dorsal/arxiv
View SchemaMonte Carlo simulation of melting transition on DNA nanocompartment
| Authors | Song Chang, Youdong Mao, Zhengwei Xie, Chunxiong Luo, Qi Ouyang |
|---|---|
| Categories | |
| ArXiv ID | physics/0510004 |
| URL | https://arxiv.org/abs/physics/0510004 |
| DOI | 10.1088/1742-6596/29/1/004 |
Abstract
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force microscopy. Interesting and novel phenomena emerged during the switching of the device. We have found that DNAs in this system exhibit a much steep melting transition compared to ones in bulk solution or conventional DNA array. To achieve an understanding to this discrepancy, we introduced DNA-DNA interaction potential to the conventional Ising-like Zimm-Bragg theory and Peyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation caused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the DNA-DNA interaction, we established coarse-gained Monte Carlo recursion relations by elucidation of five components of energy change during melting transition. The result suggests that DNA-DNA interaction potential accounts for the observed steep transition.
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"abstract": "DNA nanocompartment is a typical DNA-based machine whose function is\ndependent of molecular collective effect. Fundamental properties of the device\nhave been addressed via electrochemical analysis, fluorescent microscopy, and\natomic force microscopy. Interesting and novel phenomena emerged during the\nswitching of the device. We have found that DNAs in this system exhibit a much\nsteep melting transition compared to ones in bulk solution or conventional DNA\narray. To achieve an understanding to this discrepancy, we introduced DNA-DNA\ninteraction potential to the conventional Ising-like Zimm-Bragg theory and\nPeyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation\ncaused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the\nDNA-DNA interaction, we established coarse-gained Monte Carlo recursion\nrelations by elucidation of five components of energy change during melting\ntransition. The result suggests that DNA-DNA interaction potential accounts for\nthe observed steep transition.",
"arxiv_id": "physics/0510004",
"authors": [
"Song Chang",
"Youdong Mao",
"Zhengwei Xie",
"Chunxiong Luo",
"Qi Ouyang"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1088/1742-6596/29/1/004",
"title": "Monte Carlo simulation of melting transition on DNA nanocompartment",
"url": "https://arxiv.org/abs/physics/0510004"
},
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