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Biotech

The Birth of Quantum Biology 108

Posted by Zonk from the i-am-an-exo-necro-extra-quantum-biologist dept.
Roland Piquepaille writes "Just when you finally have grasped the concept of quantum mechanics, it's time to wake up and to see the arrival of a nascent field named quantum biology. This is the scientific study of biological processes in terms of quantum mechanics and it uses today's high-performance computers to precisely model these processes. And this is what researchers at Rensselaer Polytechnic Institute (RPI) are doing, using powerful computer models to reveal biological mechanisms. Right now, they're working on a "nanoswitch" that might be used for a variety of applications, such as targeted drug delivery to sensors."
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The Birth of Quantum Biology More

The Birth of Quantum Biology

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  • Re: (Score:2, Interesting)

    by account_deleted ( 4530225 )
    Comment removed based on user account deletion

    • Re: (Score:3, Funny)

      by JeanPaulBob ( 585149 )
      Just doesn't carry the same sex-appeal as Quantum Physics.

      Same-sex appeal? I didn't know quantum physicists were mostly gay...

    • Re: (Score:3, Interesting)

      by JabberWokky ( 19442 )
      As a quantum chemist, my wife (and all associates) tend to prefer the term "quantum mechanics" rather than "quantum physics". I've noticed that seems to be the term used in papers anyway.

      .

      I also wonder how this is at all new... she models inter-molecular protein reactions using high speed computers and the field has been doing so for quite awhile. The code is in Fortran77, as that seems to be the popular language for such research. It's not that it's not an interesting field, it's just not really a "nas

  • Sense of Smell Tied To Quantum Physics? [slashdot.org]

    Animal, vegetable, mineral -- we are all made of matter.

  • How is this any different? (Score:5, Interesting)

    by dorpus ( 636554 ) on Friday January 19, 2007 @05:40PM (#17688804)
    Scientists have been building 3-D computer models of organic molecules since at least the 1980s, using the same equations to predict likely reactions. It sounds like plain biochemistry given a new window dressing.

    • Re: (Score:3, Informative)

      by exp(pi*sqrt(163)) ( 613870 )
      Most of those models have used classical mechanics with really primitive ball and spring models and a bunch of ad hoc rules for bonding.
      • Mods, are you on crack? The parent has made a perfectly valid point about the limited physical sophistication of many models of biochemical processes. Definitely not a troll...

        • Re:HOW IS THIS A TROLL?? (Score:5, Informative)

          by exp(pi*sqrt(163)) ( 613870 ) on Friday January 19, 2007 @09:23PM (#17690836) Journal
          I think many people really don't appreciate how difficult quantum simulations are. I was pretty surprised when I worked in pharmaceuticals for a bit and saw how much CPU time was being expended on fundamentally simple ball-and-stick simulations. (Ball-and-stick seemed to be standard terminology, even though it looks like a derogatory term.) I was also pretty shocked by how many tunable parameters there were - mainly because things like bonds were added ad hoc rather than emerging naturally from the simulation. Bonding is fundamentally a quantum phenomenon so it can never emerge from a classical simulation without being explicitly added as a kind of spring. And because bonding doesn't really make sense in a classical context, it actually behaves very differently from any kind of spring, and that's why you have to keep tuning the spring parameters to make things look reasonable.

          But when I realised how hard quantum simulations could be it started seeming reasonable again. Quantum simulations aren't just an order of magnitude more difficult. The order of magnitude of difficulty can itself be an order of magnitude bigger!

    • Re:How is this any different? (Score:5, Interesting)

      by wass ( 72082 ) on Friday January 19, 2007 @06:30PM (#17689362)
      Scientists have been modelling chemical systems within the quantum realm for almost a century now. The problem is that there are very few problems which can be exactly solved. Eg, the hydrogen atom is one of the few solvable ones, but in reality that's only solvable when ignoring all the fine structure corrections (no spin-orbit, relativistic, or spin-spin perturbations). Once you get to the 'difficult' problem of only a mere helium atom, which in its simplest form neglecting fine structure is 'only' two interacting electrons orbiting a nucleus that you model as just a point mass with charge +2e, things get very complicated very quickly. Now imagine modelling something more complicated like a benzen ring, then imagine an actual protein.

      This isn't anything new per se, just that the complexity of the modelled systems is getting larger, and due to the numercal estimation processes needed to get anything remotely usable these realms haven't been accessible until lately with the increase of computing power. So where does one draw the line between physics, chemistry, biochemistry, and biology? In these cases, what's being modelled are primarily systems consisting of electrons, neutrons, and protons, interacting with Coulomb force (like-charges repel), spin-orbit interactions, spin-spin interactions, Pauli-exclusion principle, etc. Add more atoms, system gets more complicated, and needs bigger computers.

      So it's an age-old problem, using almost age-old numerical techniques, running on new shiny computing clusters

      • This isn't anything new per se, just that the complexity of the modelled systems is getting larger, and due to the numercal estimation processes needed to get anything remotely usable these realms haven't been accessible until lately with the increase of computing power
        http://boinc.berkeley.edu/ [berkeley.edu]

         

      • Re: (Score:2)

        by jotok ( 728554 )
        I've read that physics in general is a discipline in which you can figure out the way systems work relatively easily, but have a hard time accounting for specific forms or structures...so you have freshman ballistics problems that begin "Imagine a spherical or point-shaped cow launched from a catapult..." Is this why so few problem can be exactly solved? The more intricate the structure, the less the generalized functional model describes it?

        • Re:How is this any different? (Score:4, Informative)

          by MoxFulder ( 159829 ) on Friday January 19, 2007 @09:18PM (#17690808) Homepage
          Being able to solve physics problems analytically depends a lot on what "symmetry". It's kind of a misleading term... basically what we physicists mean by symmetry is that a system is unchanged by changing the value of some property. So a square cut down the middle is symmetric in that both halves have the same shape. As a result we can solve problems involving the square without worrying about which half we're dealing with.

          The "spherical cow" case is similar. A uniform-density sphere is great for ballistics problems because you can characterize it with only 2 parameters: its radius and its mass. If it's a realistic cow, it becomes a lot more complicated... its mass is distributed non-uniformly, and it's got a complicated shape (and it can move!!).

          The real art in physics is figuring out when you can use approximations! If a cow is orbiting the moon, it's probably an excellent approximation to treat it as a sphere in order to determine its orbit. But if a cow is dropped off a cliff, it's not such a good approximation... since its air resistance will depend a lot on its shape.

          • But if a cow is dropped off a cliff, it's not such a good approximation... since its air resistance will depend a lot on its shape.
            Not that it makes any difference to the cow :)

        • Re:How is this any different? (Score:5, Informative)

          by wass ( 72082 ) on Friday January 19, 2007 @09:57PM (#17691088)
          Well, physics is much more than freshman ballistics problems, but you're correct in that the complexity becomes significantly more difficult. Eg, in elementary quantum mechanics one can build a 'Hamiltonian' for any system, and usually you approximate things such as excluding the Coulomb force between every set of electrons, and that neutrons, electrons, and protons act as tiny magnets so they interact that way, and that there are spin-relational effcts, etc. Each of these adds terms to the Hamiltonian, but usually there's a convergence as the correction terms are smaller and smaller and can be neglected. Actually, that's why QED is so easy but QCD gets harder, because secondary and higher interactions in QED have decreasing significance but no so much in QCD where things diverge.

          So in some sense you know the basic 'laws' of the universe, and right now we have pretty reasonable understanding of most things, neglecting large scales (dark matter, dark energy) and large energies (Higgs boson, gravitons, etc). But for stuff within our local spheres of observation, we have basic laws that account for most things we can see, so we should theoretically be able to model anything in this frame. The problem is that it becomes super complex very quickly.

          Okay, so why there are so few solvable problems is mathematical. Eg, in the hydrogen atom, we can easily solve the differential equation that comes from the Schrodinger equation. Ie, you write the kinetic energy as T=p^2/2m, you write the potential energy as U=-e^2/r, giving a total energy of E=p^2/2m - e^2/r. You should recognize this as the standard kinetic energy written using momentum instead of velocity, and the Coulomb potential energy between the electron and proton. The system is an electron orbiting a proton, and in the center-of-mass units r is the distance between the two, and m is the reduced mass, which is fairly close to the electron. This is all well and good, and when put into the realm of quantum mechanics, r and p go from being canonical coordinates to being canonical operators. When put into the position basis, the p operator acts as a derivative of the r coordinate, and this yields a differential equation that must be solved to give the eigenstates of the solution. The system is spherically-symmetric which makes things much easier, and after solving the three-dimensional 2nd-order differential equations you get the solutions of atomic orbitals that you probably studied about in high-school chemistry class.

