Molecular Dynamics Simulations and the Mechanisms of Protein Complexes

John Kuriyan from UC Berkeley is giving a NERSC Nobel Lecture describing the research behind the Nobel Prize, one of four lectures this year sponsored by National Energy Research Computing Center in honor of its 40th anniversary.

I thought to highlight memorable moments from the lecture.

John Kuriyan – May 20th, 2014

The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations that are much too complicated to be soluble.
It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to explanation of the main features of complex atomic systems without too much computation.
‒ Paul Dirac

On the laws of motion for the atoms
Although the laws governing the motions of atoms are quantum mechanical, the essential realization that made possible the treatment of the dynamics of complex systems was that a classical mechanical description of the atomic motions is adequate in most cases. This realization was derived from simulations of the dynamics of the H+H2 exchange reaction

…everything that living things do can be understood in terms of the jigglings and wigglings of atoms.
‒ Richard Feynman

The atoms are eternal and always moving. Everything comes into existence simply because of the random movement of atoms, which, given enough time, will form and reform, constantly experimenting with different configurations of matter from which will eventually emerge everything we know.
‒ Richard Feynman

Cell: A Collection of Machines
Many of the cellular elements are motors: they convert energy into motion. Myosins walk on actin, and Kinesins walk on microtubules to transport materials in an organized fashion. One motor is special: it does not walk but is responsible for the synthesis of ATP.



References

  1. Paul Dirac
  2. Richard Feynman
  3. NERSC
  4. Cellular Biochemistry
  5. Kuriyan Lab
  6. John Kuriyan
  7. Martin Karplus

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