Search Results - "Snodin, Benedict E. K"

Coarse-graining DNA for simulations of DNA nanotechnology by Doye, Jonathan P K, Ouldridge, Thomas E, Louis, Ard A, Romano, Flavio, Šulc, Petr, Matek, Christian, Snodin, Benedict E K, Rovigatti, Lorenzo, Schreck, John S, Harrison, Ryan M, Smith, William P J

“…To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different…”
Get more information

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA by Snodin, Benedict E K, Randisi, Ferdinando, Mosayebi, Majid, Šulc, Petr, Schreck, John S, Romano, Flavio, Ouldridge, Thomas E, Tsukanov, Roman, Nir, Eyal, Louis, Ard A, Doye, Jonathan P K

“…We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and…”
Get more information

Direct Simulation of the Self-Assembly of a Small DNA Origami by Snodin, Benedict E. K, Romano, Flavio, Rovigatti, Lorenzo, Ouldridge, Thomas E, Louis, Ard A, Doye, Jonathan P. K

“…By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from…”
Get full text

Coarse-grained modelling of the structural properties of DNA origami by Snodin, Benedict E K, Schreck, John S, Romano, Flavio, Louis, Ard A, Doye, Jonathan P K

“…Abstract We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on…”
Get full text

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami by Doye, Jonathan P K, Fowler, Hannah, Prešern, Domen, Bohlin, Joakim, Rovigatti, Lorenzo, Romano, Flavio, Šulc, Petr, Wong, Chak Kui, Louis, Ard A, Schreck, John S, Engel, Megan C, Matthies, Michael, Benson, Erik, Poppleton, Erik, Snodin, Benedict E K

“…This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model…”
Get more information

Coarse-grained modelling of the structural properties of DNA origami by Snodin, Benedict E. K, Schreck, John S, Romano, Flavio, Louis, Ard A, Doye, Jonathan P. K

“…Nucleic Acids Res. 47, 1585-1597 (2019) We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties…”
Get full text

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA by Snodin, Benedict E. K, Randisi, Ferdinando, Mosayebi, Majid, Sulc, Petr, Schreck, John S, Romano, Flavio, Ouldridge, Thomas E, Tsukanov, Roman, Nir, Eyal, Louis, Ard A, Doye, Jonathan P. K

“…J. Chem. Phys. 142, 234901 (2015) We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural…”
Get full text

Coarse-graining DNA for simulations of DNA nanotechnology by Doye, Jonathan P. K, Ouldridge, Thomas E, Louis, Ard A, Romano, Flavio, Sulc, Petr, Matek, Christian, Snodin, Benedict E. K, Rovigatti, Lorenzo, Schreck, John S, Harrison, Ryan M, Smith, William P. J

“…Phys. Chem. Chem. Phys. 15, 20395-20414 (2013) To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained…”
Get full text

Simulating large dna nanostructures with a coarse-grained model by Snodin, Benedict E. K

“…In this thesis we investigate the self-assembly and structural properties of DNA origamis, which are large-scale DNA nanostructures comprising thousands of DNA…”
Get full text

The oxDNA coarse-grained model as a tool to simulate DNA origami by Doye, Jonathan P. K, Fowler, Hannah, Prešern, Domen, Bohlin, Joakim, Rovigatti, Lorenzo, Romano, Flavio, Šulc, Petr, Wong, Chak Kui, Louis, Ard A, Schreck, John S, Engel, Megan C, Matthies, Michael, Benson, Erik, Poppleton, Erik, Snodin, Benedict E. K

“…This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model…”
Get full text