, and indeed, the economy, if nothing is done.

It wasn't all negative though as we also suggested ways to improve the situation, namely by introducing permanent positions for advanced post-docs alongside principal investigator roles and allowing post-docs to be able to apply for their own project grants.

We wait now, with bated breath, for a response. 

What are your thoughts? Do you have any grand ideas for reforming the academic career structure? Please enlighten us below

 

via newscientist.com

My new desktop on my laptop - windows 7

How to disappear two Nobel Prize medals (and how to bring them back)

When the Nazis invaded Copenhagen in 1940, physicist Niels Bohr was in possession of two Nobel Prize medals. But they were not his medals. The first belonged to Max von Laue, winner of the 1914 Prize for physics, the second to James Franck, the physics winner in 1925.

Not wanting to attract unwanted attention to themselves, each had sent his medal to Bohr's lab in Copenhagen for safekeeping. But with Nazis marching through the streets of the city, the medals now posed a particularly serious threat to Bohr. NPR's Robert Krulwich writes:

Inconveniently, [these medals were] now sitting in Bohr's building, clearly inscribed "Von Laue"...and "Franck" — like two death warrants. Bohr's institute had attracted and protected Jewish scientists for years. The Nazis knew that, and Niels Bohr knew (now that Denmark was suddenly part of the Reich) that he was a target. He had no idea what to do.

On the day the Nazis came to Copenhagen, a Hungarian chemist named Georgy de Hevesy (he would one day win a Nobel of his own) was working in Bohr's lab. He wrote later, "I suggested that we should bury the medal(s)," but Bohr thought no, the Germans would dig up the grounds, the garden, search everywhere in the building. Too dangerous.

So Hevesy's thoughts turned to chemistry. Maybe he could make the medals disappear. He took the first one, he says, and "I decided to dissolve it. While the invading forces marched in the streets of Copenhagen, I was busy dissolving Laue's and also James Franck's medals."

It was a painstakingly slow process (gold is a notoriously stable element), but Hevesy managed to pull it off; when the Nazis ransacked Bohr's institute, they found no trace of the medals.

Or rather, they never noticed them. The gold from the two medals had been dissolved into a bright orange, but otherwise unassuming, liquid. A liquid that the Nazis left untouched. A liquid that Hevesey later extracted the gold from and sent back to the Nobel Foundation to have recast into two brand-spanking-new medals.

The moral of the story? Science wins, bitches.

Check out the full story on how Hevesy saved the day, including a video on how to dissolve gold, over at NPR
Top image by Benjamin Arthur via NPR

via io9.com

Kalina and Yamato are 1 year old

See the full gallery on Posterous

Barcelona Conference Blog - Days 2 + 3

OK, so let's see if I can write this quick?

First day was a midday start. I had popped over to the Temple de la Sagrada Familia. An immense modern church. It just was utterly unreal. As if it were something from the setting of Warhammer 40000.

Lunch at the conference was a little bit xmas like. It was some roast duck, with stewed apples and figs. Yeah! Food at this conference has been amazing and I feel so stuffed.

That night we were taken to Casa Batllo, which like the church, was a construction of Gaudi. Casa Batllo is as if elves on crack had made it. Surreal curving surfaces everywhere. Literally as if the building was alive. Dinner that night was held there! Queue stupid amounts of wine and food.

Starters were (each being a mouthful only!) ;

Prawns and caviar, a shot of apple and cucumber vinegar, duck liver in chocolate, feta wrapped in ham, tempura asparagus, fried rice ball, beef and satay dip.

The main course, when it arrived after all the above, was a nice piece of steamed sea bass.

Dessert was some sort of sponge with a mango like ice cream and the after that chocolates.

So yeah, stuffed, and after that I led, but did not join, some chemists to the old town so they could drink more.

Today was an early start, and with my boss doing his presentation... so I had to be awake.

Lunch again was impressive and woke me up fully.

Most of the presentations were interesting, but more what you could use the programs for, rather than how you design them, which is what I do.

There was a cool toy there being a 3D viewer station connected to a haptic feedback device. It means, by hand, you can move molecules about a protein and the device gives you force feedback. Weird but very cool.

So this evening has been back to the quiet of the hotel, a brief sit up on the terrace (I should have used the pool here!) and now just resting my legs more before sorting everything out for the morning and heading home.

I really can't wait to come back to Barcelona and bring my wife along too!

Barcelona Day 2 - Audio Blog #barcelona

recording-20110927092814.3gpp Listen on Posterous

Barcelona - Day 2 - Gothic Quarter and Beach - Audio Blog

Barcelona Conference - Day 1 - Bloody Zurich

Barcelona Conference - Day 1 - Bloody Zurich!

So I, like the modern techno savvy gentleman that I am of course ensured that I had done all my booking online. This means I can have a lot more time to check in, something useful when you are just taking hand luggage. This time, fortunately, my mobile check-in worked. Easily scanned the image off the phone screen.

But that was too easy.

My flight had been delayed, in good old rainy Birmingham International. This was not good. I had the best part of 50 mins to get through Zurich (which from my last experince when going to Germany seems to be frequented by dawdling idiots). Oh Boy! However I was told that this should not be an issue for me, as the delayed aircraft would be flying faster to make up time.

Now Zurich is a funny fucking airport. The planes seem to never taxi to the actual gates. No it is all done using buses. A bus from the plane. A bus to the plane. So more time wasted as idiots pile on and off. Now fortunately I am not lazy and so when I have the option of escalators or stairs I choose stairs. So I thought I was going to speed through transfer. Nope.

See transfer for most other airports I have been to does not require to go through security again. This however is Zurich, and so I feared I waould have more sow moving idiots going through the x-rays. This happened to me, again, last time when I was going to Germany. I had already gotten annoyed with a wonderful couple of old people in Brum when they seem to fail at how the liquids on airlines rule works. Even though Brum has numerous of these weird pseudo holograms that talk and tell you what to do. Sigh.

Surely it could not get worse?

Well having dodged the expected idiots (hey lets all walk together across the width of the corridor), I got to the gate with about 10 mins to spare (I should power walk at the Olympics). So I brought up my boarding pass on my phone and scanned it.

Bzzrrt!

Denied! Shit I thought. However, after a quick look at their database and sorting out a few things, bam, business class upgrade. WTF! I have nevered had that before.

Next, another bus to the fucking plane (WTF Zurich. W. T. F. ???) and half way along that came to a very abrupt halt, sending people off their feet. Fuck knows why? Phew.

So here I am now, in business class, enjoying the refreshments. Seems like the Swiss like have cool little flat screens that flip down from the overhead and showing info on the flight (air speed, altitude, time, weather, google map stuff of where the hell we are - oh yeah we flew over Kunsten.... I think - and other bits).

Wine please!

Landing in Barcelona, and wow, that is one massive airport. Designed more like a hanger, it shits on anything in the UK. And yes, the heat and humidity hits you. Not crazy levels (as I landed in the evening) but very noticable. From there it was very easy to get to where I wanted, grabbing the shuttle bus to University Square, which even from there you could spot the hotel (I love having a good sense of direction).

Now the hotel looks amazing. Look it up, Hotel Jazz. Yeah... jazzy. The decor is all monocrhome and the bedroom is fantastic (I slept like a log). I will add photos to this.

So for my first day here? Go get a small bag (I need it to carry a few things to the conference) and get some sunscreen.

And yeah. A phone in the bathroom.

See the full gallery on Posterous

What's so bad about sugar? #chemistry

We blame sugar for adding extra calories to almost anything we purchase in the grocery store, call sugary snacks "junk food." But is sugar really junk? Let's take a look at some common myths about sugar, and find out why there are good reasons for you to keep natural sugars as a part of your diet.

Myth: All sugars are the same.

Fact: Different sugars have different properties and degrees of sweetness.

Sugar comes in many forms. Common table sugar is sucrose, a disaccharide of glucose and fructose, each of which have different properties. Fructose is often called a "fruit sugar" as it is found in honey, berries, and vegetables. Glucose and galactose also accompany fructose as a naturally occurring sugar, however, these naturally occurring sugars are often forsaken for artificial sweeteners, which lack the caloric and other bodily advantages of naturally occurring sugars.
Fructose is considerably sweeter than other naturally-occurring sugars, with fructose being over 1.5 times as sweet as sucrose, over twice as sweet as glucose, and six times sweeter than galactose. Fructose also has a reasonably low manufacturing cost, leading it to be one of the main natural sweeteners used in manufacturing processes.

Myth: Sugar is bad and not a useful part of your diet.

Fact: You need glucose.

Glucose is used by as an energy source by almost every organism. Glucose is used by your body's cells as a very efficient energy source. For example, via the the Krebs Cycle, a single molecular of glucose yields a net gain of two molecules of ATP through anaerobic respiration, and 34 molecules of ATP through aerobic respiration.

Glucose is also a valuable precursor for several types biological molecules; including lipids, amino acids, and cellulose, providing a valuable building block that can be readily used by almost any molecule. The synthesis of glucose was not able to be reproduced in vitro until the late 1800s, with Emil Fischer winning the 1902 Nobel Prize in Chemistry for his contributions to the synthesis of glucose and other naturally occurring sugars.

Myth: Sugar has little impact on humans other than acting as a sweetener.

Fact: Your brain runs on sugar.

You brain's main supply of energy is the monosaccharide glucose. While your brain only weighs between 3 to 5 pounds, it makes use of approximately 15-20% of your body's daily caloric needs. It has been long thought that the glucose was consumed as a function of cognitive experience, and research on rats shows that when a more cognitively challenging task is placed before them, more glucose is depleted. This phenomenon also appears to extend to humans.

In the journal article Glucose, memory, and aging, published by the American Journal of Clinical Nutrition, researchers observed that elderly patients who were given lemonade sweetened with glucose experienced a nearly two fold increase in short term memory when asked to recall a prose passage compared to those who drank lemonade sweetened with the artificial sweetener saccharin (also known by the brand name of "Sweet'N Low"). Additionally, saccharin has no calories.

Glucose has also been shown to have a large impact on self-control and behavior, with limited supplies causing a quick falloff in behavioral stability at times. I like to call this phenomenon "hanger", hungry-anger, when observed in friends and loved ones.

In Sum, Sugar is your Friend

So, sugar isn't all that bad, and honestly, if you want to perform a series of cognitively difficult tasks, you'll be depleting your resources quickly. Individuals with pre-existing conditions like diabetes need to watch their sugar intake, but for the individuals without such ailments, sugar is your friend, not your enemy.

Top photo by Liv friis-larsen via Shutterstock.

via io9.com

Thank fuck fr a nice streamlined article on the subject

You know when your really nerdy when....

Your boss complains there is a rogue exit statement, your ask him to show the output from the program and then you immediately now which file of the code to check for the statement.

Admire The Deglon Meeting Knife Set | Design Sojourn #knives

A warm welcome to you dear reader! If you have not already, why not subscribe to The Design Sojourn Newsletter and get my latest thoughts on Strategies for Good Design conveniently delivered right to your inbox? It's free! You can also follow me on Twitter and Facebook as well.

Thanks for visiting and please keep in touch?

Please take a moment to admire the beauty and elegance of Deglon’s Meeting Knife Set.

Don’t worry, I’ll wait.

Done?

Why not take another minute?

Ok, ready? Let’s continue.

Designed by Mia Schmallenbach, this design is a wonderful exercise of merging utility with aesthetics. A sublimely beautiful design that stopped me dead in my tracks, and compelled me to study how to lines and shapes worked together. Furthermore this design is not just “form for form’s sake”. The knives cleverly tuck back into each other like Russian dolls thereby organizing and removing clutter on your kitchen counter. Some people have concerns on the functionality, but I’ll reserve judgment on this until I get a chance to hold one myself.

