Multiscale simulations of complex systems: Computation meets reality

Scientific Modeling and Simulation SMNS

Volumn 15, Issue 1-3, 2008, Pages 59-65

  Kaxiras, Efthimios ^a   Succi, Sauro ^b,c  

^a HARVARD UNIVERSITY   (United States)

^b CNR   (Italy)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Biomolecules; Corrosion; Multiscale simulations

Indexed keywords

COMPLEX SYSTEMS; DNA SEQUENCING; MACROSCOPIC BEHAVIORS; MASSIVELY PARALLEL COMPUTERS; MULTI-SCALE SIMULATION; MULTISCALE METHOD; MULTISCALE SIMULATIONS; NOVEL DEVICES; PHYSICAL PHENOMENA; ULTRA-FAST;

BIOMOLECULES; COMPUTER ARCHITECTURE;

STRESS CORROSION CRACKING;

EID: 73449132931     PISSN: 18748554     EISSN: 18748562     Source Type: Journal    
DOI: 10.1007/s10820-008-9096-y     Document Type: Article

References (31)

1. Lu, G., Kaxiras, E.: Overview of multiscale simulations of materials. In: Rieth, M., Schommers, W. (eds.) Handbook of Theoretical and Computational Nanothechnology, vol. X, pp. 1-33. American Scientific Publishers (2005)
2. N. Winzer A. Artens G. Song E. Ghali W. Dietzel K. Ulrich N. Hortand C. Blawert 2005 A critical review of the stress corrosion cracking (SCC) of Magnesium alloys Adv. Eng. Mater. 7 659 10.1002/adem.200500071 1:CAS:528:DC%2BD2MXhtVGiu7jN (Pubitemid 41356631)
3. Hirth J.P., Lothe J.: Theory of Dislocations. Krieger Publshing Co., Malabar, Florida (1992)
4. Peierls, R.: The size of a dislocation. Proc. Phys. Soc. London 52, 34-37 (1940);
5. Nabarro, F.R.N.: Dislocations in a simple cubic lattice. Proc. Phys. Soc. London 59, 256-272 (1947)
6. B. Devincre L. Kubin 1994 Mesoscopic simulations of dislocations and plasticity Mater. Sci. Eng. A 234-236 8 14
7. V. Bulatov F.F. Abraham L. Kubin S. Yip 1998 Connecting atomistic and mesoscopic simulations of crystal plasticity Nature 391 669 681 10.1038/35577 1998Natur.391..669B 1:CAS:528:DyaK1cXht1Gmtrw%3D (Pubitemid 28113207)
8. R. Car M. Parrinello 1985 Unified approach for molecular-dynamics and density-functional theory Phys. Rev. Lett. 55 2471 2474 10032153 10.1103/PhysRevLett.55.2471 1985PhRvL..55.2471C 1:CAS:528:DyaL28XhtVOlug%3D%3D
9. T.D. Kuhne M. Krack F.R. Mohamed M. Parrinello 2007 Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics Phys. Rev. Lett. 98 066401 17358962 10.1103/PhysRevLett.98.066401 2007PhRvL..98f6401K (Pubitemid 46220444)
10. Abraham, F., Broughton, J., Bernstein, N., Kaxiras, E.: Spanning the length scales in dynamic simulation. Comput. Phys. B. 12, 538-546 (1998);
11. Broughton, J., Abraham, F., Bernstein, N., Kaxiras, E.: Concurrent coupling of length scales: methodology and application. Phys. Rev. B. 60, 2391-2403 (1999)
12. E.B. Tadmor M. Ortiz R. Phillips 1996 Quasicontinuum analysis of defects in solids Philos. Mag. A. 73 1529 1563 10.1080/01418619608243000 1996PMagA..73.1529T (Pubitemid 126310376)
13. G.S. Smith E.B. Tadmor N. Bernstein E. Kaxiras 2001 Multiscale simulation of silicon nanoindentation Acta Mater. 49 4089 10.1016/S1359-6454(01)00267-1 1:CAS:528:DC%2BD3MXnslSntbY%3D (Pubitemid 33018779)
14. E.B. Tadmor U.V. Waghmare G.S. Smith E. Kaxiras 2002 Polarization switching in PbTiO3: an ab initio finite element simulation Acta Mater. 50 2989 10.1016/S1359-6454(02)00127-1 1:CAS:528:DC%2BD38XkslSgtL0%3D (Pubitemid 34704385)
15. Voter, A.F.: A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106, 4665-4677 (1997);
16. Voter, A.F.: Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys. Rev. Lett. 78, 3908-3911 (1997)
17. Kasianowicz, J.J., Brandin, E., Branton, D., Deamer, D.: Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA 93, 13770-13773 (1996)
18. Meller, A., Nivon, L., Brandin, E., Golovchenko, J., Branton, D.: Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. 97, 1079-1084 (2000)
19. Li, J., Gershow, M., Stein, D., Brandin, E., Golovchenko, J.A.: DNA molecules and configurations in a solid-state nanopore microscope. Nat. Mater. 2, 611-615 (2003)
20. Storm, A.J., Storm, C., Chen, J., Zandbergen, H., Joanny, J.-F., Dekker, C.: Fast DNA translocation through a solid-state nanopore. Nanoletter 5, 1193-1197 (2005)
21. C. Dekker 2007 Solid state nanopores Nat. Nanotech. 2 209 215 10.1038/nnano.2007.27 2007NatNa...2..209D 1:CAS:528:DC%2BD2sXjvVOgtrY%3D (Pubitemid 46739810)
22. Succi, S.: The Lattice Boltzmann Equation for Fluid Dynamics and Beyond. Clarendon Press, Oxford (2001);
23. Benzi, R., Succi, S., Vergassola, M.: The lattice Boltzmann equation: theory and applications. Phys. Rep. 222, 145-197 (1992)
24. Fyta, M.G., Melchionna, S., Kaxiras, E., Succi, S.: Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore. Multiscale Model. Sim. 5, 1156-1173 (2006);
25. Fyta, M.G., Melchionna, S., Kaxiras, E., Succi, S.: Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann molecular-dynamics methodology. Int. J. Mod. Phys. C. 18, 685-692 (2007)
26. Fyta, M.G., Kaxiras, E., Melchionna, S., Succi, S.: Multiscale modeling of biological flows. Comput. Sci. Eng. 20 (2008)
27. M. Bernaschi S. Melchionna S. Succi M. Fyta E. Kaxiras 2008 Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations Nano Lett. 8 1115 1119 18302329 10.1021/nl073251f 1:CAS:528:DC%2BD1cXisVWlu7Y%3D
28. Öttinger, H.C.: Stochastic Processes in Polymeric Fluids: Tools and Examples for Developing Simulation Algorithms. Springer, Berlin (1996); Beyond Equilibrium Thermodynamics. Wiley, New York (2005)
29. M. Praprotnik K. Kremer L. Delle Site 2007 Adaptive molecular resolution via a continuous change of the phase space dimensionality Phys. Rev. E. 75 017701 10.1103/PhysRevE.75.017701 2007PhRvE..75a7701P (Pubitemid 46134174)
30. E,W., Engquist, B., Li, X.T.: Heterogeneous multiscale methods: a review. Commun. Comp. Phys. 2, 367-450 (2007); and in Kevrekidis
31. I.G., Gear, C.W., Hummer, G.: Equation-free: the computer-aided analysis of complex multiscale systems. AiChe J. 50, 1346-1355 (2004)