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Kim JM. Influence of chain stiffness on semiflexible polymer melts in two dimensions via molecular dynamics simulation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1970155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jun Mo Kim
- Department of Chemical Engineering, Kyonggi University, Suwon, South Korea
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Kim J, Kim JM, Baig C. Intrinsic chain stiffness in flexible linear polymers under extreme confinement. POLYMER 2021. [DOI: 10.1016/j.polymer.2020.123308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Wang X, Limpouchová Z, Procházka K. Separation of polymers differing in their chain architecture by interaction chromatography: Phase equilibria and conformational behavior of polymers in strongly adsorbing porous media. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Cheong GK, Li X, Dorfman KD. Evidence for the extended de Gennes regime of a semiflexible polymer in slit confinement. Phys Rev E 2018; 97:022502. [PMID: 29479576 PMCID: PMC5823612 DOI: 10.1103/physreve.97.022502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We use off-lattice, pruned-enriched Rosenbluth method (PERM) simulations to compute the confinement free energy of a real wormlike chain of effective width w and persistence length lp in a slit of height H. For slit heights much larger than the persistence length of the polymer and much smaller than the thermal blob size, the excess free energy of the confined chain is consistent with a modified version of the scaling theory for the extended de Gennes regime in a channel that reflects the blob statistics in slit confinement. Explicitly, for channel sizes [Formula: see text], the difference between the confinement free energy of the real chain and that of an ideal chain scales like w/H.
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Affiliation(s)
- Guo Kang Cheong
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Xiaolan Li
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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Huang A, Hsu HP, Bhattacharya A, Binder K. Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles. J Chem Phys 2016; 143:243102. [PMID: 26723587 DOI: 10.1063/1.4929600] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs"-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.
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Affiliation(s)
- Aiqun Huang
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Hsiao-Ping Hsu
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Kurt Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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Glagoleva AA, Vasilevskaya VV, Khokhlov AR. Polymer globule with fractal properties caused by intramolecular nanostructuring and spatial constrains. SOFT MATTER 2016; 12:5138-5145. [PMID: 27198966 DOI: 10.1039/c6sm00747c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
By means of computer simulation, we studied macromolecules composed of N dumbbell amphiphilic monomer units with attractive pendant groups. In poor solvents, these macromolecules form spherical globules that are dense in the case of short chains (the gyration radius RG∼N(1/3)), or hollow inside and obey the RG∼N(1/2) law when the macromolecules are sufficiently long. Due to the specific intramolecular nanostructuring, the vesicle-like globules of long amphiphilic macromolecules posses some properties of fractal globules, by which they (i) could demonstrate the same scaling statistics for the entire macromolecule and for short subchains with m monomer units and (ii) possess a specific territorial structure. Within a narrow slit, the globule loses its inner cavity, takes a disk-like shape and scales as N(1/2) for much shorter macromolecules. However, the field of end-to-end distance r(m) ∼m(1/2) dependence for subchains becomes visibly smaller. The results obtained were compared with the homopolymer case.
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Affiliation(s)
- Anna A Glagoleva
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia.
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Li X, Dorfman KD. Effect of excluded volume on the force-extension of wormlike chains in slit confinement. J Chem Phys 2016; 144:104902. [PMID: 26979704 DOI: 10.1063/1.4943195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use pruned-enriched Rosenbluth method simulations to develop a quantitative phase diagram for the stretching of a real wormlike chain confined in a slit. Our simulations confirm the existence of a "confined Pincus" regime in slit confinement, analogous to the Pincus regime in free solution, where excluded volume effects are sensible. The lower bound for the confined Pincus regime in the force-molecular weight plane, as well as the scaling of the extension with force and slit size, agree with an existing scaling theory for this regime. The upper bound of the confined Pincus regime depends on the strength of the confinement. For strong confinement, the confined Pincus regime ends when the contour length in the Pincus blob is too short to have intrablob excluded volume. As a result, the chain statistics become ideal and the confined Pincus regime at low forces is connected directly to ideal chain stretching at large forces. In contrast, for weak confinement, the confined Pincus regime ends when the Pincus blobs no longer fit inside the slit, even though there is sufficient contour length to have excluded volume inside the Pincus blob. As a result, weak confinement leads to a free-solution Pincus regime intervening between the confined Pincus regime for weak forces and ideal chain stretching at strong forces. Our results highlight shortcomings in existing models for the stretching of wormlike chains in slits.
