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Milchev A, Binder K. Adsorption of Semiflexible Polymers in Cylindrical Tubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11759-11770. [PMID: 34581575 DOI: 10.1021/acs.langmuir.1c01715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Conformations of wormlike chains in cylindrical pores with attractive walls are explored for varying pore radius and strength of the attractive wall potential by molecular dynamics simulations of a coarse-grained model. Local quantities such as the fraction of monomeric units bound to the surface and the bond-orientational order parameter as well as the radial density distribution are studied, as well as the global chain extensions parallel to the cylinder axis and perpendicular to the cylinder surface. A nonmonotonic convergence of these properties to their counterparts for adsorption on a planar substrate is observed due to the conflict between pore surface curvature and chain stiffness. Also the interpretation of partially adsorbed chains in terms of trains, loops, and tails is discussed.
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Affiliation(s)
- A Milchev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - K Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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2
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Milchev A, Binder K. Cylindrical confinement of solutions containing semiflexible macromolecules: surface-induced nematic order versus phase separation. SOFT MATTER 2021; 17:3443-3454. [PMID: 33646224 DOI: 10.1039/d1sm00172h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Solutions of semiflexible polymers confined in cylindrical pores with repulsive walls are studied by Molecular Dynamics simulations for a wide range of polymer concentrations. Both the case where both lengths are of the same order and the case when the persistence length by far exceeds the contour length are considered, and the enhancement of nematic order along the cylinder axis is characterized. With increasing density the character of the surface effect changes from depletion to the formation of a layered structure. For binary 50 : 50 mixtures of the two types of polymers an interplay between surface enrichment of the stiffer component and the isotropic-nematic transition is found, and a phase separated structure with cylindrical symmetry occurs, with the isotropic phase located around the cylinder axis. For melt densities the mixed nematic phase forms at the wall a layer with a screw-like structure of a tilted smectic phase. The observed behavior is tentatively interpreted in terms of the competition of the chain orientational entropy with entropy of mixing and excluded volume due to the wall.
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Affiliation(s)
- Andrey Milchev
- Institute for Physical Chemistry, Bulgarian Academia of Sciences, 1113, Sofia, Bulgaria.
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3
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Tagliabue A, Izzo L, Mella M. Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/polb.24806] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Andrea Tagliabue
- Dipartimento di Scienza ed Alta TecnologiaUniversità degli Studi dell'Insubria via Valleggio 9, 22100, Como Italy
| | - Lorella Izzo
- Dipartimento di Biotecnologie e Scienze della VitaUniversità degli Studi dell'Insubria via J. H. Dunant 3, 21100, Varese Italy
| | - Massimo Mella
- Dipartimento di Scienza ed Alta TecnologiaUniversità degli Studi dell'Insubria via Valleggio 9, 22100, Como Italy
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4
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Azote S, Müller-Nedebock KK. Density fields for branching, stiff networks in rigid confining regions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:23. [PMID: 30788631 DOI: 10.1140/epje/i2019-11784-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin filaments with branching due to the Arp2/3 complex. We develop a grand ensemble formalism that enables the computation of segment density and polarisation profiles within the confines of the cell. This is expressed in terms of the solution to nonlinear integral equations for auxiliary functions. We find three specific classes of behaviour depending on filament length, degree of branching and the ratio of persistence length to the dimensions of the geometry. Our method allows a numerical approach for semi-flexible filaments that are networked.
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Affiliation(s)
- Somiéalo Azote
- Institute of Theoretical Physics, Department of Physics, Stellenbosch University, Stellenbosch, South Africa.
| | - Kristian K Müller-Nedebock
- Institute of Theoretical Physics, Department of Physics, Stellenbosch University, Stellenbosch, South Africa
- National Institute for Theoretical Physics, Stellenbosch, South Africa
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5
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Rišpanová L, Benková Z, Cifra P. Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array. Polymers (Basel) 2018; 10:E1301. [PMID: 30961226 PMCID: PMC6401765 DOI: 10.3390/polym10121301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022] Open
Abstract
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information.
