The Community for Technology Leaders
RSS Icon
Issue No.04 - July/August (2008 vol.10)
pp: 10-19
Simone Melchionna , National Research Council, Italy
Efthimios Kaxiras , Harvard University
Sauro Succi , National Research Council, Italy
A new multiscale approach for simulating nanobiological flows uses concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The approach is based on a simple scheme of space–time information exchange between the atomistic and mesoscopic scales.
multiscale modeling, multiscale coupling, multiscale modeling, Lattice Boltzmann equation, nanopores, atomistic dynamics, nanoscale modeling, nanoscale
Simone Melchionna, Efthimios Kaxiras, Sauro Succi, "Multiscale Simulation of Nanobiological Flows", Computing in Science & Engineering, vol.10, no. 4, pp. 10-19, July/August 2008, doi:10.1109/MCSE.2008.100
1. D.A. Wolf-Gladrow, Lattice Gas Cellular Automata and Lattice Boltzmann Models, Springer Verlag, 2000.
2. R. Benzi, S. Succi, and M. Vergassola, "The Lattice Boltzmann Equation—Theory and Applications," Physics Reports, vol. 222, Dec. 1992, pp. 145–197.
3. S. Succi et al., "Applying the Lattice Boltzmann Equation to Multiscale Fluid Problems," Computing in Science &Eng., vol. 3, no. 6, 2001, pp. 26–37.
4. M.G. Fyta et al., "Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore," Multiscale Modeling and Simulation, vol. 5, no. 4, 2006, pp. 1156–1173.
5. P. Ahlrichs and B. Duenweg, "Simulation of a Single Polymer Chain in Solution by Combining Lattice Boltzmann and Molecular Dynamics," J. Chemical Physics, vol. 111, no. 17, 1999, pp. 8225–8239.
6. A.J.C. Ladd and R. Verberg, "Lattice-Boltzmann Simulations of Particle-Fluid Suspensions," J. Statistical Physics, vol. 104, no. 5–6, 2001, pp. 1191–1251.
7. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, "Numerical-Integration of Cartesian Equations of Motion of a System with Constraints—Molecular-Dynamics of n-alkanes," J. Computational Physics, vol. 23, no. 3, 1977, pp. 327–341.
8. H.C. Andersen, "Rattle—A Velocity Version of the SHAKE Algorithm for Molecular-Dynamics Calculations," J. Computational Physics, vol. 52, no. 1, 1983, pp. 24–34.
9. R. Adhikari et al., "Fluctuating Lattice Boltzmann," Europhysical Letters, vol. 71, no. 3, 2005, pp. 473–477.
10. S. Ansumali, I.V. Karlin, and H.C. Öttinger, "Minimal Entropic Kinetic Models for Hydrodynamics," Europhysical Letters, vol. 63, no. 6, 2003, pp. 798–804.
11. S. Melchionna, "Design of Quasi-Symplectic Propagators for Langevin Dynamics," J. Chemical Physics, vol. 127, 2007, article 044108.
12. J.J. Kasianowicz et al., "Characterization of Individual Polynucleotide Molecules Using a Membrane Channel," Proc. Nat'l Academy of Science, vol. 93, no. 24, 1996, pp. 13770–13773.
13. J. Li et al., "DNA Molecules and Configurations in a Solid-state Nanopore Microscope," Nature Materials, vol. 2, no. 9, 2003, pp. 611–615.
14. S. Matysiak et al., "Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment," Physical Rev. Letters, vol. 96, no. 11, 2006, article 118103.
15. D.K. Lubensky and D.R. Nelson, "Driven Polymer Translocation through a Narrow Pore" Biophysical J., vol. 77, no. 4, 1999, pp. 1824–1838.
16. C. Forey and M. Muthukumar, "Langevin Dynamics Simulations of Genome Packing in Bacteriophage," Biophysical J., vol. 91, no. 1, 2006, pp. 25–41.
17. J.S. Hur, E.S.G. Shaqfeh, and R.G. Larson, "Brownian Dynamics Simulations of Single DNA Molecules in Shear Flow," J. Rheology, vol. 44, no. 4, 2000, pp. 713–742.
18. H. Yamakawa, Modern Theory of Polymer Solutions, Harper &Row, 1971.
19. P.J. Hagerman, "Flexibility of DNA," Ann. Rev. Biophysics and Biophysical Chemistry, vol. 17, 1988, pp. 265–286.
20. A.J. Storm et al., "Fast DNA Translocation through a Solid-State Nanopore," Nanoletters, vol. 5, no. 7, 2005, pp. 1193–1197.
18 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool