Size and shape of excluded volume polymers confined between parallel plates

Chaudhuri, Debasish; Mulder, Bela M.

doi:10.1103/physreve.83.031803

Cited by 17 publications

(11 citation statements)

References 32 publications

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“…Accordingly, by substituting the expression for R G (x) provided by Ref. [54] into Eq. (13) the agreement between the analytical predictions and the outcome of A).…”

Section: Resultsmentioning

confidence: 99%

“…11). avoiding polymer, where RG, as function of channel width, h(x), exhibits a non monotonic behavior that can be captured by RG(x) 2 ∼ a2h(x) 2 + a3h(x) −1/2 , where a2 and a3 are fitting parameters [54].…”

Section: Discussionmentioning

confidence: 99%

“…In particular, in our simulations we found that R G is not constant, rather it depends on position. In order to take into account such a dependence we exploit an explicit expression for the dependence of the gyration radius of a Gaussian polymer [58] confined between parallel plates [54] …”

Section: Appendix A: Position Dependent Radius Of Gyrationmentioning

confidence: 99%

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Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Bianco

Malgaretti

2016

The Journal of Chemical Physics

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We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like particle under the action of an effective potential. Such a model allows us to identify the relevant parameters controlling the polymers dynamics and, in particular, their translocation time. By comparing our analytical results with numerical simulations we show that, under suitable conditions, our model provides reliable predictions of the dynamics of both Gaussian and self-avoiding polymers, in two-and three-dimensional confinement. Moreover, both theoretical predictions, as well Brownian dynamic results, show a non-monotonous dependence of polymer translocation velocity as a function of polymer size, a feature that can be exploited for polymer separation.

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“…Accordingly, by substituting the expression for R G (x) provided by Ref. [54] into Eq. (13) the agreement between the analytical predictions and the outcome of A).…”

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Bianco

Malgaretti

2016

The Journal of Chemical Physics

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“…Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured.…”

mentioning

confidence: 99%

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

et al. 2015

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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.An understanding of the many factors influencing the size of dsDNA under nanoscale confinement is highly relevant to rationally designing measurement technologies for genomic sequencing and medical sensing and for accurately describing crowding effects on dsDNA organization in living systems. Consequently, there have been many recent theoretical and experimental studies of this phenomenon. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In particular, it has been possible for two decades to image individual fluorescently labeled dsDNA under conditions of nanoscale confinement in nanofluidic devices with slit-like geometries. In this way, the in-plane radius of gyration of dsDNA as a function of slit height has been recently measured. Fig. 1 summarizes the results of these experimental measurements, which exhibit a puzzling scatter under nominally similar experimental conditions. Scaling arguments and continuum chain models have dominated the majority of the recent theoretical treatments of this problem, which generally ignore polymer-surface interactions and hav...

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“…Mesoscale modeling of DNA has granted insights into DNA mechanics, conformation, and dynamics in free solution [82][83][84][85][86][87][88][89][90][91][92][93][94] and for DNA in nanoslits [95][96][97][98][99][100][101][102][103][104][105][106][107][108][109][110][111] and nanochannels [112][113][114][115][116][117][118][119][120][121][122][123][124]. In particular, there has been significant interest in the validation of polymer theory using DNA as a model polymer due to ease of direct observation of single DNA molecules and its highly monodisperse nature [104,[125][126][127][128]…”

Section: Mesoscale Modeling Of Dna Dynamicsmentioning

confidence: 99%

Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

et al. 2015

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Computational modeling has become increasingly important in biophysics, but the great challenge in numerical simulations due to the multiscale feature of biological systems limits the capability of modeling in making discoveries in biology. Innovative multiscale modeling approaches are desired to bridge different scales from nucleic acids and proteins to cells and tissues. Although all-atom molecular dynamics has been successfully applied in many microscale biological processes such as protein folding, it is still prohibitively expensive for studying macroscale problems such as biophysics of cells and tissues. On the other hand, continuum-based modeling has become a mature procedure for analysis and design in many engineering fields, but new insights for biological systems in the microscale are limited when molecular details are missing in continuum-based modeling. In this context, mesoscale modeling approaches such as Langevin dynamics, lattice Boltzmann method, and dissipative particle dynamics have become popular by simultaneously incorporating molecular interactions and long-range hydrodynamic interactions, providing insights to properties on longer time and length scales than molecular dynamics. In this review, we summarized several mesoscale simulation approaches for studying two model systems in biophysics: red blood cells (RBCs) and deoxyribonucleic acids (DNAs). The RBC is a model system for cell mechanics and biological membranes, while the DNA represents a model system for B Zhangli Peng

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Size and shape of excluded volume polymers confined between parallel plates

Cited by 17 publications

References 32 publications

Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

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