Radial distribution function for semiflexible polymers confined in microchannels

Levi, P.G.; Mecke, Klaus

doi:10.1209/0295-5075/78/38001

Cited by 18 publications

(40 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the smaller channel widths, the distribution is narrower and the maximum is found at a higher value for normalized end-to-end distances, R/L, indicating that in this case the filaments are more stretched out and aligned in the direction of the channel. An analytical equation describing the radial distribution function G R,c of semiflexible filaments confined in the Odijk regime has been obtained in reference [Le Goff et al, 2002;Levi and Mecke, 2007]; for the two-dimensional case we obtain:…”

Section: Resultsmentioning

confidence: 99%

An in vitro model system for cytoskeletal confinement

Köster

Pfohl

2009

Cell Motil. Cytoskeleton

View full text Add to dashboard Cite

The motility, shape, and functionality of the cell depend sensitively on cytoskeletal mechanics which in turn is governed by the properties of filamentous proteins - mainly actin, microtubules, and intermediate filaments. These biopolymers are confined in the dense cytoplasm and therefore experience strong geometric constraints on their equilibrium thermal fluctuations. To obtain a better understanding of the influence of confinement on cytoskeletal filaments we study the thermal fluctuations of individual actin filaments in a microfluidic in vitro system by fluorescence microscopy and determine the persistence length of the filaments by analyzing the radial distribution function. A unique feature of this method is that we obtain the persistence length without detailed knowledge of the complete contour of the filament which makes the technique applicable to a broad range of biological polymers, including those with a persistence length smaller than the optical resolution.

show abstract

Section: Resultsmentioning

confidence: 99%

An in vitro model system for cytoskeletal confinement

Köster

Pfohl

2009

Cell Motil. Cytoskeleton

View full text Add to dashboard Cite

show abstract

“…1 This scaling theory has been further extended to regimes where the intrinsic stiffness of a polymer is comparable to the confinement dimensions by Odijk and others. [2][3][4][5][6][7] However, the verification of the theories through realistic systems has not been possible until recent advances in highly sophisticated nanofabrication and single molecule detection. [8][9][10] The primary focus of these recent studies is on understanding the structural and dynamic behavior of DNA in nanochannels or nanoslits, since they potentiate a novel high-throughput and high-resolution genome analysis platform.…”

Section: Introductionmentioning

confidence: 99%

DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model

Chang

2012

The Journal of Chemical Physics

View full text Add to dashboard Cite

We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.

show abstract

“…When the polymer chain simultaneously subjects to tube confinement and force stretch in the deflection regime, as shown by [23,24] and later by [25], the effect of confinement can be approximately equivalent to an additional effective stretching force f c [23] witĥ…”

Section: Introductionmentioning

confidence: 99%

Stretching a Semiflexible Polymer in a Tube

Wang

2016

Polymers

View full text Add to dashboard Cite

How the statistical behavior of semiflexible polymer chains may be affected by force stretching and tube confinement is a classical unsolved problem in polymer physics. Based on the Odijk deflection theory and normal mode decomposition in terms of Fourier expansion, we have derived a new compact formula for the extension of a wormlike chain of finite length strongly confined in a tube and simultaneously stretched by an external force. We have also suggested a new deflection length, which together with the force-extension relation is valid for a very extended range of the tube-diameter/persistence-length ratio comparing to the classic Odijk theory. The newly derived formula has no adjustable fitting parameters for the whole deflection regime; in contrast, the classic Odijk length needs different prefactors to fit the free energy and average extension, respectively. Brownian dynamics simulations based on the Generalized Bead-Rod (GBR) model were extensively performed, which justified the theoretical predictions.

show abstract

Radial distribution function for semiflexible polymers confined in microchannels

Cited by 18 publications

References 28 publications

An in vitro model system for cytoskeletal confinement

An in vitro model system for cytoskeletal confinement

DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model

Stretching a Semiflexible Polymer in a Tube

Contact Info

Product

Resources

About