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Wiener B, Stein D. Ionic current driven by a viscosity gradient. Faraday Discuss 2023; 246:47-59. [PMID: 37464910 DOI: 10.1039/d3fd00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Gradients of voltage, pressure, temperature, and salinity can transport objects in micro- and nanofluidic systems by well-known mechanisms. This paper explores the dynamics of particles in a viscosity gradient with numerical simulations. The different stochastic rules used to integrate the random motion of Brownian particles affect the steady-state distribution of particles in a diffusivity gradient. Importantly, the simulations illuminate the important role that the boundary conditions play, disallowing a steady-state flux when the boundary conditions mimic those of a closed container, but allowing flux when they mimic electrodes. These results provide an interpretation for measurements of a steady ionic current flowing between electrodes separated by a nanofluidic channel with a liquid viscosity gradient.
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Affiliation(s)
| | - Derek Stein
- Physics Department, Brown University, Providence, RI, USA.
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2
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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: 6] [Impact Index Per Article: 6.0] [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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A theoretical understanding of ionic current through a nanochannel driven by a viscosity gradient. J Colloid Interface Sci 2022; 628:545-555. [PMID: 36007419 DOI: 10.1016/j.jcis.2022.07.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/24/2022]
Abstract
HYPOTHESIS Different thermodynamic forces owing to the gradient of temperature, electrical potential, or concentration can drive ionic current through charged membranes. It has been recently shown that a viscosity gradient can drive an electrical current through a negatively charged nanochannel (Wiener and Stein, arXiv: 1807.09106). A model description of this phenomenon, based on the Maxwell-Stefan equation will help unravel the dominating physical mechanisms in so-called visco-migration. THEORY To understand the physical mechanisms underlying this phenomenon, we employed the Maxwell-Stefan equation to develop a 1D model and obtain a relation between the flux of solvents and the driving forces. Viscosity gradients are known to drive transport, but the development of an electrical current has not been theoretically described prior to this work. FINDINGS Our 1D model shows that the ionic current depends on the ideality of the solvent, though both ideal and non-ideal scenarios demonstrated good agreement with experimental data. We employed the model to understand the impact of solution bulk ionic strength and pH on the drift of ionic species with same reservoirs solution properties. Our modeling results unveiled the significant impact of bulk solution properties on the drift of ions which is in agreement with the experiments. Moreover, we have shown that the diffusion gradient along the nanochannel contributes significantly into driving ionic species if we even apply a small ionic concentration gradient to both reservoirs. Our modeling results may pave the way for finding novel applications for drift of ions in a diffusion gradient, which can be induced by connecting reservoirs of different viscosity fluids.
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Translocation paradox of a linear polymer chain in a semi-entangled semi-free space. JOURNAL OF POLYMER RESEARCH 2021. [DOI: 10.1007/s10965-021-02547-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Chen J, Chen X, Sun LZ, Xu XJ, Luo MB. Translocation of a looped polymer threading through a nanopore. SOFT MATTER 2021; 17:4342-4351. [PMID: 33908563 DOI: 10.1039/d1sm00007a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent experiments reported that the complicated translocation dynamics of a looped DNA chain through a nanopore can be detected by ionic current blockade profiles. Inspired by the experimental results, we systematically study the translocation dynamics of a looped polymer, formed by three building blocks of a loop in the middle and two tails of the same length connected with the loop, by using Langevin dynamics simulations. Based on two entering modes (tail-leading and loop-leading) and three translocation orders (loop-tail-tail, tail-loop-tail, and tail-tail-loop), the translocation of the looped polymer is classified into six translocation pathways, corresponding to different current blockade profiles. The probabilities of the six translocation pathways are dependent on the loop length, polymer length, and pore radius. Moreover, the translocation times of the entire polymer and the loop are investigated. We find that the two translocation times show different dependencies on the translocation pathways and on the lengths of the loop and the entire polymer.
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Affiliation(s)
- Jia Chen
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Xian Chen
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiao-Jun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China.
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6
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Lee JS, Oviedo JP, Bandara YMNDY, Peng X, Xia L, Wang Q, Garcia K, Wang J, Kim MJ, Kim MJ. Detection of nucleotides in hydrated ssDNA via 2D h-BN nanopore with ionic-liquid/salt-water interface. Electrophoresis 2021; 42:991-1002. [PMID: 33570197 DOI: 10.1002/elps.202000356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 02/03/2023]
Abstract
Accomplishing slow translocation speed with high sensitivity has been the most critical mission for solid-state nanopore (SSN) device to electrically detect nucleobases in ssDNA. In this study, a method to detect nucleobases of ssDNA using a 2D SSN is introduced by considerably reducing the translocation speed and effectively increasing its sensitivity. The ultra-thin titanium dioxide coated hexagonal boron nitride nanopore was fabricated, along with an ionic-liquid 1-butyl-3-methylimidazolium hexafluorophosphate/2.0 M KCl aqueous (cis/trans) interface, for increasing both the spatial and the temporal resolutions. As the ssDNA molecules entered the nanopore, a brief surge of electrical conductivity occurred, which was followed by multiple resistive pulses from nucleobases during the translocation of ssDNA and another brief current surge flagging the exit of the molecule. The continuous detection of nucleobases using a 2D SSN device is a novel achievement: the water molecules bound to ssDNA increased the molecular conductivity and amplified electrical signals during the translocation. Along with the experiment, computational simulations using COMSOL Multiphysics are presented to explain the pivotal role of water molecules bound to ssDNA to detect nucleobases using a 2D SSN.