          Now this is the 'simple' system. When you start adding relativistic corrections to that kinetic energy and when you add the interaction of the electron's magnetic moment interacting with the magnetic field creating as it orbits the proton, this yields the fine structure. You can also add in the spin-spin interaction between the magnetic moment of the electron and the proton, which gives the hyperfine interaction. Each of these things makes the differential equations MUCH harder to solve, and at some point we just don't mathematically know how to solve these complex systems of equations. Helium atom gets much harder because there are now two position coordinates of each atom, and an extra Coulomb interaction term. This is a quantum three-body problem, and even in classical mechanics the three-body problem cannot be solved in general. Ie, there is no KNOWN exact solution for any three bodies.

          Anyway, you can see where this is going. But while we cannot know exact solutions, we can approximate them numerically to arbitrarily-small precision (at least with classical mechanics where there is no uncertainty principle). This is where the shiny computers come in. We can model easily how 10 bodies orbit around the sun AND interact with each other, but to get a general algebraic solution of them for any point in time, we cannot do.

          • Re: (Score:2)

            by jotok ( 728554 )
            Wow, I'm surprised both by the depth of the answer and my own ability to understand it :)

            So in essence we can get "good enough" approximations. Is there evidence that you can get significantly more explanatory power by trying to take into account all the additonal factors? Is it a problem of observation (data acq) or of processing power?

            When I ask this I'm thinking of a note in Brian Goodwin's book How the Leopard Changed Its Spots, in which the author (very gently IMO) takes proponents of the Modern Evol

            • Re: (Score:2)

              by wass ( 72082 )
              in classical physics, which we know isn't fully valid, given a position and momentum at one instant of time for every particle in the system, and an understanding of the equations of motion of how those particles act with each other, you can figure out where the particles will be at any time in the future. well, you'll need numerical techniques to approximate, but you can get arbitrarily accurate. quantum is now differnt, you can only know position adn momentum within some finite uncertainty so it limits

          • Re: (Score:2)

            by Manchot ( 847225 )
            I think I should clarify something in the parent's post. In a lot of situations, it's not just that we don't know the solution to a mathematical problem, it's that no general solution exists. (See the n-body problem [wikipedia.org] for an example.) This is not the same thing as saying that a solution doesn't exist, it just means that no mathematical statement can fully solve the equations.
      • Parent makes good points. However, most /. readers may not realise that there are a number of ways to approximately solve many of these problems. One of the most powerful is the so-called density functional theory [wikipedia.org]. This is (in principle) a way of computing physical properties for (bio)chemical systems. It scales as the cube of the number of electrons in the system.

        Using todays supercomputers, we can deal with about ten thousand atoms. So by Moores law, it takes eight years to double the number of atoms.

        wher

    • Re: (Score:2, Informative)

      by avelldiroll ( 813074 )

      It sounds like plain biochemistry given a new window dressing.

      Not exactly ... there's actually something new here (2-3 years old in fact).

      There are 3 "levels" of Computational chemistry :

      - ab-initio method : a resolution of the Schrödinger equation for the studied system with only a few approximations mandatory to solve problem more complex than the hydrogen atom. This method is fairly demanding on number crunching power and is applied on models of hundreds of atoms.

      - semi-empirical method

    • Re: (Score:2)

      by jotok ( 728554 )
      Not at all. Biology has the same structure-function paradox as every other discipline...so x-ray crystallographs won't tell you how the active site works, and chemical models don't tell you much about structure. This sounds a lot more like Bioinformatics [wikipedia.org], which is about modeling information flow in biological systems.

  • Uncertainty principle and medicine (Score:5, Funny)

    by Anonymous Coward on Friday January 19, 2007 @05:40PM (#17688810)
    So, when I am seriously ill and get quantum biology based medication, will I be in a superposition state of 'getting better' and 'dead'?
  • ...might or might not be dead; it also might or might not even exist???
    • Well, no. It may or may not have evolved, or it may have been Created(TM). Since we do not know, we must consider both to be true. Finally, a solution to that debate.

