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Joseph B Hubbard - One of the best experts on this subject based on the ideXlab platform.

  • sharp scalar and tensor bounds on the Hydrodynamic Friction and mobility of arbitrarily shaped bodies in stokes flow
    Physics of Fluids, 2005
    Co-Authors: Jerzy Blawzdziewicz, James A Given, Eligiusz Wajnryb, Joseph B Hubbard
    Abstract:

    We prove rigorous inequalities for the Hydrodynamic translational Friction and mobility matrices ζ and μO of an arbitrarily shaped rigid particle in terms of the electrostatic capacitance C of a conducting particle of identical shape. Specifically, we derive the scalar and matrix inequalities 13trζ−1⩽13trμO⩽C−1 and 23ζ−1⩽C−1I, where all quantities are normalized by the corresponding values for a sphere, and the mobility matrix is evaluated in the center-of-mobility reference frame. These bounds are obtained using a variational approach with the energy dissipation functional expressed in terms of the induced force distribution on the surface of the particle. To relate the Hydrodynamic problem to the solution of the corresponding electrostatic problem, the trial force field is expressed in terms of the charge distribution on the equipotential particle surface. This procedure yields the first rigorous bounds on Hydrodynamic Friction that apply to bodies with translation-rotation coupling. We demonstrate that...

  • a first passage algorithm for the Hydrodynamic Friction and diffusion limited reaction rate of macromolecules
    Journal of Chemical Physics, 1997
    Co-Authors: James A Given, Joseph B Hubbard, Jack F Douglas
    Abstract:

    Many important properties of a macromolecule can be expressed in terms of averages over the trajectories of diffusing particles that begin in the medium surrounding the molecule and terminate at its surface. These properties include its translational Hydrodynamic Friction coefficient and the Smoluchowski rate constant for diffusion-limited reactions. In this paper we introduce a first-passage algorithm (FPA) for calculating such quantities. This algorithm uses certain exact Green’s functions, or propagators, for the Laplace equation to eliminate the need to construct explicitly those portions of a diffusing particle’s trajectory that are not near an absorbing object. The algorithm is especially efficient for studying objects that contain large voids or have very irregular surfaces, such as macromolecules. Diffusion algorithms were previously shown to give accurate results for the quantities we study. In this paper, we show that first-passage methods make these algorithms more accurate and efficient. In fu...

  • Hydrodynamic Friction and the capacitance of arbitrarily shaped objects
    Physical Review E, 1994
    Co-Authors: Joseph B Hubbard, Jack F Douglas, Huanxiang Zhou
    Abstract:

    The translational Friction coefficient and the capacitance of a variety of objects are calculated with a probabilistic method involving hitting the ``probed'' objects with random walks launched from an enclosing spherical surface. This method is applied to exactly solvable examples to test the program accuracy and to physically important and analytically intractable examples (cube, chain of spheres at the vertices of self-avoiding and random walks, etc.). Large fluctuations in the Friction of polymer chains with a random coil structure are found to give large deviations from the mean-field Kirkwood-Riseman theory and ``Hydrodynamic fluctuation'' effects are found to diminish with the chain swelling accompanying excluded volume interaction. Capacity applications are reviewed and our probabilistic estimates of polymer Friction are compared with previous calculations using alternative methods. Transients to the capacity and related properties are expressed in terms of fluctuations in the ``Wiener sausage'' volume (volume swept out by a Brownian particle where a repeated visit to a spatial region does not contribute to the volume increase in time).

  • a brownian dynamics algorithm for calculating the Hydrodynamic Friction and the electrostatic capacitance of an arbitrarily shaped object
    Journal of Chemical Physics, 1994
    Co-Authors: Huanxiang Zhou, Jack F Douglas, Attila Szabo, Joseph B Hubbard
    Abstract:

    An algorithm originally devised for calculating the diffusion‐controlled reaction rate toward an arbitrarily shaped object is adapted to calculate the scalar translational Hydrodynamic Friction and the electrostatic capacitance of the object. In this algorithm Brownian particles are launched from a spherical surface enclosing the object. Each particle is propagated until it either hits the enclosed object or crosses the starting surface. In the latter case the particle is allowed to escape to infinity with an analytically known probability. If the particle does not escape to infinity, it is put back on the starting surface with the correct distribution density and the process is repeated. The scalar Friction or capacitance of the ‘‘probed’’ object is proportional to the fraction of particles that hit the object. This algorithm is illustrated on a dumbbell made of two equal‐size spheres, a cube, and a phantom spherical shell having random distributed beads embedded in its surface.

