Compression and Stretching of Confined Linear and Ring Polymers by Applying Force

We use Langevin dynamics to study the deformations of linear and ring polymers in different confinements by applying compression and stretching forces on their two sides. Our results show that the compression deformations are the results of an interplay among of polymer rigidity, degree of confinement, and force applied. When the applied force is beyond the threshold required for the buckling transition, the semiflexible chain under the strong confinement firstly buckles; then comes helical deformation. However, under the same force loading, the semiflexible chain under the weaker confinement exhibits buckling instability and shrinks from the folded ends/sides until it becomes three-folded structures. This happens because the strong confinement not only strongly reduces the buckling wavelength, but also increases the critical buckling force threshold. For the weakly confined polymers, in compression process, the flexible linear polymer collapses into condensed states under a small external force, whereas the ring polymer only shows slight shrinkage, due to the excluded volume interactions of two strands in the crowded states. These results are essential for understanding the deformations of the ring biomacromolecules and polymer chains in mechanical compression or driven transport.

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Relaxation processes and mechanical responses of ring hard-sphere polymers

Modern Physics Letters B ◽

10.1142/s0217984918502664 ◽

2018 ◽

Vol 32 (23) ◽

pp. 1850266 ◽

Cited By ~ 1

Author(s):

Zhong-Hao Tu ◽

Ji-Xuan Hou

Keyword(s):

Hard Sphere ◽

Dynamic Properties ◽

Polymer Chains ◽

Monte Carlo Algorithm ◽

Relaxation Processes ◽

Hard Sphere Model ◽

Mechanical Responses ◽

Ring Polymers ◽

Ring Polymer ◽

Time Required

A hard-sphere model strictly guaranteeing the uncrossability of polymer chains is used to simulate the relaxation process of the linear and ring polymers. The statistical and dynamic properties of both linear and ring chains are obtained by using Monte Carlo algorithm. We find that the relaxation time of a self-avoiding ring polymer is smaller than the time required for the polymer to move a distance of order of its own size. Moreover, the stretching properties of linear and ring polymers are also studied, and the results show that the elongation curve of a ring polymer is almost identical to that of a linear polymer except under the situation of small external force.

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Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations

Entropy ◽

10.3390/e23020242 ◽

2021 ◽

Vol 23 (2) ◽

pp. 242

Author(s):

Joanna Halun ◽

Pawel Karbowniczek ◽

Piotr Kuterba ◽

Zoriana Danel

Keyword(s):

Star Polymers ◽

Polymer Chains ◽

The Other ◽

Nano Particles ◽

Dilute Solution ◽

Confined Geometries ◽

Density Profiles ◽

Ideal Ring ◽

Ring Polymer ◽

Monomer Density

The calculations of the dimensionless layer monomer density profiles for a dilute solution of phantom ideal ring polymer chains and star polymers with f=4 arms in a Θ-solvent confined in a slit geometry of two parallel walls with repulsive surfaces and for the mixed case of one repulsive and the other inert surface were performed. Furthermore, taking into account the Derjaguin approximation, the dimensionless layer monomer density profiles for phantom ideal ring polymer chains and star polymers immersed in a solution of big colloidal particles with different adsorbing or repelling properties with respect to polymers were calculated. The density-force relation for the above-mentioned cases was analyzed, and the universal amplitude ratio B was obtained. Taking into account the small sphere expansion allowed obtaining the monomer density profiles for a dilute solution of phantom ideal ring polymers immersed in a solution of small spherical particles, or nano-particles of finite size, which are much smaller than the polymer size and the other characteristic mesoscopic length of the system. We performed molecular dynamics simulations of a dilute solution of linear, ring, and star-shaped polymers with N=300, 300 (360), and 1201 (4 × 300 + 1-star polymer with four arms) beads accordingly. The obtained analytical and numerical results for phantom ring and star polymers are compared with the results for linear polymer chains in confined geometries.