      DISCLAIMER: No, I am not a creationist.

    • ...actually, a person doesn't own a cat, the cat honors one with his presence. Therefore, it is more accurately described as the Cat's Schrodinger and the whole conjecture should be reversed.
  • If they can simulate proteins by simulating individual atoms in the protein, I wonder if they have the computing power to simulate a basic cell using the same process. And/Or, I wonder if they can simulate a large random chunk of atoms to see if they can create simple amino acids and other biological molecules. That would be an interesting step toward learning about the origins of life.

    • Re: (Score:2)

      by jotok ( 728554 )
      It's not really an issue of computing power. Analyzing the structure and function (behavior) of a system are two radically different things, sadly, and while a complete understanding of one really doesn't help you a whole hell of a lot with the other, you need both to really grasp the nature of the system. One great example of this is ant colony behavior: the ants interact in ways that are not readily apparent simply from studying isolated ants, leading to patterns in movement (in time as well as in space

  • Doesn't work (Score:5, Funny)

    by Intron ( 870560 ) on Friday January 19, 2007 @05:51PM (#17688944)
    I tried firing hundreds of cats through two narrow slits and I didn't get interference patterns.

  • Very funny... (Score:3, Funny)

    by xENoLocO ( 773565 ) * on Friday January 19, 2007 @05:52PM (#17688952) Homepage
    Isn't this just a geeky way of saying "small anatomy" ?

    If that's the case, I invented this 26 years ago!

  • 1966 (Score:3, Informative)

    by Bowling Moses ( 591924 ) on Friday January 19, 2007 @05:59PM (#17689024) Journal
    A quick search turned up an article from 1966 [nih.gov] which suggests quantum tunneling in a protein, so the idea of quantum mechanics in biology isn't all that new (and probably predates the article). Disclaimer: I've only read the abstract, I don't do research in that area, those without a university hookup might not get to read it even if they really wanted to.
  • "Mommmm! There are two particles in the front yard...and they look like they're quantum entangled."
  • Sounds like RPI has made a bigger breakthrough than claimed.

  • Overhyped (Score:3, Interesting)

    by AFairlyNormalPerson ( 721898 ) on Friday January 19, 2007 @06:10PM (#17689150) Journal
    "This is the scientific study of biological processes in terms of quantum mechanics and it uses today's high-performance computers to precisely model these processes."

    Precisely modeling these processes? Biggest overstatement EVER. Total hype.
    When looking at large systems you are screwed and you can generally screw yourself in 1 of 2 ways:
    1) Preciesly model few configurations, in which case, your results are not comparable to reality, which is an ensamble average over billions of configurations
    2) Model things in an emprirical/semi-empirical, yet surprisingly CRUDE way: allowing one to sufficiently sample phase space, but not in an analytically useful way.

    Quantum mechanics in biological systems are typically done with QM/MM, where the "QM" is semi-EMPIRICAL, i.e., it takes parameters. These methods and parameters were NOT designed with biological systems in mind. They were chosen to reproduce small molecule heats of formation. People have found that they work poorly for biological studies unless they are reparametrized (quite frankly, you need to know "the answer" in order to get "the answer" "right") or unless other post-priori, ad hoc corrections are applied. Only a small portion of people who use QM/MM actually reparatrize the semiempirical method and those who do find the new parameters are not very transferable for use between different types of biological systems. For crying out loud, most semiempirical hamiltonians don't even provide the functional forms needed for some of the most basic molecular interactions, e.g., London dispersion, proper polarization to external fields, hydrogen bonding, orthogonalization errors in torsional barriers, etc..

    This stuff isn't really new and it's extremely overhyped.

    • Re: (Score:3, Informative)

      by the_psilo ( 592055 )

      This stuff isn't really new and it's extremely overhyped.

