Scientific Modeling and Simulations

1. Front Matter

   Pages I-V

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2. Scientific Modeling and Simulations

   • Tomas Diaz de la Rubia, Sidney Yip

   Pages 1-2

3. A retrospective on the journal of computer-aided materials design (JCAD), 1993–2007

   • Sidney Yip

   Pages 3-4

4. Extrapolative procedures in modelling and simulations: the role of instabilities

   • Göran Grimvall

   Pages 5-20

5. Characteristic quantities and dimensional analysis

   • Göran Grimvall

   Pages 21-39

6. Accuracy of models

   • Göran Grimvall

   Pages 41-57

7. Multiscale simulations of complex systems: computation meets reality

   • Efthimios Kaxiras, Sauro Succi

   Pages 59-65

8. Chemomechanics of complex materials: challenges and opportunities in predictive kinetic timescales

   • Krystyn J. Van Vliet

   Pages 67-80

9. Tight-binding Hamiltonian from first-principles calculations

   • Cai-Zhuang Wang, Wen-Cai Lu, Yong-Xin Yao, Ju Li, Sidney Yip, Kai-Ming Ho

   Pages 81-95

10. Atomistic simulation studies of complex carbon and silicon systems using environment-dependent tight-binding potentials

    • Cai-Zhuang Wang, Gun-Do Lee, Ju Li, Sidney Yip, Kai-Ming Ho

    Pages 97-121

11. First-principles modeling of lattice defects: advancing our insight into the structure-properties relationship of ice

    • Maurice de Koning

    Pages 123-141

12. Direct comparison between experiments and computations at the atomic length scale: a case study of graphene

    • Jeffrey W. Kysar

    Pages 143-157

13. Shocked materials at the intersection of experiment and simulation

    • H. E. Lorenzana, J. F. Belak, K. S. Bradley, E. M. Bringa, K. S. Budil, J. U. Cazamias et al.

    Pages 159-186

14. Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates

    • Michele Monteferrante, Sara Bonella, Simone Meloni, Eric Vanden-Eijnden, Giovanni Ciccotti

    Pages 187-206

15. Concurrent design of hierarchical materials and structures

    • D. L. McDowell, G. B. Olson

    Pages 207-240

16. Enthalpy landscapes and the glass transition

    • John C. Mauro, Roger J. Loucks, Arun K. Varshneya, Prabhat K. Gupta

    Pages 241-281

17. Advanced modulation formats for fiber optic communication systems

    • John C. Mauro, Srikanth Raghavan

    Pages 283-312

18. Computational challenges in the search for and production of hydrocarbons

    • John Ullo

    Pages 313-337

19. Microscopic mechanics of biomolecules in living cells

    • Fabrizio Cleri

    Pages 339-362

20. Enveloped viruses understood via multiscale simulation: computer-aided vaccine design

    • Z. Shreif, P. Adhangale, S. Cheluvaraja, R. Perera, R. Kuhn, P. Ortoleva

    Pages 363-380

Although computational modeling and simulation of material deformation was initiated with the study of structurally simple materials and inert environments, there is an increasing demand for predictive simulation of more realistic material structure and physical conditions. In particular, it is recognized that applied mechanical force can plausibly alter chemical reactions inside materials or at material interfaces, though the fundamental reasons for this chemomechanical coupling are studied in a material-speci c manner. Atomistic-level s- ulations can provide insight into the unit processes that facilitate kinetic reactions within complex materials, but the typical nanosecond timescales of such simulations are in contrast to the second-scale to hour-scale timescales of experimentally accessible or technologically relevant timescales. Further, in complex materials these key unit processes are “rare events” due to the high energy barriers associated with those processes. Examples of such rare events include unbinding between two proteins that tether biological cells to extracellular materials [1], unfolding of complex polymers, stiffness and bond breaking in amorphous glass bers and gels [2], and diffusive hops of point defects within crystalline alloys [3].

• atomistic simulations
• calculus
• communication
• comparison between experiments and simulations
• complex systems
• computer-aided design (CAD)
• computer-aided vaccine design
• first-principle calculations
• glass transition
• linear optimization
• mechanics
• mo

• Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, USA

  Sidney Yip

• Lawrence Livermore National Laboratory, University of California, Livermore, USA

  Tomás Diaz Rubia

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