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  • 1
    Electronic Resource
    Electronic Resource
    SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles (1997)
    Springer
    European biophysics journal 25 (1997), S. 361-372 
    Details
    ISSN: 1432-1017
    Keywords: Key words Hydrodynamics programs ; Bead modelling ; Fluorescence ; Birefringence ; Scattering
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering form factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all these developments in a new computer program, SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002490050049
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  • 2
    Electronic Resource
    Electronic Resource
    Simulation of polymer chains in elongational flow. Steady-state properties and chain fracture (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 9384-9392 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The behavior of polymer chains in steady, uniaxial elongational flows is studied using the Brownian dynamics simulation technique. Two different types of chain models are considered. One is the bead-and-spring Rouse chain and the other is a chain with breakable connectors that obey a Morse potential. The dynamics of Rouse chains and Morse chains is simulated both without and with hydrodynamic interaction (HI) between chain elements. From the simulated trajectories, steady-state properties such as chain dimensions and elongational viscosities are calculated. When HI is accounted for by using the Rotne–Prager–Yamakawa tensor, the calculated dimensions and viscosities are appreciably lower than when it is neglected. Carrying out simulations with varying elongational rate, it is possible to observe stretching and finally the fracture of the polymer chains. The critical elongational rate, corresponding to infinite elongation in the case of Rouse chains, and the fracture of the Morse chains has been characterized as a function of chain length. When the short length of the simulated chains is accounted for adequately, we find that the elongational rate needed for fracture ε(overdot)f scales with molecular weight M as ε(overdot)f∝M−2. This result, which had already been predicted rigorously without HI, holds in practice as well when hydrodynamic interaction is considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461166
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  • 3
    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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  • 4
    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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  • 5
    Electronic Resource
    Electronic Resource
    Computer simulation of hydrodynamic properties of semiflexible macromolecules: Randomly broken chains, wormlike chains, and analysis of properties of DNA (1990)
    New York : Wiley-Blackwell
    Biopolymers 29 (1990), S. 883-900 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormilike chains have been obtained by Monte Carlo simulation in the context of the rigid-body treatment. Both approximate and rigorous rigid-body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormilike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 103 base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model-independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too high.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360290603
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  • 6
    Electronic Resource
    Electronic Resource
    Fracture of DNA in transient extensional flow. A numerical simulation study (1996)
    New York : Wiley-Blackwell
    Biopolymers 39 (1996), S. 435-444 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using the Brownian dynamics simulation technique, we studied the fracture process of DNA chains subjected to transient extensional flow, letting the solution with DNA molecules pass through a very small orifice (radius = 0.0065 cm), thus experiencing extensional flow of the convergent (sink) type. The DNA molecules were modeled as FENE bead-spring chains with the springs obeying a modified Warner force law, as proposed by Reese and Zimm. The fracture yield was strongly dependent on flow rate and molecular weight, reaching, in our setup, a level of 100% at a flow rate of around 0.001 cm3/s for DNA with molecular weight 26 × 106 (T7 DNA). There was found to exist a critical flow rate (Qcrit) below which fracture did not occur, in accordance with what was observed in studies on polystyrene in transient extensional flow. We found that for DNA, the critical flow rate depended on the molecular weight as Qcrit ∼ M-14 when the hydrodynamic interaction effect (HI) was not included in the simulations. When HI was accounted for, the relation was found to be Qcrit ∼ M-1.1, close to the theoretical prediction for fracture of partly extended chains in transient extensional flow. © 1996 John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    A bead and spring model for the stiffness of DNABased on a communication presented at the Int. Symp. on Macromolecules, Rio de Janeiro, Brazil, July 1974. (1975)
    New York : Wiley-Blackwell
    Biopolymers 14 (1975), S. 1327-1335 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The chain stiffness of linear native DNA is represented by a generalized bead and spring model recently proposed. It incorporates molecular rigidity by means of springs between beads, which are second neighbors along the contour of the chain. These springs are equivalent to elastic forces having longitudinal and transversal contributions. The model is compared with existing experimental data of sedimentation and low-angle light scattering to obtain the statistical parameters of DNA. The value of the statistical length obtained with this model is 1300 Å. The same value is obtained with the wormlike chain. Throughout this analysis, excluded volume is left out as a simplifying assumption.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1975.360140703
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  • 8
    Electronic Resource
    Electronic Resource
    Deformation, scattering, and birefringence of flexible polymer chains under external forces or electric fields (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part B: Polymer Physics 35 (1997), S. 689-697 
    Details
    ISSN: 0887-6266
    Keywords: tensile force ; electric field ; chain conformation ; birefringence ; scattering ; Physics ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The effect of a tensile stress or an electric field on the conformation of a flexible polymer chain has been studied by combining theory with numerical simulation. In the presence of such external agents, the macromolecule experiences the action of two opposite forces at the chain ends. Two models are considered: the Gaussian bead-and-spring chain, and the freely jointed chain with segments of fixed length. From simulated Brownian trajectories we calculate steady-state properties of the polymer under the continuing action of the external forces. Thus, we compute the chain deformation and expansion, measured by the square radius of gyration, and analyze the influence of the external force on low-angle scattering of radiation. The effect of the link orientation in the optical anisotropy or birefringence is also analyzed. From existing theories, we predict very simple relationships between expansion, low-angle scattering, and birefringence, valid for Gaussian chains of any length, and for long freely jointed chains. The simulation results confirm those relationships. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 689-697, 1997
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 9
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    Prediction and analysis of analytical ultracentrifugation experiments for heterogeneous macromolecules and nanoparticles based on Brownian dynamics simulation (2018)
    Springer
    Details
    Publication Date: 2018-07-20
    Print ISSN: 0175-7571
    Electronic ISSN: 1432-1017
    Topics: Biology , Physics
    Published by Springer
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  • 10
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    Simulation of polymer chains in elongational flow. Steady‐state properties and chain fracture (1991)
    American Institute of Physics
    Details
    Publication Date: 1991-12-15
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics
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