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Frontiers of Engineering Reports on Leading-Edge Engineering from the 2004 NAE Symposium on Frontiers of Engineering (2005) / Chapter Skim
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Modeling the Stuff of the Material World: Do We Need All of the Atoms?--Rob Phillips
Pages 77-86

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From page 77...
... One of the flagship techniques for examining problems involving complex materials is molecular dynamics in which the microscopic trajectories of each and every atom are followed explicitly. Despite their promise, however, these simulations sometimes generate enormous quantities of information (i.e., terabyte data sets)
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From page 78...
... And yet our computers are overflowing with terabyte data sets, and worse yet, discussions of petabyte data sets are becoming routine. For example, a molecular dynamics calculation on a 100,000-atom system run for only 10 nanoseconds, woefully inadequate for accessing most materials processes, already generates a terabyte worth of data.
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From page 79...
... A CASE STUDY IN MULTISCALE MODELING The Quasicontinuum Method One of the computational responses to problems involving multiple scales is multiresolution models that attempt to capture several scales at the same time. There has been great progress along these lines in recent years from a number of different quarters, and presently we will consider one example, namely the quasicontinuum method that permits the treatment of defects in crystalline solids.1 The main idea of the quasicontinuum method is to allow for atomic-level detail in regions where interesting physical processes, such as dislocation nucleation, dislocation intersections, and crack propagation are occurring, while exploiting a more coarse-grained description away from the key action.
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From page 80...
... To that end, the quasicontinuum method posits that the forces on the nodes can be obtained by appealing to interatomic potentials that describe interactions between individual atoms. Using the interpolated atomic positions, a neighborhood of atoms around each node is constructed, and the energies and forces are then computed using standard atomistic techniques.
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From page 81...
... So the hunt is on to find methods of modeling processes of biological relevance involving assemblies of diverse molecular actors, such as proteins, lipids, and DNA, without having to pay the price in excessive data of all-atom simulation. One way to guarantee a rich interplay between experiment and models is through the choice of case studies that are well developed from the standpoint of molecular biology and for which we have compelling quantitative data.
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From page 82...
... This statistical mechanics perspective is a natural quantitative counterpart to the cartoons describing gene regulation used in classic texts of molecular biology. As shown in Figure 3, these cartoons depict various states of occupancy of the DNA in the neighborhood of the site where RNA polymerase binds.
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From page 83...
... SUMMARY The critical question for building models of the material world is the extent to which we can suppress an atom-by-atom description of the function of materials. As emergence of "multiscale modeling" reveals, even with increasing
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From page 84...
... 84 The corre T) B (K their ap and molecules.
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From page 85...
... Although multiscale computational models are receiving most of the effort and attention right now, I believe the hunt should continue for analytic models that can capture the key features of complex materials and lead to the kind of insight that can be discussed at a blackboard. ACKNOWLEDGMENTS I am grateful to Jané Kondev, Michael Ortiz, Ellad Tadmor, Ron Miller, Vijay Shenoy, Vivek Shenoy, David Rodney, Klaus Schulten, Darren Segall, and Laurent Dupuy for collaboration and conversation.
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Key Terms

  • material world
  • quasicontinuum method
  • gene regulation
  • molecular dynamics
  • complex materials

  • terabyte data
  • statistical mechanics
  • lac operon
  • rna polymerase
  • microscopic physics

  • atomic positions
  • mediate gene
  • amino acid
  • modeling perspective
  • underlying microscopic

  • binding sites
  • genes responsible
  • mechanics perspective
  • elasticity theory
  • key action

  • lactose digestion
  • individual atoms
  • material response
  • materials setting
  • key features

  • microscopic trajectories
  • diverse molecular
  • intellectual roof
  • design complex
  • harbor laboratory


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