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Affiliation(s)
- Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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6
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Roy S, Luzhbin DA, Chen YL. Investigation of nematic to smectic phase transition and dynamical properties of strongly confined semiflexible polymers using Langevin dynamics. SOFT MATTER 2018; 14:7382-7389. [PMID: 30203825 DOI: 10.1039/c8sm01100a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We investigated the nematic to smectic phase transition for strongly confined semiflexible polymer solutions in slit-like confinements using GPU-accelerated Langevin dynamics. We characterized the phase transitions from the nematic to smectic phases for semi-flexible polymer solutions as the polymer density increased. The dependence for the lyotropic nematic to smectic transition can be collapsed by scaling exponents between 0.2 and 0.3. The smectic C phase is found for all the cases with the polymer orientation director tilted with respect to smectic layer lateral alignment. As the chain rigidity increases, the transition density decreases for systems in which the polymer persistence length (P) to slit height (H) ratios are 1.25, 2.5, 3.75, 5 and 25. We also characterized the polymer dynamics for the isotropic-nematic-smectic transitions. The overall polymer diffusivity decreased steadily as the polymer density increased. We observed anomalous polymer diffusion along the nematic director near the isotropic-nematic transition, similar to previously reported behavior for nematic-forming ellipsoids. Polymer diffusivity decreased sharply by two orders of magnitude upon the nematic-smectic transition.
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Affiliation(s)
- Supriya Roy
- Institute of Physics, Academia Sinica, Taipei, Taiwan, Republic of China.
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7
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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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8
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Min K, Rammohan AR, Lee HS, Shin J, Lee SH, Goyal S, Park H, Mauro JC, Stewart R, Botu V, Kim H, Cho E. Computational approaches for investigating interfacial adhesion phenomena of polyimide on silica glass. Sci Rep 2017; 7:10475. [PMID: 28874757 PMCID: PMC5585183 DOI: 10.1038/s41598-017-10994-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/15/2017] [Indexed: 12/12/2022] Open
Abstract
This manuscript provides a comprehensive study of adhesion behavior and its governing mechanisms when polyimide undergoes various modes of detachment from silica glass. Within the framework of steered molecular dynamics, we develop three different adhesion measurement techniques: pulling, peeling, and sliding. Such computational methodologies can be applied to investigate heterogeneous materials with differing interfacial adhesion modes. Here, a novel hybrid potential involving a combination of the INTERFACE force field in conjunction with ReaxFF and including Coulombic and Lennard-Jones interactions is employed to study such interfaces. The studies indicate that the pulling test requires the largest force and the shortest distance to detachment as the interfacial area is separated instantaneously, while the peeling test is observed to exhibit the largest distance for detachment because it separates via line-by-line adhesion. Two kinds of polyimides, aromatic and aliphatic type, are considered to demonstrate the rigidity dependent adhesion properties. The aromatic polyimide, which is more rigid due to the stronger charge transfer complex between chains, requires a greater force but a smaller distance at detachment than the aliphatic polyimide for all of the three methodologies.
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Affiliation(s)
- Kyoungmin Min
- Platform Technology Lab, Samsung Advanced Institute of Technology, 130 Samsung-ro, Suwon, Gyeonggi-do, 443-803, Republic of Korea
| | - Aravind R Rammohan
- Science and Technology Division, Corning Incorporated, One Science Center Drive, Corning, New York, 14831, United States
| | - Hyo Sug Lee
- Platform Technology Lab, Samsung Advanced Institute of Technology, 130 Samsung-ro, Suwon, Gyeonggi-do, 443-803, Republic of Korea
| | - Jaikwang Shin
- Platform Technology Lab, Samsung Advanced Institute of Technology, 130 Samsung-ro, Suwon, Gyeonggi-do, 443-803, Republic of Korea
| | - Sung Hoon Lee
- Corning Technology Center Korea, Asan, Chungcheongnam-do, 31454, Republic of Korea
| | - Sushmit Goyal
- Science and Technology Division, Corning Incorporated, One Science Center Drive, Corning, New York, 14831, United States
| | - Hyunhang Park
- Corning Technology Center Korea, Asan, Chungcheongnam-do, 31454, Republic of Korea
| | - John C Mauro
- Science and Technology Division, Corning Incorporated, One Science Center Drive, Corning, New York, 14831, United States
| | - Ross Stewart
- Science and Technology Division, Corning Incorporated, One Science Center Drive, Corning, New York, 14831, United States
| | - Venkatesh Botu
- Science and Technology Division, Corning Incorporated, One Science Center Drive, Corning, New York, 14831, United States
| | - Hyunbin Kim
- Corning Technology Center Korea, Asan, Chungcheongnam-do, 31454, Republic of Korea
| | - Eunseog Cho
- Platform Technology Lab, Samsung Advanced Institute of Technology, 130 Samsung-ro, Suwon, Gyeonggi-do, 443-803, Republic of Korea.
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9
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Mella M, Izzo L. Modulation of ionization and structural properties of weak polyelectrolytes due to 1D, 2D, and 3D confinement. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/polb.24351] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia; Università degli Studi dell'Insubria; via Valleggio 9 Como 22100 Italy
| | - Lorella Izzo
- Dipartimento di Chimica e Biologia; Università degli Studi di Salerno; via Giovanni Paolo II, 132 Fisciano 84084 Italy
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10
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Hayase Y, Sakaue T, Nakanishi H. Compressive response and helix formation of a semiflexible polymer confined in a nanochannel. Phys Rev E 2017; 95:052502. [PMID: 28618466 DOI: 10.1103/physreve.95.052502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 06/07/2023]
Abstract
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length l_{p} is much longer than the channel diameter D:l_{p}/D≫1. Using numerical simulations, we show that the polymer undergoes a sequence of recurring structural transitions upon longitudinal compression: random deflection along the channel, a helix going around the channel wall, double-fold random deflection, double-fold helix, etc. We find that the helix transition can be understood as buckling of deflection segments, and the initial helix formation takes place at very small compression with no appreciable weak compression regime of the random deflection polymer.
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Affiliation(s)
- Yumino Hayase
- Department of Mathematical and Live Sciences, Hiroshima University, Hiroshima 739-8526, Japan
| | - Takahiro Sakaue
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
- JST, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hiizu Nakanishi
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan
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11
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Affiliation(s)
- G. D’Adamo
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - E. Orlandini
- Dipartimento
di Fisica e Astronomia, Università di Padova and Sezione INFN, Via Marzolo 8, I-35100 Padova, Italy
| | - C. Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
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12
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Leith JS, Kamanzi A, Sean D, Berard D, Guthrie AC, McFaul CMJ, Slater GW, de Haan HW, Leslie SR. Free Energy of a Polymer in Slit-like Confinement from the Odijk Regime to the Bulk. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | - David Sean
- University of
Ottawa, Ottawa, Ontario, Canada K1N 6N5
| | | | | | | | | | - Hendrick W. de Haan
- Institute
of Technology, University of Ontario, Oshawa, Ontario, Canada L1H 7K4
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13
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Benková Z, Námer P, Cifra P. Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel. SOFT MATTER 2016; 12:8425-8439. [PMID: 27722460 DOI: 10.1039/c6sm01507g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension-confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension-confinement strength dependence for both topologies conforms to the de Gennes regime in a stripe, a linear chain undergoes gradual transition to the pseudoideal regime as the slab height increases in the slab-like confinement. For a confined circle, the onset of the pseudoideal regime is shifted to larger slab heights. The structure factor confirms the absence of the pseudoideal and extended de Gennes regime in a stripe and the transition from the extended to the pseudoideal regime of a circular and linear chain upon increasing the slab heights.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia. and LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Pavol Námer
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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14
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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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15
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Jain A, Sheats J, Reifenberger JG, Cao H, Dorfman KD. Modeling the relaxation of internal DNA segments during genome mapping in nanochannels. BIOMICROFLUIDICS 2016; 10:054117. [PMID: 27795749 PMCID: PMC5065570 DOI: 10.1063/1.4964927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/04/2016] [Indexed: 06/01/2023]
Abstract
We have developed a multi-scale model describing the dynamics of internal segments of DNA in nanochannels used for genome mapping. In addition to the channel geometry, the model takes as its inputs the DNA properties in free solution (persistence length, effective width, molecular weight, and segmental hydrodynamic radius) and buffer properties (temperature and viscosity). Using pruned-enriched Rosenbluth simulations of a discrete wormlike chain model with circa 10 base pair resolution and a numerical solution for the hydrodynamic interactions in confinement, we convert these experimentally available inputs into the necessary parameters for a one-dimensional, Rouse-like model of the confined chain. The resulting coarse-grained model resolves the DNA at a length scale of approximately 6 kilobase pairs in the absence of any global hairpin folds, and is readily studied using a normal-mode analysis or Brownian dynamics simulations. The Rouse-like model successfully reproduces both the trends and order of magnitude of the relaxation time of the distance between labeled segments of DNA obtained in experiments. The model also provides insights that are not readily accessible from experiments, such as the role of the molecular weight of the DNA and location of the labeled segments that impact the statistical models used to construct genome maps from data acquired in nanochannels. The multi-scale approach used here, while focused towards a technologically relevant scenario, is readily adapted to other channel sizes and polymers.
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Affiliation(s)
- Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | | | - Han Cao
- BioNano Genomics , 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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16
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Luzhbin DA, Chen YL. Shifting the Isotropic–Nematic Transition in Very Strongly Confined Semiflexible Polymer Solutions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00986] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dmytro A. Luzhbin
- Institute of Physics, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan, R.O.C
- Department of Physics, National Taiwan University, Taipei, Taiwan, R.O.C
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan, R.O.C
- Department of Physics, National Taiwan University, Taipei, Taiwan, R.O.C
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17
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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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18
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Alishahi M, Kamali R, Abouali O. Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility behaviour. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:92. [PMID: 26314258 DOI: 10.1140/epje/i2015-15092-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 06/30/2015] [Accepted: 07/17/2015] [Indexed: 06/04/2023]
Abstract
The essential and effective characteristics of a double-stranded DNA (dsDNA) confined in a nanochannel is revisited by employing the rigorous full numerical approach of Molecular Dynamics (MD). The deformation of dsDNA and wall-biomolecule interaction which is critical in highly confined regime has been precisely imposed in numerical simulations. The numerical approach has been justified against available theoretical outcomes. A new and general expression for DNA electrophoretic mobility versus DNA length is extracted from numerical simulation which is out of reach of experimental methods due to practical shortcomings. The newly derived expression suggests an essential correction in the previously proposed expression for the critical case of small DNA molecules and reveals an astonishingly unbeknown trend of small DNA's mobility. Sub-molecular phenomenon of dsDNA melting under the condition of large external force is also studied. Assuming strong electric field exertion, the MD approach aptly demonstrates the elaborate melting phenomenon for dsDNA in sub-molecular scale.
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Affiliation(s)
- Marzieh Alishahi
- School of Mechanical Engineering, Shiraz University, Shiraz, Iran
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19
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Wang X, Tang M, Wang Y. Equilibrium Distribution of Semiflexible Polymer Chains between a Macroscopic Dilute Solution Phase and Small Voids of Cylindrical Shape. MACROMOL THEOR SIMUL 2015. [DOI: 10.1002/mats.201500029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaoyan Wang
- Department of Polymer Science and Engineering; College of chemistry, Chemical Engineering and Materials Science; Soochow University; 199 Ren-ai Road Suzhou 215123 P. R. China
| | - Meng Tang
- School of Electronic and Information Engineering; Soochow University; 1 Shi-zi Street Suzhou 215006 P. R. China
| | - Yanwei Wang
- Department of Polymer Science and Engineering; College of chemistry, Chemical Engineering and Materials Science; Soochow University; 199 Ren-ai Road Suzhou 215123 P. R. China
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20
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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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21
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Liao GJ, Chien FT, Luzhbin D, Chen YL. Entropic attraction: Polymer compaction and expansion induced by nano-particles in confinement. J Chem Phys 2015; 142:174904. [DOI: 10.1063/1.4919650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Guo-Jun Liao
- Department of Physics, National Taiwan University, Taipei, Taiwan
| | - Fan-Tso Chien
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Dmytro Luzhbin
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Yeng-Long Chen
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
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22
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Benková Z, Námer P, Cifra P. Stripe to slab confinement for the linearization of macromolecules in nanochannels. SOFT MATTER 2015; 11:2279-2289. [PMID: 25651783 DOI: 10.1039/c4sm02382j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigated the recently suggested advantageous analysis of chain linearization experiments with macromolecules confined in a stripe-like channel (Huang and Battacharya, EPL, 2014, 106, 18004) using Monte Carlo simulations. The enhanced chain extension in a stripe, which is due to the significant excluded volume interactions between the monomers in two dimensions, weakens considerably on transition to an experimentally feasible slit-like channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for a chain in a stripe, we infer the excluded volume regime (de Gennes regime) typical for two-dimensional systems. On widening of the stripe in a direction perpendicular to the stripe plane, i.e. on the transition to the slab geometry, the advantageous chain extension decreases and a Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on four indicators: the extension curves, variation of the extension with the persistence length P, estimated limits for the regimes in the investigated systems, and the structure factor behavior. The slab behavior can be observed when the two-dimensional stripe (originally of a one-monomer thickness) reaches a reduced thickness D larger than approximately D/P ≈ 0.2 in the third dimension. This maximum height of a slab at which the advantage of a stripe is retained is very low and has implications for DNA linearization experiments.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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23
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Muralidhar A, Tree DR, Dorfman KD. Backfolding of Wormlike Chains Confined in Nanochannels. Macromolecules 2014. [DOI: 10.1021/ma501687k] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Abhiram Muralidhar
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
| | - Douglas R. Tree
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
- Materials
Research Laboratory, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering and Materials Science, University of Minnesota−Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, United States
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24
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van der Maarel JRC, Zhang C, van Kan JA. A Nanochannel Platform for Single DNA Studies: From Crowding, Protein DNA Interaction, to Sequencing of Genomic Information. Isr J Chem 2014. [DOI: 10.1002/ijch.201400091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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25
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Lee J, Kim S, Jeong H, Jung GY, Chang R, Chen YL, Jo K. Nanoslit Confined DNA at Low Ionic Strengths. ACS Macro Lett 2014; 3:926-930. [PMID: 35596361 DOI: 10.1021/mz500396t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We present nanoslit confined DNA conformations at very low ionic strengths and a theory to explain most measurements for single DNA molecule size under strong nanoslit confinement. Very low ionic strength conditions not only increase the DNA persistence length dramatically, but also cause DNA molecules to swell to the extent that the effective diameter of DNA becomes larger than the nanoslit height. By accounting for these effects, our results and theory provide a reasonable clue for a current controversy regarding the dependence of the DNA conformation on slit height (h), persistence length (p), and effective diameter (w).
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Affiliation(s)
- Jinyong Lee
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Sulhwa Kim
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Huisu Jeong
- School
of Material Science and Engineering, Gwanju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Gun Young Jung
- School
of Material Science and Engineering, Gwanju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Rakwoo Chang
- Department
of Chemistry, Kwangwoon University, Seoul, Republic of Korea
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department
of Physics, National Taiwan University, Taipei, Taiwan
- Department
of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Kyubong Jo
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
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26
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Affiliation(s)
- Douglas R. Tree
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wesley F. Reinhart
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering
and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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27
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Roushan M, Kaur P, Karpusenko A, Countryman PJ, Ortiz CP, Fang Lim S, Wang H, Riehn R. Probing transient protein-mediated DNA linkages using nanoconfinement. BIOMICROFLUIDICS 2014; 8:034113. [PMID: 25379073 PMCID: PMC4162420 DOI: 10.1063/1.4882775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/30/2014] [Indexed: 05/16/2023]
Abstract
We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Parminder Kaur
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Alena Karpusenko
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | | | - Carlos P Ortiz
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Shuang Fang Lim
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Hong Wang
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Robert Riehn
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
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28
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Chen YL, Lin YH, Chang JF, Lin PK. Dynamics and Conformation of Semiflexible Polymers in Strong Quasi-1D and -2D Confinement. Macromolecules 2014. [DOI: 10.1021/ma401923t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yeng-Long Chen
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
- Department
of Physics, National Taiwan University, Taipei, Taiwan
- Department
of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Yu-Hui Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Po-keng Lin
- Institute
of Physics, Academia Sinica, Taipei, Taiwan
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29
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Hsu HP, Binder K. Semiflexible Macromolecules with Discrete Bond Angles Confined in Nanoslits: A Monte Carlo Test of Scaling Concepts. Macromolecules 2013. [DOI: 10.1021/ma401374e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hsiao-Ping Hsu
- Institut
für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg
7, D-55099 Mainz, Germany
| | - Kurt Binder
- Institut
für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg
7, D-55099 Mainz, Germany
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30
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Affiliation(s)
| | - Jia-Wei Yeh
- Institute
of Physics, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute
of Physics, Academia Sinica, Nangang, Taipei 11529, Taiwan
- Research Center for Applied Sciences, Nangang, Taipei 11529, Taiwan
- Genomics
Research Center, Academia Sinica, Nangang, Taipei 11529, Taiwan
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31
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Tree DR, Wang Y, Dorfman KD. Extension of DNA in a nanochannel as a rod-to-coil transition. PHYSICAL REVIEW LETTERS 2013; 110:208103. [PMID: 25167455 PMCID: PMC4156158 DOI: 10.1103/physrevlett.110.208103] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Indexed: 05/14/2023]
Abstract
DNA confinement in nanochannels is emerging as an important tool for genomics and an excellent platform for testing the theories of confined wormlike polymers. Using cutting-edge, large scale Monte Carlo simulations of asymptotically long wormlike chains, we show that, in analogy to the rod-to-coil transition for free wormlike polymers, there exists a universal, Gauss-de Gennes regime that connects the classic Odijk and de Gennes regimes of channel-confined chains. For DNA in a nanochannel, this Gauss-de Gennes regime spans practically the entire experimentally relevant range of channel sizes, including the nanochannels used in an incipient genome mapping technology.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
| | - Yanwei Wang
- Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou, 215123, P.R. China
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota ― Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455
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32
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Račko D, Cifra P. Segregation of semiflexible macromolecules in nanochannel. J Chem Phys 2013; 138:184904. [DOI: 10.1063/1.4803674] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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33
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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34
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Reinhart WF, Tree DR, Dorfman KD. Entropic depletion of DNA in triangular nanochannels. BIOMICROFLUIDICS 2013; 7:24102. [PMID: 24309518 PMCID: PMC3598824 DOI: 10.1063/1.4794371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 05/14/2023]
Abstract
Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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35
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Dai L, Ng SY, Doyle PS, van der Maarel JRC. Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel. ACS Macro Lett 2012; 1:1046-1050. [PMID: 35607035 DOI: 10.1021/mz300323a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Currently, no theory is available to describe the conformation of DNA confined in a channel when the nanochannel diameter is around the persistence length. Back-folded hairpins in the undulating wormlike chain conformation result in the formation of loops, which reduces the stretch of the molecule in the longitudinal direction of the channel. A cooperativity model is used to quantify the frequency and size of the loop domains. The predictions agree with results from the Monte Carlo simulation.
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
| | - Siow Yee Ng
- Department of Physics, National University of Singapore, Singapore 117542
| | - Patrick S. Doyle
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Johan R. C. van der Maarel
- BioSystems and Micromechanics, Singapore−MIT Alliance for Research and Technology, Singapore
- Department of Physics, National University of Singapore, Singapore 117542
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