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Affiliation(s)
- Xiaolan Li
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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Vargas-Lara F, Stavis SM, Strychalski EA, Nablo BJ, Geist J, Starr FW, Douglas JF. Dimensional reduction of duplex DNA under confinement to nanofluidic slits. SOFT MATTER 2015; 11:8273-8284. [PMID: 26353028 DOI: 10.1039/c5sm01580d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.
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Affiliation(s)
- Fernando Vargas-Lara
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Samuel M Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Elizabeth A Strychalski
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Brian J Nablo
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jon Geist
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Francis W Starr
- Department of Physics and Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Welch D, Lettinga MP, Ripoll M, Dogic Z, Vliegenthart GA. Trains, tails and loops of partially adsorbed semi-flexible filaments. SOFT MATTER 2015; 11:7507-7514. [PMID: 26279011 DOI: 10.1039/c5sm01457c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Polymer adsorption is a fundamental problem in statistical mechanics that has direct relevance to diverse disciplines ranging from biological lubrication to stability of colloidal suspensions. We combine experiments with computer simulations to investigate depletion induced adsorption of semi-flexible polymers onto a hard-wall. Three dimensional filament configurations of partially adsorbed F-actin polymers are visualized with total internal reflection fluorescence microscopy. This information is used to determine the location of the adsorption/desorption transition and extract the statistics of trains, tails and loops of partially adsorbed filament configurations. In contrast to long flexible filaments which primarily desorb by the formation of loops, the desorption of stiff, finite-sized filaments is largely driven by fluctuating filament tails. Simulations quantitatively reproduce our experimental data and allow us to extract universal laws that explain scaling of the adsorption-desorption transition with relevant microscopic parameters. Our results demonstrate how the adhesion strength, filament stiffness, length, as well as the configurational space accessible to the desorbed filament can be used to design the characteristics of filament adsorption and thus engineer properties of composite biopolymeric materials.
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Affiliation(s)
- David Welch
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, MA 02454, USA
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de Haan HW, Shendruk TN. Force-Extension for DNA in a Nanoslit: Mapping between the 3D and 2D Limits. ACS Macro Lett 2015; 4:632-635. [PMID: 35596406 DOI: 10.1021/acsmacrolett.5b00138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The force-extension relation for a semiflexible polymer confined in a nanoslit is investigated. Both the effective correlation length and force-extension relation change as the chain goes from 3D (large slit heights) to 2D (tight confinement). At low forces, correlations along the polymer give an effective dimensionality. The strong force limit can be interpolated with the weak force limit for two regimes: when confinement dominates over extensile force and vice versa. These interpolations give good agreement with simulations for all slit heights and forces. We thus generalize the Marko-Siggia force-extension relation for DNA and other semiflexible biopolymers in nanoconfinement.
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Affiliation(s)
- Hendrick W. de Haan
- University of Ontario Institute of Technology, Faculty
of Science, 2000 Simcoe
Street North, Oshawa, Ontario L1H 7K4, Canada
| | - Tyler N. Shendruk
- The
Rudolf Peierls Centre for Theoretical Physics, Department of Physics,
Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, United Kingdom
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Li S, Zhang W, Yao W, Shi T. Structure and dynamics of confined polymer melts from attractive interaction to repulsive interaction between polymer and smooth wall. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-4455-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gao J, Tang P, Yang Y, Chen JZY. Free energy of a long semiflexible polymer confined in a spherical cavity. SOFT MATTER 2014; 10:4674-4685. [PMID: 24839199 DOI: 10.1039/c4sm00605d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The free energy and conformational properties of a wormlike chain confined inside a spherical surface are investigated. We show that in the weak-confinement limit, the wormlike chain model exactly reproduces the confinement properties of a Gaussian chain; in such a case the confinement entropy dominates the free energy; in the strong-confinement limit, the free energy is dominated by the bending energy of the chain, which is forced to wrap around the confining surface. We also present a numerical solution within the crossover region between the two limits, solving the differential equation that the probability distribution function satisfies.
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Affiliation(s)
- Jie Gao
- Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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