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 "...

Cur síos iomlán

Sonraí bibleagrafaíochta
Príomhchruthaitheoir:	Snodin, B
Rannpháirtithe:	Doye, J
Formáid:	Tráchtas
Foilsithe / Cruthaithe:	2016

Míreanna comhchosúla

Coarse-graining DNA for simulations of DNA nanotechnology.
de réir: Doye, J, et al.
Foilsithe / Cruthaithe: (2013)

Coarse-grained modelling of the structural properties of DNA origami
de réir: Snodin, B, et al.
Foilsithe / Cruthaithe: (2019)

Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
de réir: Sharma, R, et al.
Foilsithe / Cruthaithe: (2017)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
de réir: Snodin, B, et al.
Foilsithe / Cruthaithe: (2015)

Coarse-grained simulations of DNA overstretching.
de réir: Romano, F, et al.
Foilsithe / Cruthaithe: (2013)

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
de réir: Schreck, J, et al.
Foilsithe / Cruthaithe: (2016)

Coarse-grained modeling of DNA and DNA nanotechnology
de réir: Ouldridge, T, et al.
Foilsithe / Cruthaithe: (2012)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
de réir: Šulc, P, et al.
Foilsithe / Cruthaithe: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
de réir: Sulc, P, et al.
Foilsithe / Cruthaithe: (2012)

Coarse-grained modelling of DNA and DNA self-assembly
de réir: Ouldridge, T
Foilsithe / Cruthaithe: (2011)

Coarse-grained modelling of DNA-RNA hybrids
de réir: Ratajczyk, EJ, et al.
Foilsithe / Cruthaithe: (2023)

Coarse-Grained Modelling of Extreme DNA Bending
de réir: Harrison, R, et al.
Foilsithe / Cruthaithe: (2014)

Bottom-up coarse-grained modeling of DNA
de réir: Sun, Tiedong, et al.
Foilsithe / Cruthaithe: (2021)

A coarse-grained bonded particle model for large-scale rock simulation
de réir: Chengshun Shang, et al.
Foilsithe / Cruthaithe: (2024-10-01)

DNA nanotweezers studied with a coarse-grained model of DNA.
de réir: Ouldridge, T, et al.
Foilsithe / Cruthaithe: (2010)

DNA nanotweezers studied with a coarse-grained model of DNA
de réir: Ouldridge, T, et al.
Foilsithe / Cruthaithe: (2010)

Simulation data associated with "Coarse-grained modelling of the structural properties of DNA origami"
de réir: Schreck, J
Foilsithe / Cruthaithe: (2018)

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models
de réir: Mohsen Sadeghi, et al.
Foilsithe / Cruthaithe: (2020-06-01)

Sequence-dependent thermodynamics of a coarse-grained DNA model.
de réir: Šulc, P, et al.
Foilsithe / Cruthaithe: (2012)

Coarse-grained modelling of a DNA origami force sensor
de réir: Sen, N
Foilsithe / Cruthaithe: (2021)

A coarse-grained DNA model parameterized from atomistic simulations by inverse Monte Carlo
de réir: Korolev, Nikolay, et al.
Foilsithe / Cruthaithe: (2014)

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

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
de réir: Ouldridge, T, et al.
Foilsithe / Cruthaithe: (2011)

Influence of ionic conditions on knotting in a coarse-grained model for DNA
de réir: Sarah Wettermann, et al.
Foilsithe / Cruthaithe: (2023-01-01)

Study on the Surface Modification of Nanostructured Ti Alloys and Coarse-Grained Ti Alloys
de réir: Hsuan-Kai Lin, et al.
Foilsithe / Cruthaithe: (2022-05-01)

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
de réir: Choon-Peng Chng, et al.
Foilsithe / Cruthaithe: (2008-03-01)

Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
de réir: Lee-Wei Yang, et al.
Foilsithe / Cruthaithe: (2008-01-01)

Coarse-grained molecular dynamics simulations of biomolecules
de réir: Ken Takahashi, et al.
Foilsithe / Cruthaithe: (2014-03-01)

Coarse-grained molecular dynamics simulations of biomolecules
de réir: Ken Takahashi, et al.
Foilsithe / Cruthaithe: (2014-03-01)

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
de réir: Rodrigo V. Honorato, et al.
Foilsithe / Cruthaithe: (2019-10-01)

Data-driven coarse graining of large biomolecular structures.
de réir: Yi-Ling Chen, et al.
Foilsithe / Cruthaithe: (2017-01-01)

A Coarse Grained Model for Viscoelastic Solids in Discrete Multiphysics Simulations
de réir: Iwan H. Sahputra, et al.
Foilsithe / Cruthaithe: (2020-05-01)

A Coarse-Grained Molecular Model for Simulating Self-Healing of Bitumen
de réir: Liang He, et al.
Foilsithe / Cruthaithe: (2022-10-01)

Protein-DNA docking with a coarse-grained force field
de réir: Setny Piotr, et al.
Foilsithe / Cruthaithe: (2012-09-01)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
de réir: Ouldridge, T, et al.
Foilsithe / Cruthaithe: (2013)

Exploring peptide-membrane interactions with coarse-grained MD simulations.
de réir: Hall, B, et al.
Foilsithe / Cruthaithe: (2011)

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin
de réir: Jules Nde, et al.
Foilsithe / Cruthaithe: (2021-08-01)

Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models
de réir: Genki Shino, et al.
Foilsithe / Cruthaithe: (2021-11-01)

Coarse-grained modelling of nucleic acids
de réir: Sulc, P
Foilsithe / Cruthaithe: (2014)

Coarse-grained modelling of supercoiled RNA
de réir: Matek, C, et al.
Foilsithe / Cruthaithe: (2015)