PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
Tytuł artykułu

Simulation of [delta]-phage DNA in microchannels using dissipative particle dynamics

Wybrane pełne teksty z tego czasopisma
Identyfikatory
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Dissipative Particle Dynamics (DPD) is a simulation method at mesoscopic sca1es that bridges the gap between molecular dynamics and continuum hydrodynamics. It call simulate efficiently complex liquids and dense suspensions using only a few thousands of virtual particle s and at speed-up factors of more than one hundred thousands compared to Molecular Dynamics. Lowe's approach provides a powerful alternative to the usual DPD integrating schemes. Here, we demonstrate the details and potential of Lowe's scheme. We compute viscosity, , diffusivity and Schmidt number values and we present comparison of wormlike chain model s under shear with experimental and Brownian I Dynamics results for A-phage DNA.
Rocznik
Strony
395--403
Opis fizyczny
Bibliogr. 29 poz., 10 rys.
Twórcy
autor
Bibliografia
  • [1] G.E. Karniadakis, A. Beskok, and N. Aluru, Microflows and Nanoflows: Fundamentals and Simulation, Springer, New York, 2005.
  • [2] X.B. Nie, S.Y. Chen, W.N.E and M.O. Robbins, A continuum and molecular hybrid method for micro- and nano-fluid flow, J. Fluid Mech. 500, 55–64 (2004).
  • [3] S. Succi, The Lattice Boltzmann Equation for Fluid Dynamics and Beyond, Oxford University Press, 2001.
  • [4] P.J. Hoogerbrugge and J.M. Koelman, “Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics”, Europhys. Lett. 19(3), 155–160 (1992).
  • [5] P. Espa~nol and P. Warren, “Statistical mechanics of dissipative particle dynamics”, Europhys. Lett. 30(4), 191–196 (1995).
  • [6] B.M. Forrest and U.W. Suter, “Accelerated equilibration of polymer melts by time-coarse-graining”, J. Chem. Phys. 102(18), 7256–7266 (1995).
  • [7] R.D. Groot and P.B. Warren, “Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation”, J. Chem. Phys. 107(11), 4423–4435 (1997).
  • [8] R.D. Groot and K.L. Rabone, “Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants”, Biophys. J. 81, 725–736 (2001).
  • [9] C.P. Lowe, “An alternative approach to dissipative particle dynamics”, Europhys. Lett. 47(2), 145–151 (1999).
  • [10] L. Verlet, “Computer ‘experiments’ on classical fluids. I: Thermodynamical properties of Lennard-Jones molecules”, Phys. Rev. 159, 98–103 (1967).
  • [11] P. Nikunen, M. Karttunen, and I. Vattulainen, “How would you integrate the equations of motion in dissipative particle dynamic simulations?”, Computer Physics Communications 153, 407–423 (2003).
  • [12] H.C. Andersen, “Molecular dynamics simulations at constant pressure and/or temperature”, J. Chem. Phys. 72(4), 2384–2396 (1980).
  • [13] E.A.J.F. Peters, “Elimination of time step effects in DPD”, Europhys. Lett. 66(3), 311–317 (2004).
  • [14] O. Kratky and G. Porod, “Rentgenuntersuchung geloster fadenmolekÄule, Rec. Trav. Chim. 68, 1106–1115 (1949).
  • [15] H. Yamakawa, Modern Theory of Polymer Solutions, Harper and Row, New York, 1971.
  • [16] S.F. Sun, Physical Chemistry of Macromolecules, John Wiley & Sons, 1994.
  • [17] J.F. Marko and E.D. Siggia, “Stretching DNA”, Macromolecules 28, 8759–8770 (1995).
  • [18] R.G. Larson, T.T. Perkins, D.E. Smith, and S. Chu, “Hydrodynamics of a DNA molecule in a flow field”, Phys. Rev. E 55(2), 1794–1797 (1997).
  • [19] P.T. Underhill and P.S. Doyle, “On the coarse-graining of polymers into bead-spring chains”, J. Non-Newtonian Fluid Mech. 122(1), 3–31 (2004).
  • [20] C. Bouchiat, M.D. Wang, J.F. Allemand, T. Strick, S.M. Block, and V. Croquette, “Estimating the persistence length of a wormlike-chain molecule from force-extension measurements”, Biophys. J. 76, 409–413, (1999).
  • [21] D.E. Smith, H.P. Babcock, and S. Chu, “Single polymer dynamics in steady shear flo”, Science 283, 1724 (1999).
  • [22] J.S. Hur, E.S.G. Shaqfeh, and R.G. Larson, “Brownian dynamics simulations of single DNA molecules in shear flow”, J. Rheol. 44(4), 713–742 (2000).
  • [23] R.M. Jendrejack, J.J. de Pablo, and M.D. Graham, “Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions”, J. Chem. Phys. 116, 7752–7759 (2002).
  • [24] A.W. Lees and S.F. Edwards, “The computer study of transport processes under extreme conditions, J. Phys. C 5, 1921 (1972).
  • [25] J.H. Irving and J.G. Kirkwood, “The statistical mechanical theory of transport processes. IV. The equations of hydrodynamics”, J. Chem. Phys. 18, 817–829 (1950).
  • [26] J.A. Backer, C.P. Lowe, H.C.J. Hoefsloot, and P.D. Iedema, “Poiseuille flow to measure the viscosity of particle model fluids”, J. Chem. Phys. 122, 154503 (2005).
  • [27] V. Symeonidis, Numerical Methods for Multi-scale Modeling of Non-Newtonian Flows, Phd thesis, Brown University, 2006.
  • [28] C.A. Marsh, Theoretical Aspects of Dissipative Particle Dynamics, Phd thesis, University of Oxford, 1998.
  • [29] M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids, Oxford University Press, 1989.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPG5-0012-0057
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.