      I agree on the overhype. What the article fails to properly elucidate is that this is a common expansion of existing molecular modeling techniques. All modern molecular modeling simulations are based on equations of force and motion experienced by the individual atoms. Even with "simple" interactions such as electrostatics, the equations are often rendered into power series approximations of the more complicated higher order equations. This makes it easier to do computationally intensive calculations

    • Re: (Score:1, Interesting)

      by Anonymous Coward
      I totally agree. I am a computational chemist who uses QM/MM modelling of biological systems and the field is definitely not new. It is an exciting field of scientific study with a lot of promise, and I do commend the scientists involved for popularising their research. The best thing about this type of science is that it combines the best parts of chemistry, physics, maths and computer science. In my opinion, the biggest challenge at the moment is how do we (a) increase the detail (expense) of the QM calcu

    • Re: (Score:2)

      by jotok ( 728554 )
      Isn't there some value in trying to apply the methods? Most of the advances in analytical technique in biology in the past 100 years seem to have been applications of techniques that originated in physics and engineering circles.

    • Quantum mechanics in biological systems are typically done with QM/MM, where the "QM" is semi-EMPIRICAL, i.e., it takes parameters. These methods and parameters were NOT designed with biological systems in mind. They were chosen to reproduce small molecule heats of formation. People have found that they work poorly for biological studies unless they are reparametrized (quite frankly, you need to know "the answer" in order to get "the answer" "right") or unless other post-priori, ad hoc corrections are applied.

      By the sounds of it, you are just parameterizing yourself practically back to MM with fudged factors to allow bond-breaking etc. Are you saying QM/MM cannot be used to predict an enzyme mechanism? Is this a limit of current quantum theory or a limit because of calculation times? I'd appreciate any good recent references.

    • Re: (Score:1, Interesting)

      by Anonymous Coward
      The beauty of QM/MM simulations is that you can use MM to find the relatively few conformations that are worthy of full QM analysis. MM simulations do a pretty good job of predicting biologically relevant conformers. With that information you can then do full blown QM simulations on selected conformers to predict/model covalent chemistry. This approach has been particularly successful at modeling hydrogen tunneling (see the works of Prof. Truhlar at the U. of Minnesota). Suggesting that current efforts

      • Re: (Score:2, Informative)

        by AFairlyNormalPerson ( 721898 )
        It's more accurate than what most people believe because they spend so much time jerking each other off.

        That's the big variational transistion state theory guy, right? Pay special attention to the details of how those potential energy surfaces are contructed - especially from the groups at that university. All of their QM/MM results match experiment almost perfectly (because after doing a QM/MM simulation they either "correct" the resulting "potential of mean force" curves or "correct" the effective PES o
  • Wasn't this an episode of Star Trek???
  • I was never totally sure I was a sprout.
  • I think that "in terms of quantum mechanics" we do not have any "high-performance computers" yet.
  • I think that the term Quantum Biology is somewhat misleading in this instance. I do not think that we are anywhere close to being able to simulate anything at the biological level Quantum Mechanically (QM). Well simulate it and obtain reliable data anyways. In the field of Molecular Modeling, we have a pretty good grasp of how to simulate an entire protein at the atomistic level (MM). Right now Quantum Mechanical simulations can provide us with reasonable answers for systems of something like 400 to 4000

  • Puhleease: Put Roland Piquepaille blog elsewhere (Score:5, Insightful)

    by viking80 ( 697716 ) on Friday January 19, 2007 @06:29PM (#17689352) Journal
    would like to just suggest a link to Roland Piquepailles blog somewhere where those who are interested can click. And *no more articles please*

    I read /. to get real news and facts, and see discussions from people with insight.
    Roland Piquepailles submissions has not met this criterium. At least filter away the combination "Piquepailles", "nano" and "quantum".

    Take a bottle of nano-beer (yes the water molecules are nano particles), eat some nano-pretzels (the baking soda produced a nano-gas that puffed them up), and run this script.

    Here is one of many greasemonkey script to remove piquepaille stories
    http://userscripts.org/scripts/show/5735/ [userscripts.org]

    You should mod this up if you agree or mod away as flamebait/offtopic/troll if you dont agree, but at least mod it.
  • Just when you finally have grasped the concept of quantum mechanics

    My physics professors always made fun of people who talked like this. Nobody has ever "finally grasped the concept of quantum mechanics".
  • >> The Birth of Quantum Biology

    Won't need an epidural for that.
    1. Find a way to prefix the terminology in your research with Hyper-, Nano-, or Quantum-..
    2. ??? (not necessary)
    3. Profit!!!

