Simulating large DNA nanostructures with a coarse-grained model

Simulating large DNA nanostructures with a coarse-grained model

<p>In this thesis we investigate the self-assembly and structural properties of DNA origamis, which are large-scale DNA nanostructures comprising thousands of DNA base pairs, using the coarse-grained model of DNA called oxDNA.</p> <p>We use simulations of oxDNA, with both a "...

Disgrifiad llawn

Manylion Llyfryddiaeth
Prif Awdur:	Snodin, B
Awduron Eraill:	Doye, J
Fformat:	Traethawd Ymchwil
Cyhoeddwyd:	2016

Eitemau Tebyg

Coarse-graining DNA for simulations of DNA nanotechnology.
gan: Doye, J, et al.
Cyhoeddwyd: (2013)

Coarse-grained modelling of the structural properties of DNA origami
gan: Snodin, B, et al.
Cyhoeddwyd: (2019)

Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
gan: Sharma, R, et al.
Cyhoeddwyd: (2017)

Coarse-grained simulations of DNA overstretching.
gan: Romano, F, et al.
Cyhoeddwyd: (2013)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
gan: Snodin, B, et al.
Cyhoeddwyd: (2015)

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
gan: Schreck, J, et al.
Cyhoeddwyd: (2016)

Coarse-grained modeling of DNA and DNA nanotechnology
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2012)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
gan: Šulc, P, et al.
Cyhoeddwyd: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
gan: Sulc, P, et al.
Cyhoeddwyd: (2012)

Coarse-grained modelling of DNA and DNA self-assembly
gan: Ouldridge, T
Cyhoeddwyd: (2011)

Coarse-grained modelling of DNA-RNA hybrids
gan: Ratajczyk, EJ, et al.
Cyhoeddwyd: (2023)

Coarse-Grained Modelling of Extreme DNA Bending
gan: Harrison, R, et al.
Cyhoeddwyd: (2014)

Bottom-up coarse-grained modeling of DNA
gan: Sun, Tiedong, et al.
Cyhoeddwyd: (2021)

DNA nanotweezers studied with a coarse-grained model of DNA.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2010)

DNA nanotweezers studied with a coarse-grained model of DNA
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2010)

A coarse-grained bonded particle model for large-scale rock simulation
gan: Chengshun Shang, et al.
Cyhoeddwyd: (2024-10-01)

Simulation data associated with "Coarse-grained modelling of the structural properties of DNA origami"
gan: Schreck, J
Cyhoeddwyd: (2018)

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models
gan: Mohsen Sadeghi, et al.
Cyhoeddwyd: (2020-06-01)

Sequence-dependent thermodynamics of a coarse-grained DNA model.
gan: Šulc, P, et al.
Cyhoeddwyd: (2012)

Coarse-grained modelling of a DNA origami force sensor
gan: Sen, N
Cyhoeddwyd: (2021)

A coarse-grained DNA model parameterized from atomistic simulations by inverse Monte Carlo
gan: Korolev, Nikolay, et al.
Cyhoeddwyd: (2014)

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
gan: Cheng Tan, et al.
Cyhoeddwyd: (2022-04-01)

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2011)

Influence of ionic conditions on knotting in a coarse-grained model for DNA
gan: Sarah Wettermann, et al.
Cyhoeddwyd: (2023-01-01)

Study on the Surface Modification of Nanostructured Ti Alloys and Coarse-Grained Ti Alloys
gan: Hsuan-Kai Lin, et al.
Cyhoeddwyd: (2022-05-01)

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
gan: Rodrigo V. Honorato, et al.
Cyhoeddwyd: (2019-10-01)

Coarse-grained molecular dynamics simulations of biomolecules
gan: Ken Takahashi, et al.
Cyhoeddwyd: (2014-03-01)

Coarse-grained molecular dynamics simulations of biomolecules
gan: Ken Takahashi, et al.
Cyhoeddwyd: (2014-03-01)

Data-driven coarse graining of large biomolecular structures.
gan: Yi-Ling Chen, et al.
Cyhoeddwyd: (2017-01-01)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2013)

A Coarse Grained Model for Viscoelastic Solids in Discrete Multiphysics Simulations
gan: Iwan H. Sahputra, et al.
Cyhoeddwyd: (2020-05-01)

A Coarse-Grained Molecular Model for Simulating Self-Healing of Bitumen
gan: Liang He, et al.
Cyhoeddwyd: (2022-10-01)

Exploring peptide-membrane interactions with coarse-grained MD simulations.
gan: Hall, B, et al.
Cyhoeddwyd: (2011)

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin
gan: Jules Nde, et al.
Cyhoeddwyd: (2021-08-01)

Coarse-grained modelling of nucleic acids
gan: Sulc, P
Cyhoeddwyd: (2014)

Coarse-grained modelling of supercoiled RNA
gan: Matek, C, et al.
Cyhoeddwyd: (2015)

Towards coarse-grained modelling of proteins
gan: M.Stepanova
Cyhoeddwyd: (2007-09-01)

Coarse-Graining of Observables
gan: Stan Gudder
Cyhoeddwyd: (2022-10-01)

Exploration of DNA systems under internal and external forcing using coarse-grained modelling
gan: Engel, M
Cyhoeddwyd: (2018)

Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
gan: Doye, JPK, et al.
Cyhoeddwyd: (2022)