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Affiliation(s)
- Jung Soo Lee
- Applied Science Program, Lyle School of Engineering, Southern Methodist University, Dallas, TX, USA
| | - Juan Pablo Oviedo
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | | | - Xin Peng
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Department of Physical Chemistry, University of Science and Technology, Beijing, P. R. China
| | - Longsheng Xia
- Department of Electrical Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Qingxiao Wang
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Kevin Garcia
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Monterrey Institute of Technology and Higher Education, Mexico City, Mexico
| | - Jinguo Wang
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Min Jun Kim
- Applied Science Program, Lyle School of Engineering, Southern Methodist University, Dallas, TX, USA.,Deparment of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Moon Jae Kim
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
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8
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Sun LZ, Wang CH, Luo MB, Li H. Trapped and non-trapped polymer translocations through a spherical pore. J Chem Phys 2019; 150:024904. [PMID: 30646715 DOI: 10.1063/1.5063331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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9
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Sun LZ, Li H, Xu X, Luo MB. Simulation study on the translocation of polyelectrolyte through conical nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:495101. [PMID: 30431017 DOI: 10.1088/1361-648x/aaeb19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experiments have suggested that the conical nanopore may be a reasonable sensor for the biopolymer analysis as it can provide high-resolution current signal. In this paper, we use Langevin dynamics simulation to study the translocation of charged polymer (polyelectrolyte) through three different conical nanopores, a single-conical nanopore with large entry and small exit (pore I), a single-conical nanopore with small entry and large exit (pore II), and a double-conical nanopore with the tip (narrowest place) at the middle (pore III). Simulation shows that the detailed translocation behaviors are of pore structure dependence. Pore I might be the most reasonable one for the polyelectrolyte analysis, especially at strong monomer-pore attraction, since it can efficiently reduce the polyelectrolyte speed at the tip. The simulation results are interpreted by the free energy profiles of the polyelectrolyte translocation through different pores and the time of individual monomer passing through the tips.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, People's Republic of China
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10
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Qiu Y, Siwy ZS, Wanunu M. Abnormal Ionic-Current Rectification Caused by Reversed Electroosmotic Flow under Viscosity Gradients across Thin Nanopores. Anal Chem 2018; 91:996-1004. [DOI: 10.1021/acs.analchem.8b04225] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yinghua Qiu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zuzanna S. Siwy
- Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
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11
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Sun LZ, Luo MB, Cao WP, Li H. Theoretical study on the polymer translocation into an attractive sphere. J Chem Phys 2018; 149:024901. [PMID: 30007381 DOI: 10.1063/1.5025609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report a non-sampling model, combining the blob method with the standard lattice-based approximation, to calculate the free energy for the polymer translocation into an attractive sphere (i.e., spherical confined trans side) through a small pore. The translocation time is then calculated by the Fokker-Planck equation based on the free energy profile. There is a competition between the confinement effect of the sphere and the polymer-sphere attraction. The translocation time is increased due to the confinement effect of the sphere, whereas it is reduced by the polymer-sphere attraction. The two effects offset each other at a special polymer-sphere attraction which is dependent on the sphere size, the polymer length, and the driving force. Moreover, the entire translocation process can be divided into an uncrowded stage where the polymer does not experience the confinement effect of the sphere and a crowded stage where the polymer is confined by the sphere. At the critical sphere radius, the durations of the two (uncrowded and crowded) stages are the same. The critical sphere radius R* has a scaling relation with the polymer length N as R* ∼ Nβ. The calculation results show that the current model can effectively treat the translocation of a three-dimensional self-avoiding polymer into the spherical confined trans side.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Wei-Ping Cao
- Institute of Optoelectronic Technology, Lishui University, Lishui 323000, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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12
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VandeSande MC, Pasut DJ, de Haan HW. Sorting polymers by size via an array of viscous posts. Electrophoresis 2017; 38:2488-2497. [PMID: 28975695 DOI: 10.1002/elps.201700136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 11/07/2022]
Abstract
DNA fragments can be sorted according to size by forcing them through an array of nanoposts. Whereas previous studies have explored solid nanoposts, this work examines nanoposts constructed out of viscous inclusions. Langevin dynamics simulations are used to study the dynamics of polymers driven through arrays of these viscous nanoposts for a range of post viscosities. The results are compared to the solid post case. Increasing post viscosity causes a decrease in the mobility of polymers traversing the array. In the limit of high post viscosity, the mobility becomes lower than in the solid post arrays, rather than converging to it. Analysis of the distributions of event times also shows that the viscous case is fundamentally different from the solid post case. The decrease in mobility in the viscous case arises from slowing down the polymer as it interacts with or even moves through the nanoposts, whereas the solid post case exhibits wrapping and unwrapping dynamics, yielding escape-like statistics. This work suggests that it may be possible to use viscous inclusions within nanofluidic and microfluidic devices to sort biomolecules with high resolution.
