dorsal/arxiv
View SchemaMechanisms of DNA separation in entropic trap arrays: A Brownian dynamics simulation
| Authors | Martin Streek, Friederike Schmid, Thanh Tu Duong, Alexandra Ros |
|---|---|
| Categories | |
| ArXiv ID | physics/0405152 |
| URL | https://arxiv.org/abs/physics/0405152 |
Abstract
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a device has been designed and fabricated recently by Han et al. for the separation of DNA molecules (Science, 2000). Our simulation reproduces the experimental observation that the mobility increases with the length of the DNA. A detailed data analysis allows to identify the reasons for this behavior. Two distinct mechanisms contribute to slowing down shorter chains. One has been described earlier by Han et al.: the chains are delayed at the entrance of the constriction and escape with a rate that increases with chain length. The other, actually dominating mechanism is here reported for the first time: Some chains diffuse out of their main path into the corners of the box, where they remain trapped for a long time. The probability that this happens increases with the diffusion constant, i.e., the inverse chain length.
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"abstract": "Using Brownian dynamics simulations, we study the migration of long charged\nchains in an electrophoretic microchannel device consisting of an array of\nmicroscopic entropic traps with alternating deep regions and narrow\nconstrictions. Such a device has been designed and fabricated recently by Han\net al. for the separation of DNA molecules (Science, 2000). Our simulation\nreproduces the experimental observation that the mobility increases with the\nlength of the DNA. A detailed data analysis allows to identify the reasons for\nthis behavior. Two distinct mechanisms contribute to slowing down shorter\nchains. One has been described earlier by Han et al.: the chains are delayed at\nthe entrance of the constriction and escape with a rate that increases with\nchain length. The other, actually dominating mechanism is here reported for the\nfirst time: Some chains diffuse out of their main path into the corners of the\nbox, where they remain trapped for a long time. The probability that this\nhappens increases with the diffusion constant, i.e., the inverse chain length.",
"arxiv_id": "physics/0405152",
"authors": [
"Martin Streek",
"Friederike Schmid",
"Thanh Tu Duong",
"Alexandra Ros"
],
"categories": [
"physics.bio-ph",
"q-bio.QM"
],
"title": "Mechanisms of DNA separation in entropic trap arrays: A Brownian dynamics simulation",
"url": "https://arxiv.org/abs/physics/0405152"
},
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