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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

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 13y ago
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 13y ago
  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 13y ago
    He means ab initio from the electrons and nuclei, not from heats of reaction and elemental entropies.
    - pa5tabear 13y ago
      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 13y ago
        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.
- Xcelerate 13y ago
  Hey! That sounds very interesting, but I'm already buried in a bunch of research projects as it is. Maybe if I get some free time at some point I'll contact you.
  - dnautics 13y ago
    I have no idea if there are software packages and the like for this, too, but melting point, liquid density, vapor point, would be really helpful too.
rprospero 13y ago
I love computational research more than most, seeing as I'm a scientist and a coder. However, I feel the need to weigh in with a counterpoint on this. I've spent the last eight years measuring a system that was well described by both theory and computational experiments. It was exactly one of those systems where the results could not be measured experimentally and simulation was the only path forward. We then built an instrument which could measure the results experimentally. Since this system was so well described by simulation and theory, we used it as a calibration sample before doing real science. Except the results didn't match the computations at all. I spent years tracking down problems in the instrument (some of which were real) before finally setting in on the fact that the theory and calculations were simply wrong. Just as you're always experimentally limited in what you can measure, you're resource constrained in what you can calculate. Sometimes, you need to drop down another physics abstraction level before you can get the right answer. However, experiments don't care about your abstraction level and get it right every time. Performing physical experiments is a waste of time and money if you can just simulate the results. However, you don't know if you can simulate it until you've performed the experiment. Every scientist I've known has, at least once, run a simulation and later found that it wasn't even close to the experimental results. Sometimes it's a leaky abstraction in the simulation (e.g. Ignoring the anti-reflective coating on a mirror). Sometimes it's a leaky abstraction in the experiment (e.g. ignoring the pH differences between H2O and D2O). Sometimes it's new physics, but not very often. Sometimes it's exactly like you predicted. Until you leave the keyboard and enter the lab, you won't know.
johncagula 13y ago
"...our understanding of the laws of physics is advanced enough nowadays to describe almost perfectly everything we observe in everyday life." -- nope. (sorry for the sheepish comment but this thinking is dangerous; look into some of the current problems in http://en.wikipedia.org/wiki/Quantum_biology http://en.wikipedia.org/wiki/Quantum_biology)
- darkmighty 13y ago
  What's about those that we can't describe? Some of these effects are very computation-intensive, but doesn't mean their basis isn't well understood already.
  - acadien 13y ago
    >very computation-intensive This is a gross understatement and fallacious. Many of the problems being studied today would take millions/billions/trillions of years of computation in order to model... with approximations. Using even the largest clusters on the planet we can't even find the ground state of even the smallest protein (with ab-initio). DFT scales cubically with system size, and DFT is an approximation to actual first principles calculations that are impossibly enormous and can never be fully calculated. The number of systems we can accurately model is minuscule, the number of open problems in computational chemistry and materials science is enormous.
    - Xcelerate 13y ago
      > impossibly enormous and can never be fully calculated. I wouldn't go so far as to say that. A quantum computer can handle the fermion sign problem by scaling polynomially with the number of particles instead of exponentially. Estimates for if/when such a practical device will be created vary wildly but I would think the possibility of this, along with new techniques that take advantage of the redundancy inherent to certain categories of problems and efficiently diagonalize the Hamiltonian could accelerate the rate at which we can handle larger and larger systems. It's kind of hard to predict what breakthroughs will be made, but I'm staying optimistic. EDIT: Then again, looking at your posts on here, I suspect you already know all that ;)

dnautics 13y ago

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 13y ago
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 13y ago
  He means ab initio from the electrons and nuclei, not from heats of reaction and elemental entropies.
  - pa5tabear 13y ago
    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 13y ago
      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.
Xcelerate 13y ago
Hey! That sounds very interesting, but I'm already buried in a bunch of research projects as it is. Maybe if I get some free time at some point I'll contact you.
- dnautics 13y ago
  I have no idea if there are software packages and the like for this, too, but melting point, liquid density, vapor point, would be really helpful too.

rprospero 13y ago

I love computational research more than most, seeing as I'm a scientist and a coder. However, I feel the need to weigh in with a counterpoint on this. I've spent the last eight years measuring a system that was well described by both theory and computational experiments. It was exactly one of those systems where the results could not be measured experimentally and simulation was the only path forward. We then built an instrument which could measure the results experimentally. Since this system was so well described by simulation and theory, we used it as a calibration sample before doing real science. Except the results didn't match the computations at all. I spent years tracking down problems in the instrument (some of which were real) before finally setting in on the fact that the theory and calculations were simply wrong. Just as you're always experimentally limited in what you can measure, you're resource constrained in what you can calculate. Sometimes, you need to drop down another physics abstraction level before you can get the right answer. However, experiments don't care about your abstraction level and get it right every time. Performing physical experiments is a waste of time and money if you can just simulate the results. However, you don't know if you can simulate it until you've performed the experiment. Every scientist I've known has, at least once, run a simulation and later found that it wasn't even close to the experimental results. Sometimes it's a leaky abstraction in the simulation (e.g. Ignoring the anti-reflective coating on a mirror). Sometimes it's a leaky abstraction in the experiment (e.g. ignoring the pH differences between H2O and D2O). Sometimes it's new physics, but not very often. Sometimes it's exactly like you predicted. Until you leave the keyboard and enter the lab, you won't know.

johncagula 13y ago

"...our understanding of the laws of physics is advanced enough nowadays to describe almost perfectly everything we observe in everyday life." -- nope. (sorry for the sheepish comment but this thinking is dangerous; look into some of the current problems in http://en.wikipedia.org/wiki/Quantum_biology http://en.wikipedia.org/wiki/Quantum_biology)

darkmighty 13y ago
What's about those that we can't describe? Some of these effects are very computation-intensive, but doesn't mean their basis isn't well understood already.
- acadien 13y ago
  >very computation-intensive This is a gross understatement and fallacious. Many of the problems being studied today would take millions/billions/trillions of years of computation in order to model... with approximations. Using even the largest clusters on the planet we can't even find the ground state of even the smallest protein (with ab-initio). DFT scales cubically with system size, and DFT is an approximation to actual first principles calculations that are impossibly enormous and can never be fully calculated. The number of systems we can accurately model is minuscule, the number of open problems in computational chemistry and materials science is enormous.
  - Xcelerate 13y ago
    > impossibly enormous and can never be fully calculated. I wouldn't go so far as to say that. A quantum computer can handle the fermion sign problem by scaling polynomially with the number of particles instead of exponentially. Estimates for if/when such a practical device will be created vary wildly but I would think the possibility of this, along with new techniques that take advantage of the redundancy inherent to certain categories of problems and efficiently diagonalize the Hamiltonian could accelerate the rate at which we can handle larger and larger systems. It's kind of hard to predict what breakthroughs will be made, but I'm staying optimistic. EDIT: Then again, looking at your posts on here, I suspect you already know all that ;)