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Journal ArticleDOI

Rotational dynamics of rigid, symmetric top macromolecules. Application to circular cylinders

15 Aug 1980-Journal of Chemical Physics (American Institute of Physics)-Vol. 73, Iss: 4, pp 1986-1993
TL;DR: Tirado et al. as mentioned in this paper extended the formalism for the calculation of translational friction coefficients of symmetric top macromolecules and derived analytical solutions that reduce to those obtained by other authors when the unmodified interaction tensor is used.
Abstract: The formalism for the calculation of translational friction coefficients of symmetric top macromolecules presented in a previous paper [M. M. Tirado and J. Garcia de la Torre, J. Chem. Phys. 71, 2585 (1979)] is here extended to the evaluation of rotational friction and diffusion coefficients. We show how the introduction of symmetry considerations leads to a great reduction of the computational requirements needed to solve the hydrodynamic interaction equations. We also obtain the translation–rotation coupling tensor from which the center of hydrodynamic stress can be obtained. For a rigid ring we have derived analytical solutions that reduce to those obtained by other authors when the unmodified interaction tensor is used. The general formalism is finally applied to the calculation of the rotational diffusion coefficients of circular cylinders modeled as stacks of rings and extrapolated to zero bead size. The resulting values are critically compared with those from earlier studies.
Citations
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Journal ArticleDOI
TL;DR: An overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function and the unifying theme in this review is energetics.
Abstract: In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function The unifying theme in this review is energetics The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides We provide an overview of the principles of stability and where available the experimental data that report on these principles Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence

640 citations

Journal ArticleDOI
TL;DR: In this paper, the translational and rotational brownian dynamics of dissolved macromolecules were analyzed using quasielastic light scattering, transient electric birefringence and fluorescence anisotropy decay.
Abstract: Among the Various methods for characterizing macromolecules in solution, hydrodynamic techniques play a major role. Since the advent of the ultracentrifuge and the development of viscometric apparatus, sedimentation coefficients and intrinsic viscosities have been extensively used to learn about the size and shape of synthetic and biological polymers. More recently, refined techniques such as quasielastic light scattering, transient electric birefringence and fluorescence anisotropy decay have made it possible to obtain in a simple and rapid way quantitative information of high precision on the translational and rotational brownian dynamics of dissolved macromolecules.

588 citations

Journal ArticleDOI
TL;DR: In this paper, the translational and rotational diffusion coefficients of a rod-like macromolecule were compared with the Tirado-Garcia de la Torre theory for a particle of given dimensions.
Abstract: Two theories relating the translational and rotational diffusion coefficients Dt and Dr of a rod‐like macromolecule to its length and diameter, proposed by Broersma [J. Chem. Phys. 74, 6989 (1981)], and Tirado and Garcia de la Torre [J. Chem. Phys. 71, 2581 (1979); 73, 1986 (1980)] are shown to predict different values of the coefficients for a particle of given dimensions. Next, we use the two theories to analyze existing experimental data of sedimentation coefficients s and translational and rotational diffusion coefficients of short DNA fragments, and obtain values of the hydrated diameter of DNA d which is treated as an adjustable parameter. The results are compared with the expected value, d≂26A. This comparison favors clearly the Tirado–Garcia de la Torre theory in the case of Dt and s. For Dr, and using a rise per base pair r=3.4 A, this theory gives best agreement for all the data examined, while when r=3.3 A, the agreement depends on the source of data.

504 citations

Journal ArticleDOI
09 Feb 1990-Cell
TL;DR: It is confirmed an earlier observation that overproduction of MotA leads to accumulation of the protein in the cytoplasmic membrane and to significant decreases in growth rate, and results suggest that MotA conducts protons.

291 citations

References
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Book
01 Jan 1965
TL;DR: Low Reynolds number flow theory finds wide application in such diverse fields as sedimentation, fluidization, particle-size classification, dust and mist collection, filtration, centrifugation, polymer and suspension rheology, and a host of other disciplines.
Abstract: Low Reynolds number flow theory finds wide application in such diverse fields as sedimentation, fluidization, particle-size classification, dust and mist collection, filtration, centrifugation, polymer and suspension rheology, flow through porous media, colloid science, aerosol and hydrosal technology, lubrication theory, blood flow, Brownian motion, geophysics, meteorology, and a host of other disciplines. This text provides a comprehensive and detailed account of the physical and mathematical principles underlying such phenomena, heretofore available only in the original literature.

