The Experts below are selected from a list of 315 Experts worldwide ranked by ideXlab platform
Tetsuo Deguchi - One of the best experts on this subject based on the ideXlab platform.
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Mean-square Radius of gyration and the Hydrodynamic Radius for topological polymers expressed with graphs evaluated by the method of quaternions revisited
Reactive and Functional Polymers, 2018Co-Authors: Erica Uehara, Tetsuo DeguchiAbstract:Abstract We revisit the numerical quaternionic study on the mean-square Radius of gyration and the Hydrodynamic Radius for topological or graph-shaped polymers. We show that it is consistent with other approaches although we apply a nontrivial modification of the quaternionic method [51] for generating random polygons. In the modified method we generate random walks that connect two given points by rescaling the bond length and assign them some weight. We evaluate by it the mean-square Radius of gyration and the Hydrodynamic Radius for several topological polymers. We correct the plots of Ref. [46] for the Hydrodynamic Radius versus the segment number and for the ratio of the gyration to the Hydrodynamic Radius versus the segment number. The estimated ratios are close to the values derived from an analytic assumption of the pair distribution function. The gyration Radius of the multi-theta chain evaluated by the modified method agrees with exact Gaussian results [48]. We derive the moments of the bond vectors' coordinates distribution in random polygons generated by the quaternionic method.
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Mean-square Radius of gyration and Hydrodynamic Radius for topological polymers evaluated through the quaternionic algorithm
Reactive and Functional Polymers, 2014Co-Authors: Erica Uehara, Ryota Tanaka, Mizue Inoue, Fukiko Hirose, Tetsuo DeguchiAbstract:Abstract We evaluate numerically the mean-square (MS) Radius of gyration and the diffusion coefficient for topological polymers such as ring, tadpole, double-ring, and caged polymers and catenanes. We consider caged polymers with any given number of subchains, and catenanes consisting of two linked ring polymers with a fixed linking number. Through Kirkwood’s approximation we evaluate the Hydrodynamic Radius, which is proportional to the inverse of the diffusion coefficient, for various topological polymers. Here we take the statistical averages over configurations of topological polymers constructed through the quaternionic algorithm, which generates uniform random walks connecting given two points. It gives ideal chains with no excluded volume. We evaluate numerically the ratio of the square root of the MS Radius of gyration to the Hydrodynamic Radius for several topological polymers, and show for them that the ratio decreases as the topology becomes more complex.
Hervé Cottet - One of the best experts on this subject based on the ideXlab platform.
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Investigating the Influence of Phosphate Ions on Poly(l-lysine) Conformations by Taylor Dispersion Analysis
Macromolecules, 2014Co-Authors: Laurent Leclercq, Nicolas Sisavath, Hervé CottetAbstract:In this work, the influence of the ionic strength and phosphate ions on poly(l-lysine) Hydrodynamic Radius, conformation and persistence lengths has been studied for molar masses comprised between 3000 and 70 000 g/mol. Mark–Houwink coefficients have been obtained via the determination of poly(l-lysine) Hydrodynamic Radius using Taylor dispersion analysis. The influence of phosphate ions and ionic strength on the solvent quality (poor, Θ, or good solvent) for poly(l-lysine) have been studied in details. Quantitative data on Hydrodynamic Radius, persistence length, Mark–Houwink coefficients are provided at pH 7.4, in the range of 10 mM to 1 M ionic strength, and for different phosphate ion concentrations from 0.1 mM to 50 mM under physiological conditions (154 mM ionic strength, pH 7.4). The strong influence of phosphate ions on poly(l-lysine) properties was finally illustrated by studying the interactions (stoichiometry, binding constant, and cooperativity) between poly(l-lysine) of DP 50 and human serum ...
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Investigating the Influence of Phosphate Ions on Poly(L‑lysine) Conformations by Taylor Dispersion Analysis.
Macromolecules, 2014Co-Authors: Xiaoyun Jin, Laurent Leclercq, Nicolas Sisavath, Hervé CottetAbstract:In this work, the influence of the ionic strength and phosphate ions on poly(L-lysine) Hydrodynamic Radius, conformation and persistence lengths has been studied for molar masses comprised between 3000 and 70 000 g/mol. Mark−Houwink coefficients have been obtained via the determination of poly(L-lysine) Hydrodynamic Radius using Taylor dispersion analysis. The influence of phosphate ions and ionic strength on the solvent quality (poor, Θ, or good solvent) for poly(L-lysine) have been studied in details. Quantitative data on Hydrodynamic Radius, persistence length, Mark−Houwink coefficients are provided at pH 7.4, in the range of 10 mM to 1 M ionic strength, and for different phosphate ion concentrations from 0.1 mM to 50 mM under physiological conditions (154 mM ionic strength, pH 7.4). The strong influence of phosphate ions on poly(L-lysine) properties was finally illustrated by studying the interactions (stoichiometry, binding constant, and cooperativity) between poly(L-lysine) of DP 50 and human serum albumin, in the absence and in the presence of phosphate ions at pH 7.4.
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Investigating the Influence of Phosphate Ions on Poly(l-lysine) Conformations by Taylor Dispersion Analysis
Macromolecules, 2014Co-Authors: Xiaoyun Jin, Laurent Leclercq, Nicolas Sisavath, Hervé CottetAbstract:International audienceIn this work, the influence of the ionic strength and phosphate ions on poly(L-lysine) Hydrodynamic Radius, conformation and persistence lengths has been studied for molar masses comprised between 3000 and 70 000 g/mol. Mark−Houwink coefficients have been obtained via the determination of poly(L-lysine) Hydrodynamic Radius using Taylor dispersion analysis. The influence of phosphate ions and ionic strength on the solvent quality (poor, Θ, or good solvent) for poly(L-lysine) have been studied in details. Quantitative data on Hydrodynamic Radius, persistence length, Mark−Houwink coefficients are provided at pH 7.4, in the range of 10 mM to 1 M ionic strength, and for different phosphate ion concentrations from 0.1 mM to 50 mM under physiological conditions (154 mM ionic strength, pH 7.4). The strong influence of phosphate ions on poly(L-lysine) properties was finally illustrated by studying the interactions (stoichiometry, binding constant, and cooperativity) between poly(L-lysine) of DP 50 and human serum albumin, in the absence and in the presence of phosphate ions at pH 7.4
J. M. Schurr - One of the best experts on this subject based on the ideXlab platform.
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Effects of ethylene glycol on the torsion elastic constant and Hydrodynamic Radius of p30δ DNA
Biopolymers, 2007Co-Authors: David P. Rangel, Bryant S. Fujimoto, Greg P. Brewood, J. M. SchurrAbstract:Upon increasing the concentration of ethylene glycol (EG) at 37 degrees C, the twist energy parameter, E(T), which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant (alpha) of linear p30delta DNA and on the Hydrodynamic Radius (R(H)) of a synthetic 24 bp duplex DNA were examined at both 40 and 20 degrees C. The time-resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) alpha; (2) R(H); (3) the lifetimes of intercalated and non-intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40 degrees C, addition of 20 w/v % EG caused a substantial (1.27- to 1.35-fold) increase in alpha, a significant change in the CD spectrum, and a very small, marginally significant increase in R(H), but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of E(T), these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40 degrees C. At 20 degrees C, addition of 20 w/v % EG caused a marginally significant decrease in alpha and very little change in any other measured properties. Also at 20 degrees C, addition of 30 w/v % betaine caused a marginally significant increase in alpha and significant but modest change in the CD spectrum, but very little change in any other properties.
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Effects of different cations on the Hydrodynamic Radius of DNA
Biophysical journal, 1994Co-Authors: Bryant S. Fujimoto, J. M. Miller, N. S. Ribeiro, J. M. SchurrAbstract:The effects of different cations on the Hydrodynamic Radius (RH) of a 48-bp synthetic DNA are measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium. Relative statistical errors in RH are only approximately 1%. With increasing cation concentration, Na+ causes a small decrease in RH, Cs+ causes a somewhat larger decrease by up to 0.5 A at 100 mM, and (CH3CH2)4N+ causes an increase in RH by approximately 0.5 A at 100 mM. The qualitatively different effects of these monovalent cations indicates that the changes in RH with cation concentration do not arise primarily from electrolyte friction. Divalent cations cause much larger increases in RH with increasing cation concentration. Mg2+ causes an increase in RH by up to 1.0 A at 24.4 mM, and Mn2+ causes an increase in RH by up to 1.6 A at 24.4 mM. These effects are independent of DNA concentration. There is some positive correlation between the order of effects of the different cations on RH and the order of their effects on interhelical hydration forces. It is suggested that these different ions affect RH either by altering the hydration layer or possibly by some effect on DNA structure, such as stabilizing bends.
Erica Uehara - One of the best experts on this subject based on the ideXlab platform.
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Mean-square Radius of gyration and the Hydrodynamic Radius for topological polymers expressed with graphs evaluated by the method of quaternions revisited
Reactive and Functional Polymers, 2018Co-Authors: Erica Uehara, Tetsuo DeguchiAbstract:Abstract We revisit the numerical quaternionic study on the mean-square Radius of gyration and the Hydrodynamic Radius for topological or graph-shaped polymers. We show that it is consistent with other approaches although we apply a nontrivial modification of the quaternionic method [51] for generating random polygons. In the modified method we generate random walks that connect two given points by rescaling the bond length and assign them some weight. We evaluate by it the mean-square Radius of gyration and the Hydrodynamic Radius for several topological polymers. We correct the plots of Ref. [46] for the Hydrodynamic Radius versus the segment number and for the ratio of the gyration to the Hydrodynamic Radius versus the segment number. The estimated ratios are close to the values derived from an analytic assumption of the pair distribution function. The gyration Radius of the multi-theta chain evaluated by the modified method agrees with exact Gaussian results [48]. We derive the moments of the bond vectors' coordinates distribution in random polygons generated by the quaternionic method.