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Entropic Sampling of Free and Ring Polymer Chains

Macromolecular Theory and Simulations ◽

10.1002/mats.200500036 ◽

2005 ◽

Vol 14 (8) ◽

pp. 491-504 ◽

Cited By ~ 14

Author(s):

Nikolai A. Volkov ◽

Anton A. Yurchenko ◽

Alexander P. Lyubartsev ◽

Pavel N. Vorontsov-Velyaminov

Keyword(s):

Polymer Chains ◽

Ring Polymer ◽

Entropic Sampling

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Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Polymers ◽

10.3390/polym11121992 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1992 ◽

Cited By ~ 4

Author(s):

Xiaolin Zhou ◽

Fuchen Guo ◽

Ke Li ◽

Linli He ◽

Linxi Zhang

Keyword(s):

Coarse Grained ◽

Number Density ◽

Polymer Mixtures ◽

Bending Energy ◽

Volume Depletion ◽

Small Ratio ◽

The Matrix ◽

Ring Polymers ◽

Ring Polymer ◽

Dynamics Simulations

Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (Kb, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak Kb, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (Kb, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions.

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Stress relaxation of entangled ring polymer chains in a linear matrix

Journal of Rheology ◽

10.1122/8.0000061 ◽

2020 ◽

Vol 64 (6) ◽

pp. 1315-1324

Author(s):

Ji-Xuan Hou

Keyword(s):

Stress Relaxation ◽

Polymer Chains ◽

Linear Matrix ◽

Ring Polymer

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Computer Simulation of Polymer Chains in Confinement

Solid State Phenomena ◽

10.4028/www.scientific.net/ssp.138.451 ◽

2008 ◽

Vol 138 ◽

pp. 451-475 ◽

Cited By ~ 2

Author(s):

Andrzej Sikorski

Keyword(s):

Computer Simulation ◽

Brownian Dynamics ◽

Dynamic Properties ◽

Practical Importance ◽

Polymer Chains ◽

Coarse Grained ◽

Theoretical Treatment ◽

Narrow Slit ◽

Exchange Method ◽

Confined Polymers

Properties of macromolecules confined in a narrow slit, pore or capillary are important due to of their practical importance. Theoretical treatment of such systems is also interesting because the introduction of confinement has an impact on most properties of polymer chains and it gained a longstanding attention. In order to determine the properties of such systems coarse-grained models of confined polymers were designed where macromolecules were represented by united atoms. Lattice approximation was also often introduced. Different macromolecular architectures were studied: linear, cyclic and star-branched chains. Computer simulation techniques (the variants of the Monet Carlo method like the Metropolis algorithm and the Replica Exchange method as well as Molecular Dynamics and Brownian Dynamics methods) applied for studies of such models were reviewed and evaluated. The structure of the polymer film and the dynamic properties were mainly presented and discussed. The influence of the width of the slit, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that a moderate confinement stabilizes folded chains while a strong confinement does not.

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Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Frontiers in Chemistry ◽

10.3389/fchem.2021.624937 ◽

2021 ◽

Vol 9 ◽

Author(s):

Yunfeng Hu ◽

Phonemany Ounkham ◽

Ondrej Marsalek ◽

Thomas E. Markland ◽

Bala Krishmoorthy ◽

...

Keyword(s):

Molecular Dynamics ◽

Path Integral ◽

Dynamic Properties ◽

Chemical Reactivity ◽

Persistent Homology ◽

Dynamics Simulation ◽

Ab Initio Molecular Dynamics ◽

Point Energy ◽

Ring Polymers ◽

Ring Polymer

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

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Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

10.26434/chemrxiv.13618922.v1 ◽

2021 ◽

Author(s):

Yunfeng Hu ◽

Phonemany Ounkham ◽

Ondrej Marsalek ◽

Thomas E. Markland ◽

Bala Krishnamoorthy ◽

...

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Path Integral ◽

Persistent Homology ◽

Dynamics Simulation ◽

Point Energy ◽

Ring Polymers ◽

Ring Polymer ◽

Wasserstein Distances ◽

Quantum Delocalization

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position i.e. its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunnelling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions. Keywords: path integral molecular dynamics, persistent homology, quantum delocalization, proton transfer, Wasserstein distances. <br>

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