Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

No abstract is available for this paper.

• Publication year

  2002

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2002-04-16

• Fields of study

  Biology, Medicine, Physics

• Identifiers
  DOI 10.1073/pnas.032095099PMID 11959991PMCID PMC122776
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  1998cited by this paper
• Four-thirds power law for knots and links

  1998cited by this paper
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  1998cited by this paper
• Simplification of DNA topology below equilibrium values by type II topoisomerases.

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  1997cited by this paper
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  1997cited by this paper
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  1996cited by this paper
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  1996cited by this paper
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  1994cited by this paper
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  1993cited by this paper
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  1993cited by this paper
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  1992cited by this paper
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  1992cited by this paper
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  1992cited by this paper
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  1991cited by this paper
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  1989cited by this paper
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  1989cited by this paper
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  1987cited by this paper
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  1987cited by this paper
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  1986cited by this paper
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  1986cited by this paper
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  1985cited by this paper
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  1985cited by this paper
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  1985cited by this paper
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