A poisson P3M force field scheme for particle-based simulations of ionic liquids

Journal of Computational Electronics

Volumn 3, Issue 2, 2004, Pages 117-133

  Aboud, S ^a   Marreiro, D ^b   Saraniti, M ^b   Eisenberg, R ^a  

^a RUSH MEDICAL COLLEGE   (United States)

^b Illinois Institute of Technology   (United States)

Author keywords

Brownian dynamics; Force field; Ion channels; Ionic solutions; Molecular dynamics

Indexed keywords

ALGORITHMS; BOUNDARY CONDITIONS; BROWNIAN MOVEMENT; CALCULATIONS; ELECTROSTATICS; INTEGRATION; IONIC STRENGTH; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; POISSON EQUATION; THERMODYNAMIC PROPERTIES;

BROWNIAN DYNAMICS; FORCE FIELD SCHEME; ION CHANNELS; IONIC LIQUIDS; IONIC SOLUTIONS; PARTICLE BASED SIMULATION;

SEMICONDUCTING LIQUIDS;

EID: 20544451576     PISSN: 15698025     EISSN: 15728137     Source Type: Journal    
DOI: 10.1007/s10825-004-0316-8     Document Type: Article

References (70)

1. B. Hille 2001 Ionic Channels of Excitables Membranes 3rd edition Sinauer Massachusetts
2. E. Neher and B. Sakmann, "Single-Channel currents recorded from membrane of denervated frog muscle fibers," Nature, 260, 799 (1976).
3. F.M. Ashcroft 2000 Ion channels and Disease Academic Press S. Diego, CA
4. M. Goryll, S. Wilk, G.M. Laws, T. Thornton, S. Goodnick, M. Saraniti, J. Tang, and R.S. Eisenberg, "Silicon-based ion channel sensor," Superlattices and Microstructures 2004 (in press).
5. S.M. Sze 1981 Physics of Semiconductor Devices 2nd edition John Wiley & Sons New York
6. Semiconductor Industry Association 1999 International Technology Roadmap for Semiconductors chapter "Process integration, devices, and structures," International SEMATECH Austin - TX p. 83.
7. G. Lamm, The Poisson-Boltzmann Equation, vol. 19 of Reviews in Computational Chemistry (VHC Publishers, 2003) chap. 4, p. 147.
8. R.S. Eisenberg, M.M. Klosek, and Z. Schuss, "Diffusion as a chemical reaction: Stochastic trajectories between fixed concentrations," Journal of Chemical Physics, 102 (4), 1767 (1995).
9. S.-H. Chung, T.W. Allen, and S. Kuyucak, "Modeling diverse range of potassium channels with Brownian dynamics," Biophysical Journal, 83 (1), 263 (2002).
10. W. Im and B. Roux, "Ions and counterions in a biological channel: A molecular dynamics simulation of OmpF porin from escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution," Journal of Molecular Biology, 319 (5), 1177 (2002).
11. D.A. McQuarrie 2000 Statistical Mechanics University Science Books Sausalito, CA
12. C.L. Brooks, B.M. Pettitt, and M. Karplus, "Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids," Journal of Chemical Physics, 83 (11), 5897 (1985).
13. L. Perera, U. Essmann, and M.L. Berkowitz, "Effect of the treatment of long-range forces on the dynamics of ions in aqueous solutions," Journal of Chemical Physics, 102 (1) (1995).
14. J.D. Jackson 1975 Classical Electrodynamics 2nd edition John Wiley & Sons New York
15. R.W. Hockney and J.W. Eastwood 1988 Computer Simulation Using Particles Adam Hilger Bristol
16. W. Hackbush 1985 Multi-Grid Methods and Applications Springer-Verlag Berlin
17. N.W. Ashcroft and N.D. Mermin 1981 Solid State Physics Holt-Sauders International Editions Tokyo
18. M.V. Fischetti and S.E. Laux, "Monte Carlo analysis of electron transport in small semiconductor devices including band-structure and space-charge effects," Physical Review B, 38 (14), 9721 (1988).
19. W.J. Gross, D. Vasileska, and D.K. Ferry, "Ultrasmall MOSFETs: The importance of the full Coulomb interaction on device characteristics," IEEE Transactions on Electron Devices, 47 (10), 1891 (2000).
20. C.J. Wordelman and U. Ravaioli, "Integration of a particle-particle-particle-mesh algorithm with the ensamble Monte Carlo method for the simulation of ultra-small semiconductor devices," IEEE Transaction on Electron Devices, 47 (2), 410 (2000).
21. A.R. Leach 2001 Molecular Modeling. Principles and Applications 2nd edition Prentice Hall Harlow, England
