Monte Carlo Simulation of Static and Dynamic Properties of Linear Polymer in a Crowded Environment

Umeta, Deme Tesfaye; Asfaw, Solomon Negash; Didu, Solomon Hailemariam; Feyisa, Chimdessa Gashu; Feyisa, Dereje Kenea

doi:10.1155/2022/6707429

Cited by 3 publications

(15 citation statements)

References 36 publications

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“…In estimation, a 20%-30% of the total surface is occupied by the obstacles [31]. This area fraction of the crowding agents is defined as [21]:…”

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

“…Whereas, the obstacles on the cis side are systemically arranged. We simulate the polymer at various area fractions of the obstacles, which are φ ≤ 0.3, as considered in some studies [21,32]. The simulations of polymers with higher dimensions (d > 1) are necessary, to deal with the effect of self-avoidance on the entry of polymers through a nano pore within the coiled state.…”

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

“…It is tallied when the N monomers are made a neighborhood move without abusing the Self avoiding and prohibited volume confinements. In our simulations, each monomer has been relaxed for 10 6 MCS (c = 10 6 MCS) [21]. The reason, why we utilized this much MC steps for relaxation was to urge the completely relaxed polymer.…”

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

“…Polymer translocation has been tremendously studied in experiments [11][12][13], theories [14][15][16] and computer simulations [17][18][19][20][21] as it is important in science and technology. In our previous study [21], we investigated the structural and dynamical properties of linear polymer (N < 100) in a crowded environment. From our study [21], we observed that the density of the crowding agents is one of the factors that affects the polymer translocation.…”

Section: Introductionmentioning

confidence: 99%

“…In our previous study [21], we investigated the structural and dynamical properties of linear polymer (N < 100) in a crowded environment. From our study [21], we observed that the density of the crowding agents is one of the factors that affects the polymer translocation. Although a few researches have been done on the transloctaion of linear polymers for a long time, the properties of other types of polymer are rarely studied.…”

Section: Introductionmentioning

confidence: 99%

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Ring polymer translocation through nanopore in a crowded environment

Negash

Umeta

Kenea³

et al. 2023

Preprint

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In this paper, we use a Monte Carlo (MC) simulation method in two dimensions with a bond fluctuation model (BFM) to investigate the translocation of a ring polymer through a nanopore in a crowded environment . We put the two middle monomers in the center of the pore, to con- quer the entropic obstruction caused by the presence of an mpenetrable membrane wall. In our system, a fixed size and same density of crowding agents (φ ) are populated orderly on the left (cis) side and randomly on the right (trans) side of the wall. As the translocation of macromolecules is an important process to study the properties of polymers, we explored the static property of the polymer which is characterized by a radius of gyration and the dynamic properties, characterized by mean square displacement and escape time. We found that the scaling exponents of the average square of radius of gyration as a function of size of the polymer N varies with density of the obstacle beads, φ . Our current investigation appears that the universal power-law relation of escape time τ as a function of polymer size (τ ∼ N 2.50 ) is influenced by the density of the crowding agents. Furthermore, our research shows that the size of the polymer, the size of the pore, and the density of the obstacles all have a significant impact on polymer diffusion.

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“…In estimation, a 20%-30% of the total surface is occupied by the obstacles [31]. This area fraction of the crowding agents is defined as [21]:…”

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

Section: Simulation and Calculation Proceduresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Ring polymer translocation through nanopore in a crowded environment

Negash

Umeta

Kenea³

et al. 2023

Preprint

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A Semiflexible Polymer Translocation Through a Cylindrical Channel

Furi,

Asfaw,

Mekonen

2024

AJPST

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In this study, translocation of a semi flexible polymer through a cylindrical channel have been investigated. A two-dimensional Monte Carlo simulation was employed, by utilizing the bond fluctuation method (BFM) to investigate the translocation processes of a chain length N. To surmount the entropic barrier, the middle monomers of the polymer have been positioned at the center of the pore, which is situated between the CIS and TRANS regions. Consequently, the static properties of a semi-flexible polymer by calculating the mean square end-to-end distance ‹R2› and the mean square radius of gyration ‹R<sup>g</sup>2› as functions of the chain length (N) have been examined. The mean square end-to-end distance and the mean square radius of gyration are proportional to the number of monomers N as ‹R2› ~ N1.496 and ‹R2g› ~ N1.505 correspondingly for a short cylindrical channel length L = 2, which aligns with the theoretically predicted. These finding indicates that the relationships between ‹R2› and ‹R<sup>g</sup>2› and the polymer chain size N are strongly influenced by the channel length L. The dynamic properties by analyzing the translocation time of the polymers also studied. Additionally, the relationship between the escape time τ and the polymer chain length N depends on the pore width W, which is equivalent to the diameter of the cylindrical channel. These research demonstrates that the escape time τ decreases as the width increases and escape time τ increases as the chain stiffness increases.

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Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Singh

Chauhan

Bharadwaj

et al. 2023

IJMS

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Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

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Monte Carlo Simulation of Static and Dynamic Properties of Linear Polymer in a Crowded Environment

Cited by 3 publications

References 36 publications

Ring polymer translocation through nanopore in a crowded environment

Ring polymer translocation through nanopore in a crowded environment

A Semiflexible Polymer Translocation Through a Cylindrical Channel

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

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