    I think Hyper- has gone out of fashion recently just like Super- went out of fashion long time ago. Our university still has a department called Hypermedialab - now it just sounds so 90's and cheese...

    Incidently I'm looking for a grant for my biology research on Supercalifragilisticexpialidocious-cells...

    Sincerely
    Dr. Johann Gambolputty de von Ausfernschplendenschlittercrasscrenbonfri

  • I'm certainly no biologist or quantum physicist for that matter, but I have this habit of pondering about things and trying to find explanations for the weird and wonderful in our lives. I generally don't beleive in ghosts, aliens, god, psychic powers and so forth but I do try to debate with myself as to how these things could be possible because well, to me that seems the best way of deciding whether I do or don't beleive in something.

    One of the things I've wondered about in the past is that of supposed ps

    • Re: (Score:3, Insightful)

      by exp(pi*sqrt(163)) ( 613870 )
      The theory that predicts the existence of "spooky action at a distance" is the same theory that predicts you can't use it to communicate - in the sense that there is no instantaneous transmission of usable information.

      But suppose there were some fancy physics that could form the basis for direct brain-to-brain communication. What would have happened during natural selection? If such a mechanism were available, surely it would have been selected for over speech. Speech requires years before users master it

      • Maybe the telepaths have wiped the floor with us normals, and we just haven't noticed because we have no way of snooping their planning meetings.

        Maybe the curent world situation is a mess of the telepaths' making, to keep us normals distracted while they hang out in their clubhouse with their cigars and champagne and telepathic passwords.

      • Re: (Score:1)

        by bh_doc ( 930270 )

        The theory that predicts the existence of "spooky action at a distance" is the same theory that predicts you can't use it to communicate - in the sense that there is no instantaneous transmission of usable information.

        Entanglement (this "spooky action at a distance") can, however, be used to increase (double, in fact) the bandwidth of classical communication. See superdense coding [wikipedia.org]. It can be argued that since we can communicate classical information at the speed of light without entanglement, superdense c

        • Quantum teleportation allows you to piggy-back qubits on bits. But you're conflating two different senses of speed. Quantum teleportation might, in some sense, be used to increase information rate, but that is entirely different from the speed of a message. (Think of trucks full of hard drives. High data rate, low signal speed.) So there's no sense in which anything is being sent at twice lightspeed.

      • But suppose there were some fancy physics that could form the basis for direct brain-to-brain communication. What would have happened during natural selection? If such a mechanism were available, surely it would have been selected for over speech. Speech requires years before users master it and is limited by the transmission of sound. If you could short circuit that then you'd have a considerable advantage. Telepaths would have wiped the floor with us normals millions of years ago.

        Supposing there were su

  • Roger Penrose has been advocating quantum mechanics (or rather, quantum gravity) as the key to understanding the brain for some time. It's pretty hard to believe, and a lot of people dismiss him out of hand. However, if you read his entire book Shadows of the Mind, you might agree with me that he could be correct.

    Another book I read on the subject a long time ago was The Quantum Brain, by Jeffrey Satinover.
  • I can't believe they are calling this "quantum biology". It has nothing whatsoever to do with quantum mechanics. They are not studying sub-atomic particles, and quantum effects to *NOT* apply to reactions between among atoms and molecules. They are looking at classical processes, and possible have moved slightly out of chemistry into physics, but certainly not into quantum physics.

    They may be looking at smaller things, but not small enough to consider quantum effects. I wonder if the scientists themse

    • Yes, and it's especially dangerous because it will be ignorantly quoted in support of the 'quantum healing' snake-oil ripoffs that are taking over the fey fringes from the galvanic, magnetic and 'radionic' gizmos of an earlier century.
  • Quantum biology? Are they maybe getting a bit ahead of themselves? Someone give me a shout once they crack the proteome.

  • It's Roland the Plogger, trolling for his blog again. For a while, Slashdot was careful about not letting him get a link to drive traffic to his blog, but somebody slipped up.

  • They plan to precisely model quantum mechanical events? Yeah, good luck with that one.
  • between a car mechanic and a quantium mechanic? one of the two dosn't have to open the garage door (but your still not sure which)

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