4,648 citations

Journal ArticleDOI
TL;DR: In this article, the diffusion of molecules ellipsoidales dissoutes is analyzed in a mouvement brownien d'ensemble (rotation and translation) with respect to a set of molecules.
Abstract: Etude analytique du mouvement brownien de rotation d'un ellipsoide a partir d'une equation etablie anterieurement (1). Application au calcul de la depolarisation, resultant des rotations des molecules excitees pour une fluorescence emise par des molecules ellipsoidales en solution. Equation aux derivees partielles du mouvement brownien d'ensemble (rotation et translation) d'un ellipsoide. Etude de la diffusion de molecules ellipsoidales dissoutes : anisotropie locale resultant de la diffusion; — existence, pour les faibles gradients de concentration, d'un coefficient de diffusion limite. Formules et graphique donnant les valeurs de ce coefficient de diffusion pour les ellipsoides de revolution.

1,011 citations

Journal ArticleDOI
TL;DR: In this paper, the rotational diffusion constant of a closed cylinder rotating in a viscous medium has been calculated for length (2a) over width (2b) ratios larger than 3.5 to within a first order in b/a.
Abstract: The torque constant of a closed cylinder rotating in a viscous medium has been calculated for length (2a) over width (2b) ratios larger than 3.5 to within a first order in b/a. The analysis demonstrates how the contributions to the viscous dissipation tend to be underestimated in hydrodynamic considerations so that the geometrical values deduced from them come out too high. Experimental results for the torque on cylindrical rods and ellipsoids for a/b values from 3.5 to 30 are close to the theoretical results. For a/b>10 the difference is about 10%; for shorter molecules 20%. With the rotational diffusion constant given by 3kT (σ—γ)/8πηa3ω, where σ=log2a/b we obtain best fit with γ(σ>2)=1.57–7 (1/σ—0.28)2±0.25. Experimental data for the rotational diffusion constant of a cylindrical virus (a/b=20) in water, obtained by O'Konski and Haltner agree with this result within 10%. The length of the protein fits within 3%.

583 citations

Journal ArticleDOI
TL;DR: In this article, the hydrodynamic interaction equations and the interaction tensor that appear in the theoretical formalism for calculating translational friction coefficients of rigid particles modeled as assemblies of beads, are formulated in cylindrical coordinates.
Abstract: The hydrodynamic interaction equations and the interaction tensor that appear in the theoretical formalism for calculating translational friction coefficients of rigid particles modeled as assemblies of beads, are formulated in cylindrical coordinates For symmetric top particles, the cylindrical shielding tensors of symmetry‐equivalent beads are the same, and have only five nonzero components This effects a great simplification with respect to the Cartesian formalism Application is made to the end‐effect correction, for translational motion of right circular cylinders modeled as stacks of rings, extrapolated to zero bead size No appreciable changes in the translational friction coefficients are found when the hollow cylindrical models are capped at the ends with disc‐shaped plates For finite cylinders with axial ratio p≳2, our results, as well as those from other theoretical and experimental studies, are in remarkable disagreement with the previous calculations by Broersma

378 citations

Journal ArticleDOI
TL;DR: It is shown that, in the limit of a continuous surface distribution, a shell model reproduces Stoke's law for a sphere.
Abstract: The theory of Kirkwood for the translational frictional coefficients of structures composed of subunits has been generalized in two ways in order to consider aggregates of nonidentical subunits. One of these generalizations fails when the sizes of subunits are too disparate; the other, derived from a surface shell distribution of frictional elements, is effective over the whole range of relative sizes. It is shown that, in the limit of a continuous surface distribution, a shell model reproduces Stoke's law for a sphere. Comparison is made between the frictional coefficients of spheres, ellipsoids, and rods modeled by finite numbers of subunits and by continuous shells of frictional elements, and those calculated from other theories. Agreement is generally good, though the shell model for prolate ellipsoids of revolution deviates by a few per cent from the Perrin value.

349 citations