
Computer chemists win Nobel prize - nsoonhui
http://www.bbc.co.uk/news/science-environment-24458534
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timr
Wow. I'm floored that computational structural biology work is getting a
Nobel. I spent a lot of time reading their papers in grad school...they're
totally foundational for the field, but the field is still really young:

Martin Karplus' group is behind CHARMM
([http://www.charmm.org](http://www.charmm.org)), which was the first(?)
molecular dynamics package (you can think of it as a precursor to
folding@home, though it's still under active development, so that isn't a
totally fair statement).

Michael Levitt has done a bunch of things, with no one big software package,
but he was one of the earliest people trying to do _ab initio_ protein
structure prediction. He was also one of the first people to really start
categorizing protein structure in a way that allowed for computational
modeling -- back in the 70s and early 80s.

Arieh Warshel is probably best known for bridging the gap between quantum
mechanics and the (relatively quick-and-dirty) molecular mechanics work. He's
done a whole bunch of work modeling enzymatic reactions, coming up with better
electrostatic models, and other things where quantum mechanics does a good
job, but is way too slow to be used on giant molecules like proteins.

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bbgm
Yes, but I am also not surprised given this is pretty fundamental work, even
if it hasn't quite hit the sort of revolutionary goals many of us hoped for.
If Peter Kollman had been alive, I suspect he would have shared this Nobel.

This Nobel is hits very close to home. Much of my PhD work was done in CHARMM
and I come from the Karplus lineage, and at one point in time I had pretty
much read every paper Levitt and Warshel had ever written.

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varelse
Why no Harold Scheraga? Seriously...

~~~
timr
I thought the same thing.

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Xcelerate
This is so cool! This is the kind of research I do: molecular dynamics and
quantum mechanical simulation. I'm not nearly as good at it as the winners of
this prize though haha.

I'm glad to see computational research is becoming more popular and accepted.
There's a (quickly diminishing) subset of scientists who think computational
work is too theoretical, inaccurate, and inapplicable to real-life. This was
the case when the field was developed, but it is no longer true.

The exponentially increasing computational power is allowing discoveries that
simply _can not_ be performed experimentally because laboratory technology
just isn't advanced or capable enough. Who needs to actually study reality if
you can just simulate what you need -- and the end result is the same?

I'm not sure many people know this, but our understanding of the laws of
physics is advanced enough nowadays to describe almost perfectly everything we
observe in everyday life. (Exceptions include things like quantum gravity
which don't really matter [ducks to avoid physicists]).

The problem is that if you want to simulate these laws, it requires a _lot_ of
computational power. Brute-force approaches are simply ineffective and so
simplifications and clever techniques must be developed to reduce the
computational effort while giving increasingly accurate results. I think it's
the combination of improving computational resources and improving simulation
algorithms that are really driving this field.

~~~
dnautics
hey Xcelerate - I'm looking for someone to do some delta-Hf calculations on
some "theoretical molecules" for me. By theoretical molecules, I mean,
molecules that are very likely able to be made, but needs an assessment of
"whether or not it's worth it". Is that something you can do, and would be
interested in putting on ArXiV?

~~~
pa5tabear
What data do you have? Do you know the mechanisms?

We calculated heats of formation in our chemical thermodynamics course, but we
were always given ample data, and we knew what we were trying to calculate.

~~~
selimthegrim
He means ab initio from the electrons and nuclei, not from heats of reaction
and elemental entropies.

~~~
pa5tabear
Can this be explained simply? I took physical chemistry and it sounds related
to calculating energy changes for ionization or electrons moving between
orbitals.

~~~
dnautics
you are using references for already measured energies and orbital systems.
For example, if you take the measured energy change for, say, but-1-ene and
the estimated heat of formation difference for a C-H vs. C-C and hydrogen, you
will get a good estimate for {alpha,omega} octadiene.

If you think you can do the same thing for ethene -> butadiene, you'll find
yourself to be horribly wrong, because of extended conjugation networks.

So while for some cases it works, it is not always simple to go from known
empiricial results to more complex structures using tables and addition and
subraction. And in the case of the molecules I care about, there is pretty
good reason to believe that the simple linear methods will fail.