  • Hydrodynamic Friction of arbitrarily shaped brownian particles
    Physical Review E, 1993
    Co-Authors: Joseph B Hubbard, Jack F Douglas
    Abstract:

    We present a simple and accurate method of estimating the translational Hydrodynamic Friction on rigid Brownian particles of arbitrary shape. The Brownian Friction coefficient f takes the form f=6\ensuremath{\pi}\ensuremath{\eta}${\mathit{C}}_{\mathrm{\ensuremath{\Omega}}}$, where ${\mathit{C}}_{\mathrm{\ensuremath{\Omega}}}$ is mathematically equivalent to the electrostatic capacitance of the particle \ensuremath{\Omega} in units where the capacity of a sphere equals its radius. This formula is particularly useful for particles consisting of a few globular subunits, for which slender body approximations are not very accurate.

Jack F Douglas - One of the best experts on this subject based on the ideXlab platform.

  • a first passage algorithm for the Hydrodynamic Friction and diffusion limited reaction rate of macromolecules
    Journal of Chemical Physics, 1997
    Co-Authors: James A Given, Joseph B Hubbard, Jack F Douglas
    Abstract:

    Many important properties of a macromolecule can be expressed in terms of averages over the trajectories of diffusing particles that begin in the medium surrounding the molecule and terminate at its surface. These properties include its translational Hydrodynamic Friction coefficient and the Smoluchowski rate constant for diffusion-limited reactions. In this paper we introduce a first-passage algorithm (FPA) for calculating such quantities. This algorithm uses certain exact Green’s functions, or propagators, for the Laplace equation to eliminate the need to construct explicitly those portions of a diffusing particle’s trajectory that are not near an absorbing object. The algorithm is especially efficient for studying objects that contain large voids or have very irregular surfaces, such as macromolecules. Diffusion algorithms were previously shown to give accurate results for the quantities we study. In this paper, we show that first-passage methods make these algorithms more accurate and efficient. In fu...

  • Hydrodynamic Friction and the capacitance of arbitrarily shaped objects
    Physical Review E, 1994
    Co-Authors: Joseph B Hubbard, Jack F Douglas, Huanxiang Zhou
    Abstract:

    The translational Friction coefficient and the capacitance of a variety of objects are calculated with a probabilistic method involving hitting the ``probed'' objects with random walks launched from an enclosing spherical surface. This method is applied to exactly solvable examples to test the program accuracy and to physically important and analytically intractable examples (cube, chain of spheres at the vertices of self-avoiding and random walks, etc.). Large fluctuations in the Friction of polymer chains with a random coil structure are found to give large deviations from the mean-field Kirkwood-Riseman theory and ``Hydrodynamic fluctuation'' effects are found to diminish with the chain swelling accompanying excluded volume interaction. Capacity applications are reviewed and our probabilistic estimates of polymer Friction are compared with previous calculations using alternative methods. Transients to the capacity and related properties are expressed in terms of fluctuations in the ``Wiener sausage'' volume (volume swept out by a Brownian particle where a repeated visit to a spatial region does not contribute to the volume increase in time).

  • a brownian dynamics algorithm for calculating the Hydrodynamic Friction and the electrostatic capacitance of an arbitrarily shaped object
    Journal of Chemical Physics, 1994
    Co-Authors: Huanxiang Zhou, Jack F Douglas, Attila Szabo, Joseph B Hubbard
    Abstract:

    An algorithm originally devised for calculating the diffusion‐controlled reaction rate toward an arbitrarily shaped object is adapted to calculate the scalar translational Hydrodynamic Friction and the electrostatic capacitance of the object. In this algorithm Brownian particles are launched from a spherical surface enclosing the object. Each particle is propagated until it either hits the enclosed object or crosses the starting surface. In the latter case the particle is allowed to escape to infinity with an analytically known probability. If the particle does not escape to infinity, it is put back on the starting surface with the correct distribution density and the process is repeated. The scalar Friction or capacitance of the ‘‘probed’’ object is proportional to the fraction of particles that hit the object. This algorithm is illustrated on a dumbbell made of two equal‐size spheres, a cube, and a phantom spherical shell having random distributed beads embedded in its surface.

  • Hydrodynamic Friction of arbitrarily shaped brownian particles
    Physical Review E, 1993
    Co-Authors: Joseph B Hubbard, Jack F Douglas
    Abstract:

    We present a simple and accurate method of estimating the translational Hydrodynamic Friction on rigid Brownian particles of arbitrary shape. The Brownian Friction coefficient f takes the form f=6\ensuremath{\pi}\ensuremath{\eta}${\mathit{C}}_{\mathrm{\ensuremath{\Omega}}}$, where ${\mathit{C}}_{\mathrm{\ensuremath{\Omega}}}$ is mathematically equivalent to the electrostatic capacitance of the particle \ensuremath{\Omega} in units where the capacity of a sphere equals its radius. This formula is particularly useful for particles consisting of a few globular subunits, for which slender body approximations are not very accurate.

  • Hydrodynamic Friction of arbitrarily shaped brownian particles
    Physical Review A, 1993
    Co-Authors: Joseph B Hubbard, Jack F Douglas
    Abstract:

    We present a simple and accurate method of estimating the translational Hydrodynamic Friction on rigid Brownian particles of arbitrary shape. The Brownian Friction coefficient f takes the form f=6πηC Ω , where C Ω is mathematically equivalent to the electrostatistic capacitance of the particle Ω in units where the capacity of a sphere equals its radius. This formula is particularly useful for particles consisting of a few globular subunits, for which slender body approximations are not very accurate

Alexander Wittemann - One of the best experts on this subject based on the ideXlab platform.

  • 3d brownian diffusion of submicron sized particle clusters
    arXiv: Soft Condensed Matter, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Because they could be separated into fractions of well-defined configurations on a sufficient scale and their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle duplets, triplets and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficient for objects with complex shapes could be applied. Because Hydrodynamic Friction must be restricted to the cluster surface the so-called shell model, in which the surface is represented as a shell of small Friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.

  • 3d brownian diffusion of submicron sized particle clusters
    ACS Nano, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because Hydrodynamic Friction must be restricted to the cluster surface, the so-called shell model, in which the surface is represented as a shell of small Friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.

  • 3d brownian diffusion of submicron sized particle clusters
    ACS Nano, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because Hydrodynamic Friction must be...

Martin Hoffmann - One of the best experts on this subject based on the ideXlab platform.

  • 3d brownian diffusion of submicron sized particle clusters
    arXiv: Soft Condensed Matter, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Because they could be separated into fractions of well-defined configurations on a sufficient scale and their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle duplets, triplets and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficient for objects with complex shapes could be applied. Because Hydrodynamic Friction must be restricted to the cluster surface the so-called shell model, in which the surface is represented as a shell of small Friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.

  • 3d brownian diffusion of submicron sized particle clusters
    ACS Nano, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because Hydrodynamic Friction must be restricted to the cluster surface, the so-called shell model, in which the surface is represented as a shell of small Friction elements, was most suitable to describe the dynamics. A quantitative comparison of the predictions from theoretical modeling with the results obtained by DDLS showed an excellent agreement between experiment and theory.

  • 3d brownian diffusion of submicron sized particle clusters
    ACS Nano, 2009
    Co-Authors: Martin Hoffmann, Claudia Simone Wagner, Ludger Harnau, Alexander Wittemann
    Abstract:

    We report on the translation and rotation of particle clusters made through the combination of spherical building blocks. These clusters present ideal model systems to study the motion of objects with complex shape. Since they could be separated into fractions of well-defined configurations on a sufficient scale and because their overall dimensions were below 300 nm, the translational and rotational diffusion coefficients of particle doublets, triplets, and tetrahedrons could be determined by a combination of polarized dynamic light scattering (DLS) and depolarized dynamic light scattering (DDLS). The use of colloidal clusters for DDLS experiments overcomes the limitation of earlier experiments on the diffusion of complex objects near surfaces because the true 3D diffusion can be studied. When the exact geometry of the complex assemblies is known, different Hydrodynamic models for calculating the diffusion coefficients for objects with complex shapes could be applied. Because Hydrodynamic Friction must be...

Gary W Slater - One of the best experts on this subject based on the ideXlab platform.

  • optimizing end labeled free solution electrophoresis by increasing the Hydrodynamic Friction of the drag tag
    Macromolecules, 2009
    Co-Authors: Kai Grass, Christian Holm, Gary W Slater
    Abstract:

    We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for Hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels as well as transiently bound micelles. It is specifically shown that the label’s drag coefficient is determined by its Hydrodynamic size and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the Hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hy...

  • optimizing end labeled free solution electrophoresis by increasing the Hydrodynamic Friction of the drag tag
    arXiv: Soft Condensed Matter, 2009
    Co-Authors: Kai Grass, Christian Holm, Gary W Slater
    Abstract:

    We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for Hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its Hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the Hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher Hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.