Here is what Mia had to say about her design.

Meeting is a set of kitchen knives: paring knife, carving knife, chef’s knife, filleting knife and their block. They all seem to be sculpted out of one piece of steel. The proportions are determined by the Fibonacci sequence with as its base the average width of a hand.

It is refreshing to see old school design methodologies, such as the Fibonacci sequence, given a new lease of life by combining the thinking with modern manufacturing technologies. Found everywhere in nature, we know that Fibonacci sequences work well in design, as proven by the Renaissance masters in the past. And it looks like it is still relevant in today’s context.

A big thanks to Shang Lee for this wonderful find.

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Thank you!

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Speak Out With Your Geek Out - A list of my Geek #speakgeek

Final post about what I geek out over.

 

• Transformers - toys, films, cartoons
• Lego - I really want all the stuff my mum has kept safe
• Thundercats - the new anime is awesome
• Roleplay games
  • Vampire the Masquerade
  • Vampire the Dark Ages
  • Mage the Ascension
  • Vampire the Requiem
  • Werewolf the Forsaken
  • Mage the Awakening
  • Changeling the Lost
  • Geist the Sin-Eaters
  • Unhallowed Metropolis
  • Exalted
  • Fading Suns
  • Cthulhu Tech
• Wargames - I want the time and money to get back into it, but not GW stuff, just Confrontation and Warmachine.
• Science - chemistry, physics, maths, computers
• Mythology
• Scifi/fantasy films
• Gipf and Zertz board games
• Anime
  • Deathnote
  • Shadow Skill
  • Devil May Cry
  • Tower of Druaga
• Computer games
  • Devil May Cry 1-4 (fuck you DMC or DMC 5 or whatever the fuck you are!)
  • Assassin's Creed
  • Batman - Arkham Asylum/City
  • Final Fantasy 7
  • Silent Hill 2
• Superheroes
  • Batman films (old and new)
  • The Joker
  • Harley Quinn (yes please)
  • Smallville (yeah I know)
  • Spiderman
  • X-men
  • Wolverine
• Horror films
• Venice, Italy
• Carnival
• Manchester, UK
• The paranormal
• The Warhammer and Warhammer 40000 universe (I'd rather roleplay in them than play the wargames)
• Cosplay

Speak Out With Your Geek Out - From Country Kid to Computational Scientist #speakgeek #chemistry

So Speak Out With Your Geek Out is still on going this week. Last post was a history of my own gaming and geek life and how it has led to what I do now as a postdoctoral researcher.

Above image was the cover image to the Journal of Physical chemistry where my literature review on neural networks and chemical simulations appeared.

I have already estabished that at school, out in the the courtyside of Herefordshire, I was quite an enthusiast for science, technology and mathematics. That is not to say I did not enjoy art, graphical design and history, but I excelled at the sciences. For A-Levels (for those in the US that is the equivalent of the last 2 years of high school, but over here we specialize in a few subjects, and for my time that was just 3) I took Physics, Chemistry and Mathematics. My Mum to a degree forced me into doing maths, on the grounds that no matter what I did at university it would come in handy. She was not wrong.

 

My love of Physics really comes from my childhood obsession with space. I loved how the solar system was, how planets were so different and similar, and at how man had left the confines of this world to explore others. A part of me as a child wanted to be an astronaut, or some form of astronomer. But as high school went on I could see possible choices like engineer or theoretical physicist. However there was chemistry.

 

Chemistry is a weird science if ever there was one. It sits are the threshold of all the others. Not all scientists wear white lab coats, and not all chemists are the same. Not all work in labs slaving over making new colourful liquids or bubbling, steaming pots of solutions. No there are a lot of boring steps to be taken in the creation of new chemicals. However, there are many forms of chemistry. There are surface chemists, biochemists, bioinorganic chemists, nano scientists, this list being very long.

 

What captured my imagination in Chemistry, was the links between it and Physics and in turn Mathematics. Quantum Mechanics. This strange area of science, ruled by particle wave waves, and strange physics, is the very science that puts electrons in their place around atoms, and in turn determines how chemistry happens. I was just struck by the beauty of the equations that determined the motion of these particle/waves. And so it was this that made me do Chemistry as a degree. But of course a particular type of chemistry.

 

Now I had applied to the Univeristy of Manchester Institute for Science and Technology (it was a one of a few such institutes) for a Masters in Chemistry. This was originally a B B C entry requirement, that based on the interview for the course, was reduced to B C C, with a B in Chemistry. That of course was achieved (I got a A in Maths, and two Bs).

 

But the course I was doing was not normal chemistry. It was Chemistry with Chemical Physics. Chemical Physics I had learnt during my hunt for university courses, was an area of chemistry where computers were used to model and analyse chemicals. It would mean I would learn programming and deal with Quantum Mechanics.

 

Of course in an ideal world you get to study exactly the way you want to. However, being such a nerd I was one of a few who were doing that exact course. Meaning that in the first few years of the degree I got to study specialized modules in Quantum Mechanics etc.However, Chemistry has a high level of attrition amongst the students. By the later years I was really the only person doing that course. This was an issue as the specialist course were not always an option for me to take due to not enough interest in them. This meant often I was doing other optional courses that were more synthetic in focus. This was and issue as it caused a drop in my overall grade averages. One thing I did learn through team projects is that I disliked doing synthetic chemistry. It would either yeild very small amounts of the desired product, or turn to brown goo. This was why I prefered physical chemistry and theoretical chemistry. it was all the formulas that described the chemical bonds and how molecules move about.

 

So for my final thesis for my Masters, I did a project on the design of a new, multipolar electrostatic, water model. How can I explain all this concisely? Water is a the most fundamental of all molecules. It is the medium for life, and is essential for the understanding for many other important chemical systems and physical properties (like how ice freezes). So what exactly was I doing?

 

Above is the way water molecules organise in the liquid. This structure is constantly shifting in the liquid, but becomes rigid in ice.

 

Water has been modelled since the start of Computational Chemistry, back in the 70s. Water models assumed a number of things. Water molecules are rigid (molecules are anything but rigid). Water molecules don't break bonds (this is a massive simplification - water molecules are constantly exchanging hydrogen atoms and making and breaking hydrogen bonds - these being weak interactions between the water oxygen atoms and the hydrogen atoms on another water molecule. Even if we models did do this, they assumed that hydrogen atoms move like normal atoms, but in fact hydrogen atoms are so small and light they move in non-Newtonian ways i.e. Quantum Mechanically).

 

Above is a diagram to show how electrons fill atomic shells. The number of electrons in a outer shell determines the chemistry. Atoms react and bond so that they complete a shell either by losing electrons or gaining them. For example, Carbon, has 4 out electrons. It reacts to form 4 bonds. In each bond it shares one electron from itself and another from the bonding partner atom. Thus in total Carbon has 8 electrons in total. A complete shell.

Water molecules can be described using points charges placed on the atoms. Oxygen atoms carry a partial negative charge, while the hydrogen atoms carry partial positive charges (this explains the above mentioned hydrogen bonds). These partial charges simplify the true distribution of electrons about the water molecules. The old models assume these charges never. However, these charge distributions do change, in response to bonds being made and broken, and in fact changes to the local environment of the molecules. This is called polarization (something I will get back to later).

 

Above a typical water model. It has the bond lengths and geometry. Note that water has a triangular shape. The toal charge of the molecule is 0. But the oxygen atom has a partial negative charge, and the hydrogens have partial positive charges.

 

So what was my model. My model used a more realistic representation of the electrons and where they are located, something called a electron density. These are 3D representations of the charge density and you can imagine the analogue with respect to say pressure of temperature.

Above is the molecule, imidazole, and the gradient vector field of its electron density. Note the field lines are the lines tha end at the dots (atoms). The isobars represent lines containing equal electron density. The thick curved lines are interatomic boundaries. Note how they curve. This means atoms are not round things when in molecules. They deform each other. The image is the same for computational determination as it is if you measured the same thing by x-ray diffraction. In fact the computer calculated version is more accurate.

The above image is similar to the previous. This time for two water molecules. One water molecule, on the right, lies in the place of the 2D plot. The othe is at right angles to it, with the hydrogen atoms sitcking out of the image. Note how the left water molecule oxygen atom deforms the hydrogen atom of the right hand water molecule.

A 3D representation of the atomis of three water molecules within a cluster of 21 water molecules. Red volumes/atoms are oxygen atoms, white are hydrogen atoms. The solid atoms belong to the central water molecule of the cluster, while the two neighbouring molecules have transparent wire-framed atoms.

This project not only saw me learn more about quantum mechanics and use such programs to generate data using the equations of quantum mechanics, but I also learnt about programming, Fortran, in order program the models and modify them so that using Newtonian equations of motion I could test if the water models recovered the expect structures of water that have been previously been measured using X-ray diffraction.

 

The work for this revealed some interesting results which I would then make use of in my PhD with the same group. The PhD was offered to me so long as I got a 2.1. Thank fuck I did.

 

Getting a PhD was a life changing experience. First of all having funding and money is good. Especially when you go from three grand a year to twelve. My PhD involved learning more programming and the fundamentals of AI, in particular neural networks. The new project was 'The design of a novel polarizable water model trained on ab initio electron densities'.

 

What hell does that all mean?

 

Let's go back to the old work. Remember I said the model assumed that the charge densities don't change, and that was a simplification? Well this new model of mine woud address that. The neural networks are computer algorithms that can learn things from the data presented to them. So what data is that?

 

Ab initio is the latin for 'first principles' i.e. quantum mechanics. I generated thousands (and that takes some time) of quantum data for various water clusters i.e. 2-6 water molecules in different arrangements where one molecule is surrounded by the rest. The data for these clusters shows that the electron density is distorted due to the placement of the water molecules. Why? Remember I said that the atoms have partial charges? Well that means that water molecules interact in such a way that the partial charges either push (negatively charge atoms do this) or push neighbouring electron density in other molecules. This distortion of electron density is known as polarization (I hope you note that a lot of these terms can be looked up on wikipedia).

 

So this means that each water molecule, and its electron density, are unique to the environment and organisation of that environment i.e. what stuff is about it and how they are pointing at each other. A neural network can be trained to related the positions and relative orientations to the electron densities found for these examples. In effect the neural network can predict during the simulation of water the electron densities, and in effect allow for the water molecules to be polarized.

 

Above is a basic neural network. They are an analogue to how brain neurons work. The circles, nodes, pass numbers along (left to right). These numbers are multiplied by things called weights i.e. how important a the number is, and used to calculate an output. A neural network 'learns' by modifying these weights so that once it has been trained to predict the output for some test examples, it can then be used to predict the output for other sets of inputs representing the other variations you wish to use.

 

Are we still following? Well this work is now being applied to a model for peptides (short chains of amino acids that if you make big enough can curl up and become proteins) and for water with ions (salt water is a good start).

 

So then I finished at the University of Manchester (a merger of UMIST and the Victoria University of Manchester) and have almost finished a postdoc at Warwick University. Here I have been developing models for spin crossover compounds.

 

Spin Crossover???

 

OK. So there are these types of atoms in the periodic table called transtition metals. These metals are called so because they can easily under go a transition from one oxidation state to another. That means they can lose a variable number of electrons when forming different complexes. For example iron can happily form compounds where in some it has lost 2 electrons, and in some 3, and in others even more. This means that in the two states it prefers different compound geometries i.e. what shapes it forms when binding to other atoms, it also has different colours in the two states, which in turn are further modified by the atoms it is bound to. For example rust is red because it is iron in the 3+ (i.e. lost three electrons) state. This is why our blood is also red when oxygenated. Really, go look up transition metals and see why they do so much stuff and are so important to life and science.

 

Above shows the outer shell electron structure of iron. Electrons are arrows. The lines are orbitals. Transition Metals break all the rules. Sothey have a 4s shell that holds 2 electrons and a 3d shell that can hold 10 electrons. Both shells are similar in energy. When iron is oxidised, it looses the the 4s electrons first (becoming a 2+ state). It will then loose one of the pair electrons in the 3d shell to form the 3+ state.

 

Now the other thing that transition metals can do is occupy different spin states. This means that while the oxidation state is the same, the electrons in the outer shell of the atom (the outer shell of the atom determines the chemistry of an atom) can be forced to change their arrangement. In turn this means that they can favour different geometries with the atoms to which they are bound. It can also mean they can be trapped in either spin state. (Spin is a property that electrons have. It is either up or down. Electrons can only be in the same orbital if they are of opposite spin. Now per orbital there are two electrons of each spin. This is stable. But pairing electrons decreases stability because electrons are negatively charged. It's like putting two north poles against each other. So then it is also favoured to have electrons spread out, one per orbital if possible. So there can be a number of ways to spread the electrons.

One is where as many electrons are paired up - low spin, and one is where as many are not paired up - high spin).

 

Above is the 3d shell for the iron in the 2+ state. What you need to know is that when iron binds with atoms you will find some of the orbitals (those lines the electrons are on) are higher in energy than others. Now here is the trick. You gain stability with the electrons in the lower energy orbitals. But you loose energy pairing electrons. So the you can spread them out (LS being low spin as the spins are all cancelled out, HS being high spin where there are more up spin than down spin). But that means putting electrons in less stable, higher energy orbitals. So there is a clever balance here that deteremines if the high spin or low spin state is preffered. It depends on how unstable i.e. how much higher in energy the upper orbitals are. If the pay off is not enough then LS state is preffered. Of course this energy difference, and thus preference can be modified by changing what iron is bound to.

 

What does this change of spin state allow for? Well spin states can be switched between if the material adsorbs a gas, or is heated, or is compressed, or is hit by a laser light. What can we do with this? The spin state can be used as a form of switch, like in memory in hard drives. Or perhaps as sensors for gases. They can even be used for optics.

 

So what am I doing for this. Well many of these models need settings to be determined for the functions that model these systems. Now this not trivial when there are 30 or more that need to be found so that the parameters can be used to model the compounds in both low and high spin states. Now, to find these, since there are many combinations, I have been using genetic algorithms (a way of varying bit string representations of the parameters) to search the parameter space to fit the models.

 

What makes it harder is that the fitting of the parameters must achieve two goals. The first being good energy predicitions for the test compounds, and the other being good recovery of the compound geometries. These two goals are in competition i.e. you can fit the models to get one really good while getting shit results in the other. This issue is know as multi-objective fitting. This is now going to be applied to a number of problems, and will in future be used for some other things.

 

My future work in Bochum, Germany, returns to my PhD work or neural networks, and I will be using it to simulate transition metal catalytic surfaces. This means I am drawing upon my old skills and pushing the work further forward since my old work and this new work are comparable and can be combined.

 

 

But why do we do this? 

 

In 2003, the cost of developing a new drug was estimated at $800 million, with a predicted 7.4% increase in costs per year, the development of a new drug will now require around around $1 billion.

 Typically, it takes over a decade for a drug to be brought to the market because only a couple of potential drugs out of 10,000 make it to the market. Moreover, it can be difficult recoup the money put into the research and the drug may be recalled when it makes it to the patient population. Subsequently, drug development and production needs to become more efficient. This can be achieved through the use of computational chemistry Computers have become ever cheaper and faster. It is, therefore, now feasible to run moderate sized simulations on a commercially available desktop computer. By using the computational tools available, and developing new computational approaches, drug design can be made more efficient and successful.

 

So I guess that means what I do should hopefully help save lives, or save the world. No really.

 

So there we go. My Speak Out With My Geek Out about Chemistry

 

Speak Out With Your Geek Out - From Country Kid to Computational Scientist #speakgeek #chemistry

So Speak Out With Your Geek Out is still on going this week. Last post was a history of my own gaming and geek life and how it has led to what I do now as a postdoctoral researcher.

Above image was the cover image to the Journal of Physical chemistry where my literature review on neural networks and chemical simulations appeared.

I have already estabished that at school, out in the the courtyside of Herefordshire, I was quite an enthusiast for science, technology and mathematics. That is not to say I did not enjoy art, graphical design and history, but I excelled at the sciences. For A-Levels (for those in the US that is the equivalent of the last 2 years of high school, but over here we specialize in a few subjects, and for my time that was just 3) I took Physics, Chemistry and Mathematics. My Mum to a degree forced me into doing maths, on the grounds that no matter what I did at university it would come in handy. She was not wrong.

 

My love of Physics really comes from my childhood obsession with space. I loved how the solar system was, how planets were so different and similar, and at how man had left the confines of this world to explore others. A part of me as a child wanted to be an astronaut, or some form of astronomer. But as high school went on I could see possible choices like engineer or theoretical physicist. However there was chemistry.

 

Chemistry is a weird science if ever there was one. It sits are the threshold of all the others. Not all scientists wear white lab coats, and not all chemists are the same. Not all work in labs slaving over making new colourful liquids or bubbling, steaming pots of solutions. No there are a lot of boring steps to be taken in the creation of new chemicals. However, there are many forms of chemistry. There are surface chemists, biochemists, bioinorganic chemists, nano scientists, this list being very long.

 

What captured my imagination in Chemistry, was the links between it and Physics and in turn Mathematics. Quantum Mechanics. This strange area of science, ruled by particle wave waves, and strange physics, is the very science that puts electrons in their place around atoms, and in turn determines how chemistry happens. I was just struck by the beauty of the equations that determined the motion of these particle/waves. And so it was this that made me do Chemistry as a degree. But of course a particular type of chemistry.

