<i>Classical Dynamics of Particles and Systems</i>

Marion, Jerry B.; Gillis, J.

doi:10.1063/1.3048143

Cited by 270 publications

(76 citation statements)

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“…3). The dynamics are based on the free energy minimization principle (Marion and Thornton, 1995;Landau and Lifshitz, 1976), and generated by means of Monte Carlo Simulations utilizing the Metropolis algorithm (Metropolis et al, 1953). Effectively, this means that cell motion comes about from the overall minimization of the energy of deformation and stretching of the membrane through stochastic fluctuations, in which the global and local forces upon a cell edge, related to the internal structure and chemistry of the cell, are resolved (Graner, 1993).…”

Section: Cell Protrusionmentioning

confidence: 99%

“…Capturing all forces acting on a cell membrane accurately presents forbidding technical challenges. To circumvent this, we use an alternate approach based on Hamilton's principle (Marion and Thornton, 1995). This approach is used in many physical problems of classical mechanics where it is inconvenient, or even impossible, to decompose the effects on a system into a finite set of discrete point forces.…”

Section: Cell Protrusionmentioning

confidence: 99%

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Polarization and Movement of Keratocytes: A Multiscale Modelling Approach

et al. 2006

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Section: Cell Protrusionmentioning

confidence: 99%

Section: Cell Protrusionmentioning

confidence: 99%

Polarization and Movement of Keratocytes: A Multiscale Modelling Approach

et al. 2006

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“…From the atomic coordinates, the protein is placed in a reference frame whose origin is at the center of mass and also diagonalizes a tensor similar to the moment of inertia tensor. 28,29 From the maximum and minimum atom positions in the x, y, and z directions in this reference frame, it is possible to identify a plausible ellipsoidal shape of a particular protein, specifically p ) a/c. Equations 7 and 13 can then be used to determine what a and c must be employed to yield the value of D t observed experimentally.…”

Section: Methodsmentioning

confidence: 99%

Electrophoresis of Protein Charge Ladders: A Comparison of Experiment with Various Continuum Primitive Models

et al. 2004

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Detailed modeling of the free solution electrophoresis of five proteins (bovine R-lactalbumin, hen egg white lysozyme, bovine superoxide dismutase, human carbonic anhydrase II, and hen ovalbumin) is carried out within the framework of the continuum primitive model. Protein crystal structures and translational diffusion constants are used to design and parametrize the models. The modeling results are compared with experimental mobilities of protein charge ladders, collections of protein derivatives where the number of charge groups is varied by partial acylation of lysine residues or by amidation of glutamic and aspartic acid residues. The simplest model considered is the Yoon and Kim model of a prolate/oblate ellipsoid with uniform surface potential, electrostatics treated at the level of the linear Poisson-Boltzmann equation, and distortion of the ion atmosphere from equilibrium (ion relaxation) ignored (Yoon, B. J.; Kim, S. J. Colloid Interface Sci. 1989, 128, 275). This model provides good agreement with experiment but only if the net absolute protein charge is low or the average absolute surface, or , potential is less than ∼25 mV. Boundary element (BE) modeling is also carried out in which detailed surface models are employed and the electrostatics are solved at the level of the nonlinear Poisson-Boltzmann equation. Ion relaxation is also included in some of the BE studies. All of the experimental mobilities are in good (human carbonic anhydrase II and hen ovalbumin) to excellent (bovine R-lactalbumin, hen egg white lysozyme, and bovine superoxide dismutase) agreement with BE modeling that includes ion relaxation. We believe that these results taken as a whole serve to confirm the ability of the continuum primitive model to predict, with quantitative accuracy, the free solution electrophoretic mobilities of proteins, provided the underlying models are sufficiently realistic. When a discrepancy occurs, it may be due to error in modeling either the protein charge or the solution conformation. The models described in this work also provide a useful approach for determining values of ∆Z, the change in net charge of proteins due to the chemical modification of charged groups. Knowledge of ∆Z is essential for the use of protein charge ladders in the quantitative description of the electrostatic properties and interactions of proteins. This paper supports the view that the continuum primitive model may be more appropriate for the modeling of electrokinetics than for electrostatics. The main challenge to the accurate predictions of electrophoretic mobilities may lie primarily in the modeling of electrostatics, not electrokinetics.

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“…Rayleigh's principle 5,6 is applied, and the coordinate frequencies   reduce to the fundamental mode of oscillation, , having the greatest intensity. The average kinetic energy T is then equal to the average potential energy U .…”

Section: Normal Coordinatesmentioning

confidence: 99%

Normal coordinates describing coupled oscillations in the gravitational field

Christensen

2007

Gen Relativ Gravit

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The motion of a local source inducing small oscillations in the gravitational field is investigated and shown to exhibit pure rotational kinetic energy. Should the net affect of these slow, revolving oscillations cause large-scale rotations in spacetime it would certainly result in anomalous celestial accelerations. When this angular rotational frequency of spacetime is applied to the anomalous acceleration of the Pioneer 10/11 spacecrafts, the correlation is promising.

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Classical Dynamics of Particles and Systems

Cited by 270 publications

References 0 publications

Polarization and Movement of Keratocytes: A Multiscale Modelling Approach

Polarization and Movement of Keratocytes: A Multiscale Modelling Approach

Electrophoresis of Protein Charge Ladders: A Comparison of Experiment with Various Continuum Primitive Models

Normal coordinates describing coupled oscillations in the gravitational field

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