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Garg V, Mathew R, Ibrahim R, Singh K, Ghosh SK. Crowding induced switching of polymer translocation by the amalgamation of entropy and osmotic pressure. iScience 2024; 27:109348. [PMID: 38523793 PMCID: PMC10959672 DOI: 10.1016/j.isci.2024.109348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
The translocation of polymers is omnipresent in inherently crowded biological systems. We investigate the dynamics of polymer translocation through a pore in free and crowded environments using Langevin dynamics simulation. We observed a location-dependent translocation rate of monomers showcasing counterintuitive behavior in stark contrast to the bead velocity along the polymer backbone. The free energy calculation of asymmetrically placed polymers indicates a critical number of segments to direct receiver-side translocation. For one-sided crowding, we have identified a critical crowding size revealing a nonzero probability of translocation toward the crowded-side. Moreover, we have observed that shifting the polymer toward the crowded-side compensates for one-sided crowding, yielding an equal probability akin to a crowder-free system. In two-sided crowding, a slight variation in crowder size and packing fraction induces a polymer to switch its translocation direction. These conspicuous yet counter-intuitive phenomena are rationalized by minimalistic theoretical arguments based on osmotic pressure and radial entropic forces.
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Affiliation(s)
- Vrinda Garg
- Department of Physics, National Institute of Technology, Warangal 506004, India
| | - Rejoy Mathew
- Department of Physics, National Institute of Technology, Warangal 506004, India
| | - Riyan Ibrahim
- Department of Physics, National Institute of Technology, Warangal 506004, India
| | - Kulveer Singh
- Department of Physics, National Institute of Technology, Warangal 506004, India
| | - Surya K. Ghosh
- Department of Physics, National Institute of Technology, Warangal 506004, India
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Dwivedi M, Rudra S, Kumar S. Polymer translocation: Effects of confinement. Phys Rev E 2024; 109:024412. [PMID: 38491574 DOI: 10.1103/physreve.109.024412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/24/2024] [Indexed: 03/18/2024]
Abstract
We investigate the influence of varying confinement on the dynamics of polymer translocation through a cone-shaped channel. For this, a linear polymer chain is modeled using self-avoiding walks on a square lattice. The cis side of a cone-shaped channel has a finite volume, while the trans side has a semi-infinite space. The confining environment is varied either by changing the position of the back wall while keeping the apex angle fixed or altering the apex angle while keeping the position of the back wall fixed. In both cases, the effective space ϕ, which represents the number of monomers in a chain relative to the total number of accessible sites within the cone, is reduced due to the imposed confinement. Consequently, the translocation dynamics are affected. We analyze the entropy of the confined system as a function of ϕ, which exhibits nonmonotonic behavior. We also calculate the free energy associated with the confinement as a function of a virtual coordinate for different positions of the back wall (base of the cone) along the conical axis for various apex angles. Employing the Fokker-Planck equation, we calculate the translocation time as a function of ϕ for different solvent conditions across the channel. Our findings indicate that the translocation time decreases as ϕ increases, but it eventually reaches a saturation point at a certain value of ϕ. Moreover, we highlight the possibility of controlling the translocation dynamics by manipulating the solvent quality across the channel. Furthermore, our investigation delves into the intricacies of polymer translocation through a cone-shaped channel, considering both repulsive and neutral interactions with the channel wall. This exploration unveils nuanced dynamics and sheds light on the factors that significantly impact translocation within confined channels.
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Affiliation(s)
- Manish Dwivedi
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Sumitra Rudra
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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Kim S, Lee NK, Chae MK, Johner A, Park JM. Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study. Polymers (Basel) 2023; 15:polym15112550. [PMID: 37299349 DOI: 10.3390/polym15112550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker-Planck equation for the position of the head monomer.
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Affiliation(s)
- Seowon Kim
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Republic of Korea
| | - Nam-Kyung Lee
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Republic of Korea
| | - Min-Kyung Chae
- National Institute for Mathematical Sciences, Daejeon 34047, Republic of Korea
| | - Albert Johner
- Institut Charles Sadron CNRS-Unistra, 6 Rue Boussingault, CEDEX, 67083 Strasbourg, France
| | - Jeong-Man Park
- Department of Physics, the Catholic University of Korea, Bucheon 14662, Republic of Korea
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
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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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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Buyukdagli S. Dielectric Manipulation of Polymer Translocation Dynamics in Engineered Membrane Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:122-131. [PMID: 34958582 DOI: 10.1021/acs.langmuir.1c02174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The alteration of the dielectric membrane properties by membrane engineering techniques such as carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in dielectric membrane pores confining mixed electrolytes. In the giant permittivity regime of these engineered membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation and set an electroosmotic counterion flow. The drag force exerted by this flow is sufficiently strong to suppress and invert the electrophoretic velocity of anionic polymers and also to generate the mobility of neutral polymers whose speed and direction can be solely adjusted by the charge and concentration of the added multivalent ions. These features identify the dielectrically generated transport mechanism as an efficient means to drive overall neutral or weakly charged analytes that cannot be controlled by an external voltage. We also reveal that, in anionic polymer translocation, multivalent cation addition into the monovalent salt solution amplifies the electric current signal by several factors. The signal amplification is caused by the electrostatic many-body interactions replacing the monovalent polymer counterions by the multivalent cations of higher electric mobility. The strength of this electrokinetic charge discrimination points out the potential of multivalent ions as current amplifiers capable of providing boosted resolution in nanopore-based biosensing techniques.
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Lopez CG, Horkay F, Schweins R, Richtering W. Solution Properties of Polyelectrolytes with Divalent Counterions. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Carlos G. Lopez
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, Aachen 52056, Germany
| | - Ferenc Horkay
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 13 South Drive, Bethesda, Maryland 20892, United States
| | - Ralf Schweins
- Institut Laue-Langevin, DS/LSS, 71 Avenue des Martyrs, CS 20156, Grenoble Cedex 9 38042, France
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, Aachen 52056, Germany
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