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alexholehouse
I'm somewhat surprised that Warshel was included instead of Berni Alder, as a
more self-consistent group of scientists from a field point of view, and given
Alder is largely seen as the father of MD.

~~~
selimthegrim
Well then why not Ceperley too, as they helped straighten out some problems at
the core of LDA? I think the Nobel committee wanted to keep the focus on
biochem.

~~~
alexholehouse
Agreed - that's the conclusion I came to too after posting. Still, I'd imagine
Harold Scheraga and Andy McCammon are (justifiably) a little sore this
morning...

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xerophtye
I don't get it. Aren't simulations of chemical reactions based on things you
already KNOW about those reactions? How are they being used to find out new
things about the reactions?

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shiven
You are thinking about reactions as written out in a chemistry textbook. Those
representations tell you about the reactants, products and maybe a few other
details like catalysts, solvents and temperature. However, none of it explains
the mechanism at the quantum or atomic level. Simulating the reaction with
specialized software enables you to 'calculate' additional data points, such
as, free energy, enthalpy and entropy among others, using 'molecular dynamics'
(which 'solves' Classical and Quantum Mechanics equations for a given system
and is extremely essential to understand movement of different parts of a
molecule and their interaction with surrounding atoms to build a more complete
picture of 'how' a reaction proceeds).

Today is a great day for computational chemistry. It is good to see the
detailed Nobel announcement acknowledge other stalwarts of the field like
Peter Kollman (who created AMBER, a package similar to CHARMm by Karplus et
al). I have no doubt that Kollman would have received this prize had he been
alive today.

~~~
raverbashing
Exactly

Chemistry is applied physics. Chemistry answers that H2 and O2 can be joined
to form water under certain conditions, but doesn't answer the "Whys"

Physics answers that. And the answer goes around orbitals, energy states,
electrons, etc.

~~~
aristomc
"Chemistry answers that H2 and O2 can be joined to form water under certain
conditions, but doesn't answer the whys".

Chemistry does answer the whys beyond product yields, why certain elements
react is vastly covered throughout organic, inorganic & physical chemistry .
It is the basis of these sub-fields, and how this is determined is looking at
orbitals, energy states etc...

~~~
raverbashing
Yes, there's an overlap of knowledge

So, Pauli's exclusion principle is Physics or Chemistry? I'd say it's "both".

~~~
xerophtye
Physical Chemistry. (its a real thing)

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mizanrahman
health sector has more scope now to update their process and techniques. I
think they should totally rethink their existing methodologies with the power
of computation

~~~
varelse
They are.

But the previous generation of scientists came of age when Molecular Dynamics
was a disappointing tool because of limitations in the Newtonian models and
the lack of computational firepower to do sufficient sampling. The latter has
been addressed by a combination of Moore's Law and the ongoing migration of
molecular dynamics codebases to GPUs, but the former issue remains - a
Newtonian approximation to quantum chemistry.

What's surprising is how much one can get out of these simple models despite
these limitations, something that was echoed back in 1976 by one of Michael
Levitt's papers that led to today's Nobel Prize:

[http://csb.stanford.edu/levitt/Levitt_JMB76_Simplified_repre...](http://csb.stanford.edu/levitt/Levitt_JMB76_Simplified_representation.pdf)

~~~
selimthegrim
There are very deep reasons for this - the Born-Oppenheimer approximation, a
central simplifying assumption, imposes some constraints on the system that
make it easier to model with (semi)classical dynamics, even when you marry it
with modern techniques such as DFT.

Kieron Burke has a nice take on the matter.

[http://www.tddft.org/TDDFT2008/talks/KB.pdf](http://www.tddft.org/TDDFT2008/talks/KB.pdf)

see also [http://www-fourier.ujf-grenoble.fr/~joye/simon2006.pdf](http://www-
fourier.ujf-grenoble.fr/~joye/simon2006.pdf), esp. its ref. 93

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jnazario
this is pretty awesome. in grad school in the 90s i was exploring a lot of
this very early on, very few people around me were there to help and that's
ultimately how i got involved using Linux and other FLOSS, then sysadmin,
security work and now what i do in computer security research. very glad to
see this prize granted for this line of work as it truly was a leap forward
for the study of chemistry.

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fireismyflag
I initialy read it as "Chemistry Nobel Prize awarded to chemist's computer"...
Makes me wonder if that will ever happen.

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dcc1
lol @ title

