Energy/entropy partition of force at <scp>DNA</scp> stretching

Bleha, Tomáš; Cifra, Peter

doi:10.1002/bip.23487

Cited by 5 publications

(5 citation statements)

References 46 publications

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“…The constant temperature compression of single chains in an impenetrable spherical cavity of the effective radius D was computed by the bead–spring model described in previous papers. , The polymer inside a sphere is modeled by N = 300 partially fused spherical beads connected by bonds of the effective mean length l (Figure ). The potential energy U of the system is given by contributions from the bond deformation U FENE , nonbonded interactions between beads U nb , and the bead–cavity wall interaction U w .…”

Section: Methodsmentioning

confidence: 99%

Pressure of Linear and Ring Polymers Confined in a Cavity

Cifra

Bleha

2023

J. Phys. Chem. B

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Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.

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Section: Methodsmentioning

confidence: 99%

Pressure of Linear and Ring Polymers Confined in a Cavity

Cifra

Bleha

2023

J. Phys. Chem. B

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“…The choice of an NpT ensemble differentiates our approach from the previous simulation studies of polymers inside a sphere based on the NVT ensemble. ,, The applied pressure expressed in the dimensionless form pl 3 / kT determines the pressure of the polymer exerted on the inner surface of the cavity. The equilibrium conformations of a confined polymer are sampled by using the Metropolis algorithm at constant temperature kT /ε = 1, where ε is the interaction energy parameter in the nonbonded potential U nb . , The Boltzmann factor in the Metropolis scheme includes an extra volume fluctuation term − p d V / kT = ( p l 3 k T ) normald V / l 3 , where d V = 4π R 2 d R represents a small random change in the spherical volume (Figure ). The chain moves in ring polymers include the small random displacement of beads and consequential evaluation of changes in interactions with all beads and walls.…”

Section: Simulation Modelmentioning

confidence: 99%

“…The equilibrium conformations of a confined polymer are sampled by using the Metropolis algorithm at constant temperature kT/ε = 1, where ε is the interaction energy parameter in the nonbonded potential U nb . 20,27 The Boltzmann factor in the Metropolis scheme includes an extra volume fluctuation term −pdV/kT =…”

Section: ■ Simulation Modelmentioning

confidence: 99%

Continuous Crossover from the Dilute to Semidilute Concentration Regime in Spherically Confined Polymers

Cifra,

Bleha

2024

Macromolecules

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We present results of simulations of flexible polymers in a sphere that show a steady reduction in the chain dimension with concentration. The 3D confinement leads to a 40% shrinking of the chain size at the overlap concentration φ*. The chain squeezing is intensified by polymer depletion inside a sphere evaluated by a novel formula. The depletion induces the accumulation of polymers in the cavity center. Because this effect is ignored in scaling theory, its predictions are not fully consistent with the simulation results. We provide the validation arguments that the shrinking of coils packed at the threshold φ* in bulk solution is comparable to the squeezing of polymers in a cavity. The size contraction by about 10% at φ* in ring polymers in bulk lies midway between those for the linear polymers in bulk and confined polymers, in harmony with the free-energy penalty for penetration of surrounding restraints.

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“…From the point of view of artificial systems, we can mention the following phenomena characterized by multistable behaviors: the peeling of a film from a substrate [1][2][3][4], the waves propagation in bistable lattices [5,6], the energy harvesting through multistable chains [7,8], the plasticity and hysteresis in phase transitions and martensitic transformations of solids [9][10][11][12][13], the cracks and dislocations nucleation and propagation in materials and alloys [14][15][16][17], and the friction at the nanoscale [18,19]. On the other hand, from the point of view of the micro-mechanical biological phenomena, we can mention the conformational transitions in polymeric and biopolymeric chains [20][21][22][23][24][25][26][27][28][29][30], the attached and detached states of fibrils in cell adhesion [31][32][33][34], the unzipping of macromolecular hairpins [35][36][37][38], the sarcomeres behavior in skeletal muscles [39][40][41][42][43]…”

Section: Introductionmentioning

confidence: 99%

Statistical Mechanics Approaches for Studying Temperature and Rate Effects in Multistable Systems

Cannizzo,

Giordano

2024

Symmetry

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Systems with a multistable energy landscape are widespread in physics, biophysics, technology, and materials science. They are strongly influenced by thermal fluctuations and external mechanical actions that can be applied at different rates, moving the system from equilibrium to non-equilibrium regimes. In this paper, we focus on a simple system involving a single breaking phenomenon to describe the various theoretical approaches used to study these problems. To begin with, we propose the exact solution at thermodynamic equilibrium based on the calculation of the partition function without approximations. We then introduce the technique of spin variables, which is able to simplify the treatment even for systems with a large number of coordinates. We then analyze the energy balance of the system to better understand its underlying physics. Finally, we introduce a technique based on transition state theory useful for studying the non-equilibrium dynamical regimes of these systems. This method is appropriate for the evaluation of rate effects and hysteresis loops. These approaches are developed for both the Helmholtz ensemble (prescribed extension) and the Gibbs ensemble (applied force) of statistical mechanics. The symmetry and duality of these two ensembles is discussed in depth. While these techniques are used here for a simple system with theoretical purposes, they can be applied to complex systems of interest for several physical, biophysical, and technological applications.

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Energy/entropy partition of force at DNA stretching

Cited by 5 publications

References 46 publications

Pressure of Linear and Ring Polymers Confined in a Cavity

Pressure of Linear and Ring Polymers Confined in a Cavity

Continuous Crossover from the Dilute to Semidilute Concentration Regime in Spherically Confined Polymers

Statistical Mechanics Approaches for Studying Temperature and Rate Effects in Multistable Systems

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