 

Now I had applied to the Univeristy of Manchester Institute for Science and Technology (it was a one of a few such institutes) for a Masters in Chemistry. This was originally a B B C entry requirement, that based on the interview for the course, was reduced to B C C, with a B in Chemistry. That of course was achieved (I got a A in Maths, and two Bs).

 

But the course I was doing was not normal chemistry. It was Chemistry with Chemical Physics. Chemical Physics I had learnt during my hunt for university courses, was an area of chemistry where computers were used to model and analyse chemicals. It would mean I would learn programming and deal with Quantum Mechanics.

 

Of course in an ideal world you get to study exactly the way you want to. However, being such a nerd I was one of a few who were doing that exact course. Meaning that in the first few years of the degree I got to study specialized modules in Quantum Mechanics etc.However, Chemistry has a high level of attrition amongst the students. By the later years I was really the only person doing that course. This was an issue as the specialist course were not always an option for me to take due to not enough interest in them. This meant often I was doing other optional courses that were more synthetic in focus. This was and issue as it caused a drop in my overall grade averages. One thing I did learn through team projects is that I disliked doing synthetic chemistry. It would either yeild very small amounts of the desired product, or turn to brown goo. This was why I prefered physical chemistry and theoretical chemistry. it was all the formulas that described the chemical bonds and how molecules move about.

 

So for my final thesis for my Masters, I did a project on the design of a new, multipolar electrostatic, water model. How can I explain all this concisely? Water is a the most fundamental of all molecules. It is the medium for life, and is essential for the understanding for many other important chemical systems and physical properties (like how ice freezes). So what exactly was I doing?

 

Above is the way water molecules organise in the liquid. This structure is constantly shifting in the liquid, but becomes rigid in ice.

 

Water has been modelled since the start of Computational Chemistry, back in the 70s. Water models assumed a number of things. Water molecules are rigid (molecules are anything but rigid). Water molecules don't break bonds (this is a massive simplification - water molecules are constantly exchanging hydrogen atoms and making and breaking hydrogen bonds - these being weak interactions between the water oxygen atoms and the hydrogen atoms on another water molecule. Even if we models did do this, they assumed that hydrogen atoms move like normal atoms, but in fact hydrogen atoms are so small and light they move in non-Newtonian ways i.e. Quantum Mechanically).

 

Above is a diagram to show how electrons fill atomic shells. The number of electrons in a outer shell determines the chemistry. Atoms react and bond so that they complete a shell either by losing electrons or gaining them. For example, Carbon, has 4 out electrons. It reacts to form 4 bonds. In each bond it shares one electron from itself and another from the bonding partner atom. Thus in total Carbon has 8 electrons in total. A complete shell.

Water molecules can be described using points charges placed on the atoms. Oxygen atoms carry a partial negative charge, while the hydrogen atoms carry partial positive charges (this explains the above mentioned hydrogen bonds). These partial charges simplify the true distribution of electrons about the water molecules. The old models assume these charges never. However, these charge distributions do change, in response to bonds being made and broken, and in fact changes to the local environment of the molecules. This is called polarization (something I will get back to later).

 

Above a typical water model. It has the bond lengths and geometry. Note that water has a triangular shape. The toal charge of the molecule is 0. But the oxygen atom has a partial negative charge, and the hydrogens have partial positive charges.

 

So what was my model. My model used a more realistic representation of the electrons and where they are located, something called a electron density. These are 3D representations of the charge density and you can imagine the analogue with respect to say pressure of temperature.

Above is the molecule, imidazole, and the gradient vector field of its electron density. Note the field lines are the lines tha end at the dots (atoms). The isobars represent lines containing equal electron density. The thick curved lines are interatomic boundaries. Note how they curve. This means atoms are not round things when in molecules. They deform each other. The image is the same for computational determination as it is if you measured the same thing by x-ray diffraction. In fact the computer calculated version is more accurate.

The above image is similar to the previous. This time for two water molecules. One water molecule, on the right, lies in the place of the 2D plot. The othe is at right angles to it, with the hydrogen atoms sitcking out of the image. Note how the left water molecule oxygen atom deforms the hydrogen atom of the right hand water molecule.

A 3D representation of the atomis of three water molecules within a cluster of 21 water molecules. Red volumes/atoms are oxygen atoms, white are hydrogen atoms. The solid atoms belong to the central water molecule of the cluster, while the two neighbouring molecules have transparent wire-framed atoms.

This project not only saw me learn more about quantum mechanics and use such programs to generate data using the equations of quantum mechanics, but I also learnt about programming, Fortran, in order program the models and modify them so that using Newtonian equations of motion I could test if the water models recovered the expect structures of water that have been previously been measured using X-ray diffraction.

 

The work for this revealed some interesting results which I would then make use of in my PhD with the same group. The PhD was offered to me so long as I got a 2.1. Thank fuck I did.

 

Getting a PhD was a life changing experience. First of all having funding and money is good. Especially when you go from three grand a year to twelve. My PhD involved learning more programming and the fundamentals of AI, in particular neural networks. The new project was 'The design of a novel polarizable water model trained on ab initio electron densities'.

 

What hell does that all mean?

 

Let's go back to the old work. Remember I said the model assumed that the charge densities don't change, and that was a simplification? Well this new model of mine woud address that. The neural networks are computer algorithms that can learn things from the data presented to them. So what data is that?

 

Ab initio is the latin for 'first principles' i.e. quantum mechanics. I generated thousands (and that takes some time) of quantum data for various water clusters i.e. 2-6 water molecules in different arrangements where one molecule is surrounded by the rest. The data for these clusters shows that the electron density is distorted due to the placement of the water molecules. Why? Remember I said that the atoms have partial charges? Well that means that water molecules interact in such a way that the partial charges either push (negatively charge atoms do this) or push neighbouring electron density in other molecules. This distortion of electron density is known as polarization (I hope you note that a lot of these terms can be looked up on wikipedia).

 

So this means that each water molecule, and its electron density, are unique to the environment and organisation of that environment i.e. what stuff is about it and how they are pointing at each other. A neural network can be trained to related the positions and relative orientations to the electron densities found for these examples. In effect the neural network can predict during the simulation of water the electron densities, and in effect allow for the water molecules to be polarized.

 

Above is a basic neural network. They are an analogue to how brain neurons work. The circles, nodes, pass numbers along (left to right). These numbers are multiplied by things called weights i.e. how important a the number is, and used to calculate an output. A neural network 'learns' by modifying these weights so that once it has been trained to predict the output for some test examples, it can then be used to predict the output for other sets of inputs representing the other variations you wish to use.

 

Are we still following? Well this work is now being applied to a model for peptides (short chains of amino acids that if you make big enough can curl up and become proteins) and for water with ions (salt water is a good start).

 

So then I finished at the University of Manchester (a merger of UMIST and the Victoria University of Manchester) and have almost finished a postdoc at Warwick University. Here I have been developing models for spin crossover compounds.

 

Spin Crossover???

 

OK. So there are these types of atoms in the periodic table called transtition metals. These metals are called so because they can easily under go a transition from one oxidation state to another. That means they can lose a variable number of electrons when forming different complexes. For example iron can happily form compounds where in some it has lost 2 electrons, and in some 3, and in others even more. This means that in the two states it prefers different compound geometries i.e. what shapes it forms when binding to other atoms, it also has different colours in the two states, which in turn are further modified by the atoms it is bound to. For example rust is red because it is iron in the 3+ (i.e. lost three electrons) state. This is why our blood is also red when oxygenated. Really, go look up transition metals and see why they do so much stuff and are so important to life and science.

 

Above shows the outer shell electron structure of iron. Electrons are arrows. The lines are orbitals. Transition Metals break all the rules. Sothey have a 4s shell that holds 2 electrons and a 3d shell that can hold 10 electrons. Both shells are similar in energy. When iron is oxidised, it looses the the 4s electrons first (becoming a 2+ state). It will then loose one of the pair electrons in the 3d shell to form the 3+ state.

 

Now the other thing that transition metals can do is occupy different spin states. This means that while the oxidation state is the same, the electrons in the outer shell of the atom (the outer shell of the atom determines the chemistry of an atom) can be forced to change their arrangement. In turn this means that they can favour different geometries with the atoms to which they are bound. It can also mean they can be trapped in either spin state. (Spin is a property that electrons have. It is either up or down. Electrons can only be in the same orbital if they are of opposite spin. Now per orbital there are two electrons of each spin. This is stable. But pairing electrons decreases stability because electrons are negatively charged. It's like putting two north poles against each other. So then it is also favoured to have electrons spread out, one per orbital if possible. So there can be a number of ways to spread the electrons.

One is where as many electrons are paired up - low spin, and one is where as many are not paired up - high spin).

 

Above is the 3d shell for the iron in the 2+ state. What you need to know is that when iron binds with atoms you will find some of the orbitals (those lines the electrons are on) are higher in energy than others. Now here is the trick. You gain stability with the electrons in the lower energy orbitals. But you loose energy pairing electrons. So the you can spread them out (LS being low spin as the spins are all cancelled out, HS being high spin where there are more up spin than down spin). But that means putting electrons in less stable, higher energy orbitals. So there is a clever balance here that deteremines if the high spin or low spin state is preffered. It depends on how unstable i.e. how much higher in energy the upper orbitals are. If the pay off is not enough then LS state is preffered. Of course this energy difference, and thus preference can be modified by changing what iron is bound to.

 

What does this change of spin state allow for? Well spin states can be switched between if the material adsorbs a gas, or is heated, or is compressed, or is hit by a laser light. What can we do with this? The spin state can be used as a form of switch, like in memory in hard drives. Or perhaps as sensors for gases. They can even be used for optics.

 

So what am I doing for this. Well many of these models need settings to be determined for the functions that model these systems. Now this not trivial when there are 30 or more that need to be found so that the parameters can be used to model the compounds in both low and high spin states. Now, to find these, since there are many combinations, I have been using genetic algorithms (a way of varying bit string representations of the parameters) to search the parameter space to fit the models.

 

What makes it harder is that the fitting of the parameters must achieve two goals. The first being good energy predicitions for the test compounds, and the other being good recovery of the compound geometries. These two goals are in competition i.e. you can fit the models to get one really good while getting shit results in the other. This issue is know as multi-objective fitting. This is now going to be applied to a number of problems, and will in future be used for some other things.

 

My future work in Bochum, Germany, returns to my PhD work or neural networks, and I will be using it to simulate transition metal catalytic surfaces. This means I am drawing upon my old skills and pushing the work further forward since my old work and this new work are comparable and can be combined.

 

 

But why do we do this? 

 

In 2003, the cost of developing a new drug was estimated at $800 million, with a predicted 7.4% increase in costs per year, the development of a new drug will now require around around $1 billion.

 Typically, it takes over a decade for a drug to be brought to the market because only a couple of potential drugs out of 10,000 make it to the market. Moreover, it can be difficult recoup the money put into the research and the drug may be recalled when it makes it to the patient population. Subsequently, drug development and production needs to become more efficient. This can be achieved through the use of computational chemistry Computers have become ever cheaper and faster. It is, therefore, now feasible to run moderate sized simulations on a commercially available desktop computer. By using the computational tools available, and developing new computational approaches, drug design can be made more efficient and successful.

 

So I guess that means what I do should hopefully help save lives, or save the world. No really.

 

So there we go. My Speak Out With My Geek Out about Chemistry

 

Speak Out With Your Geek Out - From Wildest Herefordshire to Darker Days Radio #speakgeek

So what is this all about?

'Take a stance against baiting nerd rage and stereotypes of geeks.

Post about how much you love your geeky hobbies or vocation from Monday, September 12th, 2011 to Friday, September 16th on your blog, website, social media account or in a forum somewhere. Then come here and tell us about it. We'll have a kick-off post where you can stand and be counted.

Let's show the world why we're awesome and why there is nothing wrong with being a geek.

Initially proposed and organized by author, game designer and freelance consultant Monica Valentinelli.'

http://www.speakoutwithyourgeekout.com/

So what do I have to add. On flamesrising.com they have some great points on how to address this type of points.

I am an unapologetic geek. It has fuelled my passion for the sciences, for history, for mythology, for finding my own spirituality, and has also led to me finding jobs, friends, and also my wife.

Is being a geek bad thing? Of course not. Many people are geeks. They have a deep passion for some niche interest. Be it roleplay games, video games, or football fans. Geek has been a word negatively attached to an interest in technology, sciences and books. But as time has gone on, and the world has changed, being a geek has started to payoff big time, but in a more apparent way.

Many who meet me assume I still a student. And a student into the arts. I guess the big bleached spiky hair confuses many. They seem shocked to learn I am a doctor of chemistry. I am a geek, but not the stereotype may imagine.

So where does my proud life as a geek begin?

Transformers. It has to be Transformers. Even now I am a big fan of them. My wife bought me the Megatron toy from the Transformers Animated series a few Xmas' back. But I got my first Transformer when I was just 18 months old. My mother explained to me that back then I constantly wanted them as I saw older boys with the toys. Of course, that was the Eighties, and as I grew up there were many of the classic cartoon shows. He-Man, Thundercats etc. All of this fuelled my imagination, and that imagination was allowed to create with Lego.

During Primary school I discovered Greek myths, and then the other myths from other pantheons. Again my mother fed this need, and got me books on the subject. I was also equally obsessed with space, and knew even at the age of 9 all about the shuttle program, the planets and about stars.

It was also around this time my parents got for Xmas for my sister and myself a computer. The Amiga 500. This machine let my play games, use early publishing and art software, and also try out basic programming.

Then came High school, and it was in my first year there that a friend got me into wargaming. Warhammer 40000 to be exact. This of course led to me eventually playing all the games that Games Workshop produced at the time. Overtime my parents accepted this expensive hobby, noting how it let me be artistic, develop good logic and number skills, writing, and reading, and also let myself and my friend socialize doing something other than watching TV or playing on the computer.

It was also at High school I got into table top rpgs. My parent came back one Saturday afternoon with a black box with a red dragon upon it. This was D&D Basic. I of course got my wargaming friends into table rpgs. That Xmas I got the WEG Star Wars rpg, and a year after that Vampire the Masquerade. It was also around this time, while doing work experience at the Hereford Archaeology centre that I picked up some Magic the Gathering cards. This too also became a major hobby for my friends.

Of course all the way through school, from primary to high school, to 6th form, I was a bullied for being a geek. A nerd. I did well at lessons, and in exams, especially at maths and sciences. it wasn't that I didn't like sports, but I preferred things like Martial Arts. By the end of school I was a brown belt in Karate. But for all of it I was bullied. There were often times I even wished I was not as good at school. Is it any surprise then that I got into alternative music?

Of course these matters seem pointless in hindsight once on goes to university and finds that where before you were part of an apparent minority, you are now part of a larger, a more diverse, and accepting, body of people and peers. Of course I feel I would never have gotten to university, and even got my invitation grades lowered, if I had not been a geek.

Throughout university I was still doing wargaming, and for 3 years worked part time at a Games Workshop store. While there the parents of the kids that came in were often surprised to learn that I was a degree student. They could see that this hobby promote the types of skills and interests that would lead to their kids going to university.

Of course while at university I also joined gaming groups, joined the anime society, and became more alternative. I was a industrial/cybergoth in the making.

My degree of course is quite geeky. It started out as just chemistry, but then took a computing angle, and my final degree project was the simulation of water. So I was now a programmer/chemist. I worked in an office compiling code, reading up of quantum mechanics. I was a chemist, just not in a white coat.

Of course this led to me doing a PhD in computational chemistry. My skills expanded and I learnt about AI, neural networks, machine learning, protein folding (you know the stuff on the PS3). I was becoming an expert in my field, writing papers in a unique part of chemistry. Of course I was still roleplaying during this time, but I had also stopped wargaming. I needed the time, and the money. I also got into the industrial/goth scene around this time, and found that many of the goths in the city were also scientist geeks of some form, or artist geeks. I also met my wife half way through my PhD. We originally met over the internet. We were both members of a goth meetup, but never were at the same one at the same time. So we met up one day, geeked out over Spiderman films, and then spent a lot of the day walking around geek shops, like Forbidden Planet. Sam of course brought into my life all her geek interests, some I get, some I don't, and she in turn is now an important member of my rpg group. We also cosplay when we get the opportunity as our favourite anime characters.

So where am I now? I have almost finished my first postdoc research post at the University of Warwick, and I will be moving to Germany for my new job. I have also been married for almost 3 years, with Venice now being a geeky obsession of mine, as it is a place I got engaged in, married in, and I have also written about, both for my own games, and for the rpg Amaranthine (my first shot at freelance writing). I now also co-host the Darker Days Podcast, a World of Darkness focused podcast.
Since moving to Warwick I have set up another gaming group which consists of computer game artists, battle re-enactors and political researchers.

Now I am no paragon of geekdom. I have had my rants. Be it against those who bitch and moan about a company catering to their tastes, or having a rant a person who kills their gaming party in the first scene. I also dislike certain hobbies, but that is not to say that I do not accept that others.

So what is my message to other geeks who feel as if they are the outcast, or that their hobbies are some form of social impediment. They are not. These geek hobbies can fuel the mind and imagination in a way that can lead to finding other like minded friends, and can be turned into respectable jobs. After all in this day and age of computers and technology and computer games, don't geeks somewhat rule the world? Of all the people that have encouraged me, it has been my mother who has pushed me with my studies, accepted my hobbies and in fact got me started in them.

So there we go. I am a proud geek, and there are more out there than you realize. They just don't look like the stereotype.

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