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Mean-square Radius of gyration and Hydrodynamic Radius for topological polymers evaluated through the quaternionic algorithm
Reactive and Functional Polymers, 2014Co-Authors: Erica Uehara, Ryota Tanaka, Mizue Inoue, Fukiko Hirose, Tetsuo DeguchiAbstract:Abstract We evaluate numerically the mean-square (MS) Radius of gyration and the diffusion coefficient for topological polymers such as ring, tadpole, double-ring, and caged polymers and catenanes. We consider caged polymers with any given number of subchains, and catenanes consisting of two linked ring polymers with a fixed linking number. Through Kirkwood’s approximation we evaluate the Hydrodynamic Radius, which is proportional to the inverse of the diffusion coefficient, for various topological polymers. Here we take the statistical averages over configurations of topological polymers constructed through the quaternionic algorithm, which generates uniform random walks connecting given two points. It gives ideal chains with no excluded volume. We evaluate numerically the ratio of the square root of the MS Radius of gyration to the Hydrodynamic Radius for several topological polymers, and show for them that the ratio decreases as the topology becomes more complex.
David P. Rangel - One of the best experts on this subject based on the ideXlab platform.
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Effects of ethylene glycol on the torsion elastic constant and Hydrodynamic Radius of p30δ DNA
Biopolymers, 2007Co-Authors: David P. Rangel, Bryant S. Fujimoto, Greg P. Brewood, J. M. SchurrAbstract:Upon increasing the concentration of ethylene glycol (EG) at 37 degrees C, the twist energy parameter, E(T), which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant (alpha) of linear p30delta DNA and on the Hydrodynamic Radius (R(H)) of a synthetic 24 bp duplex DNA were examined at both 40 and 20 degrees C. The time-resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) alpha; (2) R(H); (3) the lifetimes of intercalated and non-intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40 degrees C, addition of 20 w/v % EG caused a substantial (1.27- to 1.35-fold) increase in alpha, a significant change in the CD spectrum, and a very small, marginally significant increase in R(H), but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of E(T), these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40 degrees C. At 20 degrees C, addition of 20 w/v % EG caused a marginally significant decrease in alpha and very little change in any other measured properties. Also at 20 degrees C, addition of 30 w/v % betaine caused a marginally significant increase in alpha and significant but modest change in the CD spectrum, but very little change in any other properties.
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effects of ethylene glycol on the torsion elastic constant and Hydrodynamic Radius of p30δ dna
Biopolymers, 2007Co-Authors: David P. Rangel, Bryant S. Fujimoto, Greg P. Brewood, Michael J SchurrAbstract:Upon increasing the concentration of ethylene glycol (EG) at 37°C, the twist energy parameter, ET, which governs the supercoiling free energy, was recently found to undergo a decreasing (or reverse) sigmoidal transition with a midpoint near 20 w/v % EG. In this study, the effects of adding 20 w/v % EG on the torsion elastic constant (α) of linear p30δ DNA and on the Hydrodynamic Radius (RH) of a synthetic 24 bp duplex DNA were examined at both 40 and 20°C. The time-resolved fluorescence intensity and fluorescence polarization anisotropy (FPA) of intercalated ethidium were measured in order to assess the effects of 20 w/v % EG on: (1) α; (2) RH; (3) the lifetimes of intercalated and non-intercalated dye; (4) the amplitude of dye wobble in its binding site; and (5) the binding constant for intercalation. The effects of 20 w/v % EG on the circular dichroism (CD) spectrum of the DNA and on the emission spectrum of the free dye were also measured. At 40°C, addition of 20 w/v % EG caused a substantial (1.27- to 1.35-fold) increase in α, a significant change in the CD spectrum, and a very small, marginally significant increase in RH, but little or no change in the amplitude of dye wobble in its binding site or the lifetime of intercalated dye. Together with previously reported measurements of ET, these results imply that the bending elastic constant of DNA is significantly decreased by 20 w/v % EG at 40°C. At 20°C, addition of 20 w/v % EG caused a marginally significant decrease in α and very little change in any other measured properties. Also at 20°C, addition of 30 w/v % betaine caused a marginally significant increase in α and significant but modest change in the CD spectrum, but very little change in any other properties. © 2006 Wiley Periodicals, Inc. Biopolymers 85: 222–232, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