22. P. Gibbon and G. Sutmann 2002 quot;Long-range interactions in many-particle simulation" edited by J. Grotendorst, D. Marx, and A. Muramatsu, in Quantum Simulations of Many-Body Systems: From Theory to Algorithms, Lecture Notes John von Neumann Institute for Computing Jüch, Germany p. 467 vol. 10 of NIC
23. P. Ewald, "Die Berechnung optischer und elektrostatischer Gitterpotentiale," Annalen der Physik, 64, 253 (1921).
24. D.R. Rapaport 1995 The Art of Molecular Dynamics Simulation Cambridge University Press Cambridge, UK
25. A. Brandt, "Multi-level adaptive solutions to boundary-value problems", Mathematics of Computation, 31 (138), 333 (1977).
26. M. Hoyles, S. Kuyucak, and S.-H. Chung, "Solutions of Poisson's equation in channel-like geometries," Computer Physics Communications, 115 (1), 45 (1998).
27. S.C. Li, M. Hoyles, S. Kuyucak, and S.-H. Chung, "Brownian dynamics study of ion transport in the vestibule of membrane channels," Biophysical Journal, 74 (1), 37 (1998).
28. W. Im, S. Seefeld, and B. Roux, "A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels," Biophysical Journal, 79 (2), 788 (2000).
29. D.L. Ermak, "A computer simulation of charged particles in solution. I, "Technique and equilibrium properties," Journal of Chemical Physics, 62 (10), 4189 (1975).
30. P. Turq, F. Lantelme, and H.L. Friedman, "Brownian dynamics: Its application to ionic solutions," Journal of Chemical Physics, 66 (7), 3039 (1977).
31. + motion in water," Journal of Chemical Physics, 83 (11), 5832 (1985).
32. K. Cooper, E. Jakobsson, and P. Wolynes., "The theory of ion transport through membrane channels," Progress in Biophysis and Molecular Biology, 46 (1), 51 (1985).
33. E. Jakobsson and S.-W. Chiu, "Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels," Biophysical Journal, 52 (1), 33 (1987).
34. S. Bek and E. Jakobsson, "Brownian dynamics study of a multiply-occupied cation channel: Application to understanding permeation in potassium channels," Biophysical Journal, 66(4), 1028, 1994.
35. S.-H. Chung, T.W. Allen, M. Hoyles, and S. Kuyucak, "Permeation of ions across the potassium channel: Brownian dynamics studies," Biophysical Journal, 77 (5), 2517 (1999).
36. S.-H. Chung, T.W. Allen, and S. Kuyucak, "Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations," Biophysical Journal, 82 (2), 628 (2002).
37. B. Corry, M. Hoyles, T.W. Allen, M. Walker, S. Kuyucak, and S.-H. Chung, "Reservoir boundaries in Brownian dynamics simulations of ion channels," Biophysical Journal, 82 (4), 1975 (2002).
38. C.R. Arokianathan, A. Asenov, and J.H. Davies, "An approach based on Brownian motion for the simulation of ultrasmall semiconductor devices," Journal of Applied Physics, 81 (1), 226 (1996).
39. M.P. Allen and D.J. Tildesley 1987 Computer Simulation of Liquids Clarendon Press Oxford
40. F.O. Raineri, M.D. Wood, and H.L. Friedman, "Self-diffusion coefficients of ions in electrolyte solutions by nonequilibrium Brownian dynamics," Journal of Chemical Physics, 92 (1), 649 (1990).
41. M. Canales and G. Sesé, "Generalized Langevin dynamics simulations of NaCl electrolyte solutions," Journal of Chemical Physics, 109 (14), 6004 (1998).
42. M. Jarat, O. Bernard, P. Turq, and G.R. Kneller, "Transport coefficients of electrolyte solutions from Smart Brownian Dynamics simulations," Journal of Chemical Physics, 110 (16), 7993 (1999).
43. S. Yang, H. Han, and S. Lee, "An efficient Brownian dynamics method for evaluating inertial dynamics effects on diffusion-influenced reactions," Journal of Physical Chemistry B, 105 (25), 6017 (2001).
44. J.F. Dufreche, M. Jardat, T. Olynyk, O. Bernard, and P. Turq, "Mutual diffusion coefficient of charged particles in the solvent fixed frame of reference from Brownian dynamics simulation" Journal of Chemical Physics, 117 (8), 3804 (2002).
45. J.M.G. Barthel H. Krienke and W. Kunz 1998 Physical Chemistry of Electrolyte Solutions Springer New York Number 5 in Topics in Physical Chemistry
46. W.F. van Gunsteren and H.J.C. Berendsen, "Algorithms for Brownian dynamics," Molecular Physics, 45 (3), 637 (1982).
47. E. Barth and T. Schlick, "Extrapolation versus impulse in multiple-timestepping schemes. II. Linear analysis and applications to Newtonian and Langevin dynamics," Journal of Chemical Physics, 109 (5), 1633 (1998).
48. S.K. Gray, D.W. Noid, and B.G. Sumpter, "Sympletctic integrators for large scale molecular dynamics simulations: A comparison of several explicit methods," Journal of Chemical Physics, 101 (5), 4062 (1994).
49. L. Verlet, "Computer 'experiments' on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules" Physical Review, 159 (1), 159 (1967).
50. T. Schlick 2000 Molecular Modeling and Simulation: An Interdisciplinary Guide vol. 21 of Interdisciplinary Applied Mathematics Springer New York
51. R.S. Varga 1960 "Factorization and normalized iterative methods" edited by R.E. Langer, in Boundary Problems in Differential Equations University of Wisconsin Press Madison, Wisconsin p. 121.
52. D.M. Young 1971 Iterative Solution of Large Linear Systems (Computer Science and Applied Mathematics) Academic Press New York
53. R.S. Varga 1962 Matrix Iterative Analysis Series in Automatic Computation Prentice-Hall Englewood Cliffs, N.J.
54. S. Selberherr 1984 Analysis and Simulation of Semiconductor Devices Springer-Verlag Vienna, New York
55. 3M force field scheme for particle-based simulations of ionic liquids: Complementary material. ftp://ftp.rush.edu/ pub/Eisenberg/ Saraniti/JCEL04.pdf (August 2005).
56. M. Saraniti, A. Rein, G. Zandler, P. Vogl, and P. Lugli, "An efficient multigrid poisson solver for device simulations," IEEE Transaction on Computer-aided Design of Integrated Circuits and Systems, 15 (2), 141 (1996).
57. G. Dahlquist and Å. Björck 1974 Numerical Methods Prentice-Hall Englewood Cliffs, N.J.
58. A. Brandt 1981 "Multigrid solvers on parallel computers" edited by M.H. Schultz, in Elliptic Problem Solvers Academic Press New York p. 39.
59. J.V.L. Beckers, C.P. Lowe, and S.W. De Leeuw, "An itrative PPPM method for simulating coulombic systems on distributed memory parallel computers," Molecular Simulation, 20, 369 (1998).
60. H.L. Stone, "Iterative solution of implicit approximations of multidimensional partial differential equations," SIAM Journal of Numerical Analysis, 5 (3), 530 (1968).
61. J.A. Meijerink and H.A. van der Vorst, "An iterative solution method for linear systems of which the coefficient matrix is a symmetric S-matrix," Mathematics of Computation, 31, 148 (1977).
62. J. Ayubi-Moak, S. Wigger, S. Goodnick, and M. Saraniti, 3D biconjugate gradient-multi grid coupling schemes for field equations in semiconductor device simulation, in Proceedings of 2002 International Conference on Modeling and Simulation of Microsystems - MSM2002, April 2002. Accepted for poster presentation.
63. P.S. Ramanathan and H.L. Friedman, "Study of a refined model for aqueous 1-1 electrolytes," Journal of Chemical Physics, 54 (3), 1086 (1971).
64. R.S. Berry, S.A. Rice, and J. Ross, Physical Chemistry, 2 edition. (Oxford University Press, May 2000).
65. M. Tuckerman, B.J. Berne, and G.J. Martyna, "Molecular dynamics algorithm for multiple time scales: Systems with long range forces," Journal of Chemical Physics, 94 (10), 6811 (1991).
66. C.K. Birdsall and A.B. Langdon 1991 Plasma Physics via Computer Simulation Institute of Physics Publishing Bristol and Philadelphia
67. J.P. Hansen and I.R. McDonald 1976 Theory of Simple Liquids Academic London
68. M. Patra and M. Karttunen, "Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion and structural properties," Journal of Computational Chemistry, 25, 678 (2004).
69. K.-C. Ng, "Hypernetted chain solutions for the classical one-componenet plasma up to γ = 7000," Journal of Chemical Physics, 61, 2680 (1974).
70. L. Belloni, "A hypernetted chain study of highly asymmetrical polyelectrolytes," Chemical Physics, 99, 43 (1985).