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Affiliation(s)
- Matthew C VandeSande
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Daniel J Pasut
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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13
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Li Z, Guo H. A molecular dynamics simulation study of sucking a single polymer chain into nanopores: blockage and memory effects. POLYM INT 2015. [DOI: 10.1002/pi.4929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ziqi Li
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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14
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Katkar HH, Muthukumar M. Effect of charge patterns along a solid-state nanopore on polyelectrolyte translocation. J Chem Phys 2015; 140:135102. [PMID: 24712816 DOI: 10.1063/1.4869862] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the effectiveness of charge patterns along a nanopore on translocation dynamics of a flexible polyelectrolyte. We perform a three dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte translocating under uniform external electric field through a solid-state nanopore. We maintain the total charge along the pore to be constant, while varying its distribution by placing alternate charged and uncharged sections of different lengths along the pore length. Longest average translocation time is observed for a pattern corresponding to an optimum section length, with a major delay in the translocation time during the pore ejection stage. This optimum section length is independent of lengths of polyelectrolyte and pore within the range studied. A theory based on the Fokker-Planck formalism is found to successfully describe the observed trends with reasonable quantitative agreement.
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Affiliation(s)
- H H Katkar
- Department of Polymer Science and Engineering, Room A212, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - M Muthukumar
- Department of Polymer Science and Engineering, Room A212, University of Massachusetts, Amherst, Massachusetts 01003, USA
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15
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Liu Z, Liu J, Xiao M, Wang R, Chen YL. Conformation-dependent translocation of a star polymer through a nanochannel. BIOMICROFLUIDICS 2014; 8:054107. [PMID: 25332744 PMCID: PMC4189700 DOI: 10.1063/1.4893637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/11/2014] [Indexed: 06/04/2023]
Abstract
The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time [Formula: see text] and the total number of beads N tot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time.
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Affiliation(s)
- Zhu Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Jiannan Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Mengying Xiao
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Rong Wang
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Yeng-Long Chen
- Institute of Physics , Academia Sinica, Taipei 11529, Taiwan
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16
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de Haan HW, Slater GW. Biomolecule transport across biomembranes in the presence of crowding: polymer translocation driven by concentration and disorder gradients. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:020601. [PMID: 25215678 DOI: 10.1103/physreve.90.020601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Indexed: 06/03/2023]
Abstract
The transport of biomolecules across biomembranes occurs in a complex environment where the fluid on both sides of the membrane contains many inclusions. We investigate the translocation of a polymer through a nanopore in such crowded environments via computer simulations. Modeling intracellular and extracellular inclusions as spherical obstacles, the emergence of an entropic driving force is demonstrated for (i) a gradient in the number of obstacles on either side of the pore and (ii) having the obstacles in an ordered arrangement on one side and disordered on the other. With a directional preference of ≈90% of events occurring towards the disordered side and a reduction in the translocation time of ≈30%, the latter case represents a manifestation of entropic trapping. Simple estimates for the magnitude of the driving force are developed for both cases. The effect of allowing the obstacles to move as well as systems containing opposing concentration and disorder gradients are also explored. Demonstrating a robust conclusion that translocation to lower obstacle densities and higher degrees of disorder will be accelerated, these results suggest that accounting for such effects will be critical in developing a realistic model of in vivo translocation.
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Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1H 7K4
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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17
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Linna RP, Moisio JE, Suhonen PM, Kaski K. Dynamics of polymer ejection from capsid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052702. [PMID: 25353824 DOI: 10.1103/physreve.89.052702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 06/04/2023]
Abstract
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the ejection times scale with polymer length, τ ∼ N(α). We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) ρ inside the capsid. For very low densities ρ ≤ 0.002 the polymer is only weakly confined by the capsid, and we measure α = 1.33, which is close to α=1.4 obtained for polymer translocation. At intermediate densities the scaling exponents α = 1.25 and 1.21 for ρ = 0.01 and 0.02, respectively. These scalings are in accord with a crude derivation for the lower limit α = 1.2. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, ρ ⪆ 0.25. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.
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Affiliation(s)
- R P Linna
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - J E Moisio
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - P M Suhonen
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - K Kaski
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
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