Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and len...

पूर्ण विवरण

ग्रंथसूची विवरण
मुख्य लेखकों:	Fonseca, P, Romano, F, Schreck, J, Ouldridge, T, Doye, J, Louis, A
स्वरूप:	Journal article
प्रकाशित:	AIP Publishing 2018

समान संसाधन

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द्वारा: Reinhardt, A, और अन्य
प्रकाशित: (2016)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
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प्रकाशित: (2013)

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Simulation data associated with "Coarse-grained modelling of the structural properties of DNA origami"
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द्वारा: Schreck, J, और अन्य
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द्वारा: Dannenberg, F, और अन्य
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द्वारा: Johnston, I, और अन्य
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