Symplectic quaternion scheme for biophysical molecular dynamics

Miller, T. F.; Eleftheriou, M.; Pattnaik, P.; Ndirango, A.; Newns, D.; Martyna, G. J.
May 2002
Journal of Chemical Physics;5/22/2002, Vol. 116 Issue 20, p8649
Academic Journal
Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space. © 2002 American Institute of Physics.


Related Articles

  • Construction of a generalized gradient approximation by restoring the density-gradient expansion and enforcing a tight Lieb–Oxford bound. Yan Zhao; Truhlar, Donald G. // Journal of Chemical Physics;5/14/2008, Vol. 128 Issue 18, p184109 

    Recently, a generalized gradient approximation (GGA) to the density functional, called PBEsol, was optimized (one parameter) against the jellium-surface exchange-correlation energies, and this, in conjunction with changing another parameter to restore the first-principles gradient expansion for...

  • Stress relaxation and misfit dislocation nucleation in the growth of misfitting films: A... Dong, Liang; Schnitker, Jurgen; Smith, Richard W.; Srolovitz, David J. // Journal of Applied Physics;1/1/1998, Vol. 83 Issue 1, p217 

    Analyzes the low-temperature growth and relaxation of misfitting films, on the basis of two-dimensional molecular dynamics simulations, using Lennard-Jones potentials. Monitor of the temporal evolution of the surface morphology; Information on pseudomorphic film growth.

  • Erratum: On the determination of rate constants from equilibrium molecular dynamics simulations [J. Chem. Phys. 93, 4117 (1990)]. Brown, David; Clarke, Julian H. R. // Journal of Chemical Physics;3/15/1991, Vol. 94 Issue 6, p4684 

    Reports on two errors from the article 'On the determination of rate constants from equilibrium molecular dynamics simulations,' from volume 93, p. 4117 of the 1990 edition of the 'Journal of Chemical Physics.'

  • Ultrashallow junctions in Si using decaborane? A molecular dynamics simulation study. Smith, Roger; Shaw, Marcus; Foad, Majeed A. // Journal of Applied Physics;3/15/1998, Vol. 83 Issue 6, p3148 

    Examines how the molecular dynamics simulation was used to investigate feasibility of using decaborane B10H14 in the manufacturing of shallow junctions in silicon. Methodology used to conduct the study; Analysis of the crystal and defect distribution; Conclusion on the appearance of the simulation.

  • Molecular umbrella. Srinivasan, K.R. // Chemical Business;May96, Vol. 9 Issue 10, p12 

    Reports on the development of a molecular umbrella that protects molecules from incompatible environments. Potential use as a drug delivery system; How the molecular umbrella works.

  • Molecular dynamics simulations studies of aurein 1.2 analogs water and TFE/water. Soofian, Safiyeh; Naderimanesh, Hossin // BMC Systems Biology;2007 Supplement 1, Vol. 1, p1 

    An abstract of the article "Molecular dynamics simulations studies of aurein 1.2 analogs in water and TFE/water," by Safiyeh Soofian and Hossin Naderimanesh is presented.

  • Optical control of molecular dynamics in a liquid. Demirplak, Mustafa; Rice, Stuart A. // Journal of Chemical Physics;5/8/2002, Vol. 116 Issue 18, p8028 

    We report the results of a study of the influence of solvent fluctuations on the efficiency of selective population transfer from an initial state to a designated target state of a solute molecule. Our model of the influence of liquid fluctuations on the states of the solute assumes that...

  • Highly excited states of gerade symmetry in molecular nitrogen. de Lange, Arno; Lang, Ru¨diger; van der Zande, Wim; Ubachs, Wim // Journal of Chemical Physics;5/8/2002, Vol. 116 Issue 18, p7893 

    Highly excited states of gerade symmetry in molecular nitrogen have been investigated in a resonance-enhanced XUV+Vis (extreme ultraviolet+visible) transition scheme. Nineteen bands have been observed, of which only four involve known states [k [sup 1]...[sub g] (v = 1), x [sup l]&Zigma;[sup -,...

  • Molecular dynamics simulation of interfacial electrolyte behaviors in nanoscale cylindrical pores. Cui, S. T.; Cochran, H. D. // Journal of Chemical Physics;9/22/2002, Vol. 117 Issue 12, p5850 

    Molecular simulations have been carried out on aqueous electrolytes in cylindrical pores a few nanometers in diameter, with uncharged wall or with dispersed, discrete charges modeling silica. The results show a classical Stern layer of adsorbed counterions near the wall, and then a diffuse layer...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics