Fluctuations and Persistence Length of Charged Flexible Polymers

1995 ◽  
Vol 28 (17) ◽  
pp. 5921-5927 ◽  
Author(s):  
Hao Li ◽  
T. A. Witten
Keyword(s):  
Persistence Length ◽  
Flexible Polymers

scholarly journals SEMI-FLEXIBLE COMPACT POLYMERS IN A DISORDERED ENVIRONMENT

2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Dušanka Lekić ◽  
Sunčica Elezović-Hadžić ◽  
Nataša Adžić
Keyword(s):  
Phase Transition ◽  
Molten Globule ◽  
Persistence Length ◽  
Hamiltonian Cycles ◽  
Stiffness Parameter ◽  
Bending Rigidity ◽  
Flexible Polymers ◽  
Fractal Lattice ◽  
Ring Polymer ◽  
Flexible Ring

Hamiltonian cycles with bending rigidity are studied on the first three members of the fractal family obtained by generalization of the modified rectangular (MR) fractal lattice. This model is proposed to describe conformational and thermodynamic properties of a single semi-flexible ring polymer confined in a poor and disordered (e.g. crowded) solvent. Due to the competition between temperature and polymer stiffness, there is a possibility for the phase transition between molten globule and crystal phase of a polymer to occur. The partition function of the model in the thermodynamic limit is obtained and analyzed as a function of polymer stiffness parameter s (Boltzmann weight), which for semi-flexible polymers can take on values over the interval (0,1). Other quantities, such as persistence length, specific heat and entropy, are obtained numerically and presented graphically as functions of stiffness parameter s.

scholarly journals Active Brownian Filamentous Polymers under Shear Flow

Polymers ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 837 ◽  
Author(s):  
Aitor Martín-Gómez ◽  
Gerhard Gompper ◽  
Roland Winkler
Keyword(s):  
Shear Rate ◽  
Shear Flow ◽  
Persistence Length ◽  
Relaxation Times ◽  
Shear Thinning ◽  
Weissenberg Number ◽  
Flexible Polymers ◽  
Orientation Relaxation ◽  
Independent Behavior ◽  
Analytical Expressions

The conformational and rheological properties of active filaments/polymers exposed to shear flow are studied analytically. Using the continuous Gaussian semiflexible polymer model extended by the activity, we derive analytical expressions for the dependence of the deformation, orientation, relaxation times, and viscosity on the persistence length, shear rate, and activity. The model yields a Weissenberg-number dependent shear-induced deformation, alignment, and shear thinning behavior, similarly to the passive counterpart. Thereby, the model shows an intimate coupling between activity and shear flow. As a consequence, activity enhances the shear-induced polymer deformation for flexible polymers. For semiflexible polymers/filaments, a nonmonotonic deformation is obtained because of the activity-induced shrinkage at moderate and swelling at large activities. Independent of stiffness, activity-induced swelling facilitates and enhances alignment and shear thinning compared to a passive polymer. In the asymptotic limit of large activities, a polymer length- and stiffness-independent behavior is obtained, with universal shear-rate dependencies for the conformations, dynamics, and rheology.

Flexible polymers in a nematic medium: a Monte Carlo simulation

1993 ◽  
Vol 3 (5) ◽  
pp. 603-609 ◽  
Author(s):  
J. H. van Vliet ◽  
M. C. Luyten ◽  
G. ten Brinke
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Flexible Polymers

scholarly journals A NOTE ON THE ANALYSIS OF A HETEROGENEOUS ROD-LIKE CHAIN IN DNA MODELING

2008 ◽  
Vol 22 (14) ◽  
pp. 2213-2224
Author(s):  
YAN DING ◽  
TIEJUN LI
Keyword(s):  
Path Integral ◽  
Lie Group ◽  
Persistence Length ◽  
Elastic Behavior ◽  
Suitable Model ◽  
Weak Disorder ◽  
Integral Analysis ◽  
Basic Model ◽  
Random Forcing ◽  
Sequence Dependent

Two different results concerning the elastic behavior of the heterogeneous worm-like chain (WLC) [D. Bensimon et al., Europhys. Lett.42, 97 (1998)] and rod-like chain (RLC) [P. Nelson, Phys. Rev. Lett.80, 5810 (1998)] are compared. We argue that the RLC is a more suitable model for double-stranded (ds-) DNA. As the hetero-RLC is the basic model for studying sequence-dependent ds-DNA, a rigorous path integral analysis for the effective bending persistence length is performed in the weak disorder limit. The novelty of the paper is in analyzing a path integral on the Lie group SO(3) with random forcing, which supplies a rigorous basis for the analysis of RLC type models.

scholarly journals Polyelectrolyte Gels Formed by Filamentous Biopolymers: Dependence of Crosslinking Efficiency on the Chemical Softness of Divalent Cations

Gels ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 41
Author(s):  
Katrina Cruz ◽  
Yu-Hsiu Wang ◽  
Shaina A. Oake ◽  
Paul A. Janmey
Keyword(s):  
Alkaline Earth ◽  
Divalent Cations ◽  
Transition Metal Ions ◽  
Atomic Weight ◽  
Mechanical Resistance ◽  
Flexible Polymers ◽  
Interpenetrating Networks ◽  
Charge Densities ◽  
Polyelectrolyte Gels ◽  
Different Types

Filamentous anionic polyelectrolytes are common in biological materials. Some examples are the cytoskeletal filaments that assemble into networks and bundled structures to give the cell mechanical resistance and that act as surfaces on which enzymes and other molecules can dock. Some viruses, especially bacteriophages are also long thin polyelectrolytes, and their bending stiffness is similar to those of the intermediate filament class of cytoskeletal polymers. These relatively stiff, thin, and long polyelectrolytes have charge densities similar to those of more flexible polyelectrolytes such as DNA, hyaluronic acid, and polyacrylates, and they can form interpenetrating networks and viscoelastic gels at volume fractions far below those at which more flexible polymers form hydrogels. In this report, we examine how different types of divalent and multivalent counterions interact with two biochemically different but physically similar filamentous polyelectrolytes: Pf1 virus and vimentin intermediate filaments (VIF). Different divalent cations aggregate both polyelectrolytes similarly, but transition metal ions are more efficient than alkaline earth ions and their efficiency increases with increasing atomic weight. Comparison of these two different types of polyelectrolyte filaments enables identification of general effects of counterions with polyelectrolytes and can identify cases where the interaction of the counterions and the filaments exhibits stronger and more specific interactions than those of counterion condensation.

scholarly journals Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Valery V. Prokhorov ◽  
Nikolay A. Barinov ◽  
Kirill A. Prusakov ◽  
Evgeniy V. Dubrovin ◽  
Maxim D. Frank-Kamenetskii ◽  
...  
Keyword(s):  
Electrostatic Interaction ◽  
Mechanical Response ◽  
Persistence Length ◽  
Strong Impact ◽  
List Type ◽  
Surface Charges ◽  
Monomolecular Films ◽  
Chain Approximation ◽  
The Impact ◽  
Positively Charged

Highlights DNA kinking is inevitable for the highly anisotropic 1D–1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D—> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Abstract Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

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