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  • 1
    Electronic Resource
    Electronic Resource
    A second-order algorithm for the simulation of the Brownian dynamics of macromolecular models (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 2015-2018 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Most recent works on Brownian dynamics simulation employ a first-order algorithm developed by Ermak and McCammon [J. Chem. Phys. 69, 1352 (1978)]. In this work we propose the use of a second-order algorithm in which the step is a combination of two first-order steps, like in the second-order Runge–Kutta method for differential equations. Although the computer time per step is roughly doubled, the second-order algorithm is more efficient than the previous one because a given accuracy in the results can be achieved with less than half the number of steps. The new algorithm also allows for longer time steps without divergence. The advantage of the new procedure is illustrated in the simulation of four macromolecular systems: A quasirigid dumbbell, a semiflexible trumbbell, a semiflexible hinged rod, and a Gaussian polymer chain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458034
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Brownian dynamics simulation of rotational correlation functions of simple rigid models (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 6021-6028 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we investigate the ability of the Brownian dynamics simulation technique of Ermak and McCammon to evaluate rotational correlation functions of rigid hydrodynamic models. Concretely, we obtain from simulated trajectories the functions 〈Pi[cos θ(t)]〉, i=1,2 where Pi is the ith Legendre polynomial and θ(t) is the angle between two orientations, separated by time t, of a given vector. This function is closely related to the decay of fluorescence anisotropy and other time-dependent electro-optical properties. The simulation results are compared with exact results for these functions. We first consider dimers in a variety of conditions regarding the rigid constraint, the hydrodynamic interaction and the relative size of the two spheres. We next study bent trimers, for which the decays are typically multiexponential. In all cases we find that the simulated results of the correlation functions and the exact ones are in rather good agreement up to a time which is determined by the finite length of the simulated trajectory.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.453526
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Radius of gyration of multisubunit macromolecules: application to myosin heads, myosin rod and whole myosin
    Amsterdam : Elsevier
    International Journal of Biological Macromolecules 10 (1988), S. 39-43 
    Details
    ISSN: 0141-8130
    Keywords: Radius of gyration ; flexibility ; myosinl conformation
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0141-8130(88)90065-7
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  • 4
    Electronic Resource
    Electronic Resource
    Rotational diffusion coefficients of a small, spherical subunit flexibly tethered to a larger sphere (1987)
    Springer
    European biophysics journal 14 (1987), S. 493-498 
    Details
    ISSN: 1432-1017
    Keywords: Rotational diffusion ; tethered sphere ; anisotropy decay ; segmental flexibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The rotational diffusion coefficients of a small spherical particle, which is flexibly anchored to the surface of a much larger sphere, are calculated using the hydrodynamic theory of segmentally flexible particles. The model is intended for representing the rotational mobility of a small residue or chromophore in the surface of a globular macromolecule. The coefficients are found to be essentially independent, or to vary slowly with the relative dispositions of the spheres. They are also insensitive to the size ratio when this ratio is high enough. These findings support the use of an approximative treatment proposed by Wegener in which the small conformation dependence is averaged out. The resulting averages are tentatively used in the Lipari-Szabo model for restricted rotational diffusion in a cone. It is concluded that the rotational relaxation of the small sphere has three components: (i) a torsional rotation with the same diffusion coefficient as the free sphere; (ii) a perpendicular wobbling with a diffusion coefficient several (five in a typical case) times smaller; and (iii) an overall rotation of the whole macromolecule, that will appear in a much longer time scale if the two spheres have quite distinct sizes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00293259
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  • 5
    Electronic Resource
    Electronic Resource
    Diffusion coefficients of segmentally flexible macromolecules with two subunits: A study of broken rods (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 1771-1786 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general treatment for the solution dynamics of segmentally flexible macromolecules having two subunits is presented. Bead modeling allows for a complete inclusion of hydrodynamic interactions in this treatment. The finite size of the beads is also considered, so that it is therefore possible to account properly for torsional motions of the subunits. Expressions for the components of the resistance matrix are derived. From them, the translational and rotational diffusion coefficients can be calculated. Distinction is made between hinged macromolecules, whose only internal motion is bending, and swivel-jointed macromolecules, for which torsions of the subunits are also allowed. Numerical results are presented for broken rods with the two types of flexibility. The effects of hydrodynamic interaction between arms of broken rods are about 25% for translation and under 10% for rotation. These findings give support to the treatments of Harvey, Wegener, and co-workers in which interactions were neglected. The rotational dynamics of hinged and swivel-jointed rods are compared. Although there are differences in the short-time behavior, the longest relaxation time is the same for the two cases. Finally, the validity of Wegener's rotational diffusion constants is discussed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360271107
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Hydrodynamic study of flexibility in immunoglobulin igG1 using Brownian dynamics and the Monte Carlo simulations of a simple model (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 547-554 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple bead model is proposed for the antibody molecule immunoglobulin IgG1. The partial flexibility of the hinge is represented by a quadratic potential associated to the angles between arms. Conformational and hydrodynamic properties are calculated using Monte Carlo (rigid-body) and Brownian dynamics simulations. Comparison of experimental and calculated values for some overall properties allows the assignment of dimensions and other model parameters. The Brownian dynamics technique is used next to simulate a rotational correlation function that is comparable with the decay of fluorescence emission anisotropy. This is done with varying flexibility at the hinge. The longest relaxation time shows a threefold decrease when going from the rigid Y-shaped conformation to the completely flexible case. The calculations are in good agreement with the decay times observed for IgG1. A flexibility analysis of the latter indicates that a variability of ±55° (standard deviation) in the angle between the Fab arms.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300507
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    Paper (German National Licenses)
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