×

zbMATH — the first resource for mathematics

Fluctuating hydrodynamics methods for dynamic coarse-grained implicit-solvent simulations in LAMMPS. (English) Zbl 1364.65172

MSC:
65M06 Finite difference methods for initial value and initial-boundary value problems involving PDEs
65Y15 Packaged methods for numerical algorithms
76Z05 Physiological flows
92C35 Physiological flow
Software:
Jython; LAMMPS; SELM
PDF BibTeX XML Cite
Full Text: DOI
References:
[1] D. J. Acheson, Elementary Fluid Dynamics, Oxford Applied Mathematics and Computing Science Series, Clarendon Press, Oxford University Press, New York, 1990. · Zbl 0719.76001
[2] P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford University Press, New York, 1987. · Zbl 0703.68099
[3] T. Apajalahti, P. Niemela, P. N. Govindan, M. S. Miettinen, E. Salonen, S.-J. Marrink, and I. Vattulainen, Concerted diffusion of lipids in raft-like membranes, Faraday Discuss., 144 (2010), pp. 411–430.
[4] P. J. Atzberger, A note on the correspondence of an immersed boundary method incorporating thermal fluctuations with Stokesian-Brownian dynamics, Phys. D, 226 (2007), pp. 144–150. · Zbl 1125.76057
[5] P. J. Atzberger, P. R. Kramer, and C. S. Peskin, A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales, J. Comput. Phys., 224 (2007), pp. 1255–1292. · Zbl 1124.74052
[6] P. J. Atzberger and Y. Wang, Fluctuating Hydrodynamic Methods for Fluid-Structure Interactions in Confined Channel Geometries, preprint, University of California Santa Barbara, Santa Barbara, CA, 2014; http://atzberger.org.
[7] P. J. Atzberger, Stochastic Eulerian Lagrangian methods for fluid-structure interactions with thermal fluctuations, J. Comput. Phys., 230 (2011), pp. 2821–2837. · Zbl 1316.76086
[8] P. J. Atzberger, Incorporating shear into stochastic Eulerian Lagrangian methods for rheological studies of complex fluids and soft materials, Phys. D, to appear. · Zbl 1302.76145
[9] M. Bai, A. R. Missel, W. S. Klug, and A. J. Levine, The mechanics and affine-nonaffine transition in polydisperse semiflexible networks, Soft Matter, 7 (2011), pp. 907–914.
[10] G. Booch, Best of Booch: Designing Strategies for Object Technology, SIGS Reference Library, Cambridge University Press, Cambridge, UK, 1997.
[11] J. F. Brady and G. Bossis, Stokesian dynamics, in Annual Review of Fluid Mechanics, Annu. Rev. Fluid Mech. 20, Annual Reviews, Palo Alto, CA, 1988, pp. 111–157.
[12] G. Brannigan, L. Lin, and F. Brown, Implicit solvent simulation models for biomembranes, European Biophys. J., 35 (2006), pp. 104–124, http://dx.doi.org/10.1007/s00249-005-0013-y doi:10.1007/s00249-005-0013-y.
[13] A. J. Chorin, Numerical solution of Navier-Stokes equations, Math. Comp., 22 (1968), pp. 745–762. · Zbl 0198.50103
[14] I. R. Cooke, K. Kremer, and M. Deserno, Tunable generic model for fluid bilayer membranes, Phys. Rev. E, 72 (2005), 011506.
[15] J. G. De La Torre and V. A. Bloomfield, Hydrodynamic properties of macromolecular complexes. I. Translation, Biopolymers, 16 (1977), pp. 1747–1763.
[16] J. M. Drouffe, A. C. Maggs, and S. Leibler, Computer simulations of self-assembled membranes, Science, 254 (1991), pp. 1353–1356.
[17] R. Johnson, J. Vlissides, E. Gamma, and R. Helm, Design Patterns: Elements of Reusable Object-Oriented Software, Addison–Wesley Professional, Boston, MA, 1994. · Zbl 0887.68013
[18] D. L. Ermak and J. A. McCammon, Brownian dynamics with hydrodynamic interactions, J. Chem. Phys., 69 (1978), pp. 1352–1360.
[19] O. Farago, “Water-free” computer model for fluid bilayer membranes, J. Chem. Phys., 119 (2003), pp. 596–605.
[20] P. J. Flory, Principles of Polymer Chemistry, Cornell University Press, Ithaca, NY, 1953.
[21] D. Frenkel and B. Smit, Molecular dynamics simulations, in Understanding Molecular Simulation, 2nd ed., D. Frenkel and B. Smit, eds., Academic Press, San Diego, CA, 2002, pp. 63–107.
[22] C. W. Gardiner, Handbook of Stochastic Methods, Springer Ser. Synergetics 13, Springer, Berlin, 1985.
[23] R. Goetz and R. Lipowsky, Computer simulations of bilayer membranes: Self-assembly and interfacial tension, J. Chem. Phys., 108 (1998), pp. 7397–7409.
[24] J. Gosling and H. McGilton, The Java Language Environment: A White Paper, Sun Microsystems, Santa Clara, CA, 1996.
[25] D. A. Head, A. J. Levine, and F. C. MacKintosh, Deformation of cross-linked semiflexible polymer networks, Phys. Rev. Lett., 91 (2003), 108102.
[26] J. H. Irving and J. G. Kirkwood, The statistical mechanical theory of transport processes. IV. The equations of hydrodynamics, J. Chem. Phys., 18 (1950), pp. 817–829.
[27] P. E. Kloeden and E. Platen, Numerical Solution of Stochastic Differential Equations, Springer-Verlag, New York, 1992. · Zbl 0752.60043
[28] A. W. Lees and S. F. Edwards, The computer study of transport processes under extreme conditions, J. Phys. C Solid State Phys., 5 (1972), 1921.
[29] E. H. Lieb and M. Loss, Analysis, 2nd ed., AMS, Providence, RI, 2001. · Zbl 0966.26002
[30] S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries, The martini force field: Coarse grained model for biomolecular simulations, J. Phys. Chem. B, 111 (2007), pp. 7812–7824.
[31] B. Oksendal, Stochastic Differential Equations: An Introduction, Springer, New York, 2000.
[32] S. Pedroni and N. Rappin, Jython Essentials, O’Reilly Media, Sebastopol, CA, 2002; http://www.jython.org/.
[33] F. Perrin, Mouvement Brownien d’un ellipsoide (II). Rotation libre et dépolarisation des fluorescences. Translation et diffusion de molécules ellipsoidales, J. Phys. Rad., 7 (1936), pp. 1–11. · Zbl 0013.13906
[34] C. S. Peskin, The immersed boundary method, Acta Numer., 11 (2002), pp. 1–39. · Zbl 1123.74309
[35] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys., 117 (1995), pp. 1–19. · Zbl 0830.65120
[36] P. Plunkett, J. Hu, C. Siefert, and P. J. Atzberger, Spatially adaptive stochastic methods for fluid-structure interactions subject to thermal fluctuations in domains with complex geometries, J. Comput. Phys., 277 (2014), pp. 121–137. · Zbl 1349.76252
[37] L. E. Reichl, A Modern Course in Statistical Physics, John Wiley and Sons, New York, 1998. · Zbl 0913.00015
[38] B. J. Reynwar, G. Illya, V. A. Harmandaris, M. M. Muller, K. Kremer, and M. Deserno, Aggregation and vesiculation of membrane proteins by curvature-mediated interactions, Nature, 447 (2007), pp. 461–464.
[39] H. Royden, Real Analysis, Simon & Schuster, Delran, NJ, 1988. · Zbl 0704.26006
[40] M. Rubinstein and S. Panyukov, Elasticity of polymer networks, Macromolecules, 35 (2002), pp. 6670–6686.
[41] B. Smit, K. Esselink, P. A. J. Hilbers, N. M. Van Os, L. A. M. Rupert, and I. Szleifer, Computer simulations of surfactant self-assembly, Langmuir, 9 (1993), pp. 9–11.
[42] G. Tabak and P. J. Atzberger, Stochastic reductions for inertial fluid-structure interactions subject to thermal fluctuations, SIAM J. Appl. Math., 75 (2015), pp. 1884–1914, http://dx.doi.org/10.1137/15M1019088 doi:10.1137/15M1019088. · Zbl 1342.60109
[43] L. Verlet, Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules, Phys. Rev., 159 (1967), pp. 98–103.
[44] Y. Wang, J. K. Sigurdsson, E. Brandt, and P. J. Atzberger, Dynamic implicit-solvent coarse-grained models of lipid bilayer membranes: Fluctuating hydrodynamics thermostat, Phys. Rev. E, 88 (2013), 023301.
[45] H. Yamakawa, Transport properties of polymer chains in dilute solution: Hydrodynamic interaction, J. Chem. Phys., 53 (1970), pp. 436–443.
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.