BUCKLING INSTABILITY FOR A CHARGED AND SEMIFLEXIBLE POLYMER

In this article, we address the problem of Euler's buckling instability in a charged semi-flexible polymer that is under the action of a compressive force. We consider this instability as a phase transition and investigate the role of thermal fluctuations in the buckling critical force. By performing molecular dynamic simulations, we show that the critical force decreases when the temperature increases. Repulsive electrostatic interaction in the finite temperature is in competition with thermal fluctuations to increase the buckling threshold.

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Stretched, Twisted, Supercoiled and Braided DNA

MRS Proceedings ◽

10.1557/proc-463-31 ◽

1996 ◽

Vol 463 ◽

Author(s):

John F. Marko

Keyword(s):

Single Molecule ◽

Double Helix ◽

Persistence Length ◽

Thermal Fluctuations ◽

Internal Dynamics ◽

Flexible Polymer ◽

Bending Elasticity ◽

Polymer Elasticity ◽

Dna Double Helix ◽

Semi Flexible Polymer

ABSTRACTThe DNA double helix is a semi-flexible polymer with twist rigidity. Its bending elasticity gives rise to entropie polymer elasticity, which can be precisely studied in single-molecule experiments. DNA's twist rigidity causes it to wrap around itself, or ‘supercoil’, when it is sufficiently twisted; thermal fluctuations destabilize supercoiling for DNAs twisted fewer than once per twist persistence length. Twisted DNAs under tension, braided DNAs, and the internal dynamics of supercoiled DNAs are discussed. The interplay between braiding and supercoiling free energy is argued to be important for the decatenation of duplicated DNAs in prokaryote cells.

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The role of water co-adsorption on the modification of ZnO nanowires using acetic acid

Physical Chemistry Chemical Physics ◽

10.1039/c4cp00667d ◽

2014 ◽

Vol 16 (18) ◽

pp. 8509-8514 ◽

Cited By ~ 6

Author(s):

Adriel Domínguez ◽

Svea grosse Holthaus ◽

Susan Köppen ◽

Thomas Frauenheim ◽

Andreia Luisa da Rosa

Keyword(s):

Density Functional Theory ◽

Acetic Acid ◽

Molecular Dynamic ◽

Density Functional ◽

Co Adsorption ◽

Zno Nanowires ◽

Molecular Dynamic Simulations ◽

Dynamic Simulations ◽

Functional Theory

Density functional theory (DFT) and Car–Parinello molecular dynamic simulations were employed to investigate the interaction of acetic acid with non-polar facets of ultra-thin ZnO nanowires.

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DEPENDENCE OF THE PEAK EFFECT ON THE DENSITY OF PINNING SITES

Modern Physics Letters B ◽

10.1142/s0217984908017643 ◽

2008 ◽

Vol 22 (31) ◽

pp. 3125-3134 ◽

Cited By ~ 1

Author(s):

I. M. OBAIDAT ◽

U. AL KHAWAJA ◽

M. BENKRAOUDA

Keyword(s):

Critical Current Density ◽

Driving Force ◽

Peak Effect ◽

Molecular Dynamic Simulations ◽

Zero Temperature ◽

Relative Height ◽

Dynamic Simulations ◽

One Dimensional ◽

Matching Field

We have investigated the role of pinning density on the properties of the peak effect in the critical current density in superconducting systems. This study was conducted using a series of molecular dynamic simulations on two systems of nanostructures of periodic square arrays of pinning sites with different pining densities. We have found that the peak occurred in both systems only at zero temperature and for specific values of pinning strength. The most interesting result was that in both systems, the peak was found to occur only at nearly 0.5 fraction of the first matching field for all values of pinning strength. The properties of the peak were found to depend mainly on the initial positions of the vortices with respect to the positions of the pinning sites. The critical dipping force at the peak was found to increase linearly with the pinning strength and to have larger values for the system with the smaller density of pinning sites. The dependence of the relative height of the peak on the pinning strength was found be nearly the same in both systems. One-dimensional linear channels of moving vortices along the direction of the driving force were observed at the dip just before the peak.

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Coupled dynamics of charged macromolecules and counterions mediated by binding enzymes

10.1101/2021.06.21.449292 ◽

2021 ◽

Author(s):

Murugappan Muthukumar ◽

Tapas Singha ◽

Siao-Fong Li

Keyword(s):

Electrostatic Force ◽

Effective Diffusivity ◽

Thermal Fluctuations ◽

Scattering Data ◽

Closed Form Expression ◽

Coupled Dynamics ◽

Flexible Polymer ◽

Component Systems ◽

Charged Macromolecules

We investigate the role of active coupling on the transport properties of the macromolecules. The active coupling comes due to bound enzymes with a segment of the macromolecule wherein the enzyme exerts an electrostatic force on the segment of the macromolecule, and eventually, it gets unbound due to the thermal fluctuations. This binding and unbinding process generates active fluctuations in the dynamics of the macromolecule. Starting with segment dynamics and correlations for three dynamical models with active coupling, we obtain the cooperative diffusivity for the realistic charged macromolecules with hydrodynamics. First, we construct the three models by incorporating the features of a real polymer systematically, starting from simple Rouse dynamics with active coupling. We further include segment-segment interactions and in addition, hydrodynamic interactions with active coupling. Our obtained scaling form for segment-segment correlations for the models in terms of the size exponent of the polymer indicating that hydrodynamic and segment-segment interactions along with the active coupling lead to new scaling regimes. We finally study the dynamics of a homogeneously charged flexible polymer in an infinitely dilute solution where enzymes and counterions affect the dynamics of the polymers. We analytically investigate how these active fluctuations affect the coupled dynamics of the polymer and counterions. It turns out that these active fluctuations enhance the effective diffusivity of the polymer. The derived closed-form expression for diffusivity is pertinent to accurate interpretation of light scattering data on multi-component systems with binding-unbinding equilibria.

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