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OxDNA

OxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation analysis framework. It natively supports DNA (oxDNA model), RNA (oxRNA model), Lennard-Jones and patchy particle simulations on both CPUs and NVIDIA GPUs. Groups at the University of Oxford and L. Rovigatti, formerly in the Sciortino. Group in Rome and now in the Likos. For oxDNA at sourcef...

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OxDNA | dna.physics.ox.ac.uk Reviews
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OxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation analysis framework. It natively supports DNA (oxDNA model), RNA (oxRNA model), Lennard-Jones and patchy particle simulations on both CPUs and NVIDIA GPUs. Groups at the University of Oxford and L. Rovigatti, formerly in the Sciortino. Group in Rome and now in the Likos. For oxDNA at sourcef...
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1 main page
2 from oxdna
3 jump to navigation
4 oxdna
5 and louis
6 download and installation
7 features
8 dna model introduction
9 rna model introduction
10 documentation
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OxDNA | dna.physics.ox.ac.uk Reviews

https://dna.physics.ox.ac.uk

OxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation analysis framework. It natively supports DNA (oxDNA model), RNA (oxRNA model), Lennard-Jones and patchy particle simulations on both CPUs and NVIDIA GPUs. Groups at the University of Oxford and L. Rovigatti, formerly in the Sciortino. Group in Rome and now in the Likos. For oxDNA at sourcef...

INTERNAL PAGES

dna.physics.ox.ac.uk dna.physics.ox.ac.uk
1

Changes related to "Main Page" - OxDNA

https://dna.physics.ox.ac.uk/index.php/Special:RecentChangesLinked/Main_Page

Changes related to "Main Page". This is a list of changes made recently to pages linked from a specified page (or to members of a specified category). Pages on your watchlist. This edit created a new page (also see list of new pages. This is a minor edit. This edit was performed by a bot. The page size changed by this number of bytes. Changes in last 1. Show new changes starting from 08:40, 10 March 2017. Show changes to pages linked to the given page instead.

2

RNA model introduction - OxDNA

https://dna.physics.ox.ac.uk/index.php/RNA_model_introduction

Description of the oxRNA model. Running a simulation with the oxRNA model. Visualization of RNA configurations. Description of the oxRNA model. The RNA model, oxRNA, treats each RNA nucleotide as a single rigid body with multiple interaction sites, following the coarse-graining approach adopted for the DNA model. The nucleotides interact with the following pairwise interaction potentials:. Cross-stacking in a duplex. Which are schematically illustrated in the picture:. 1 unit of length. 1 unit of energy.

3

Gallery of studied systems - OxDNA

https://dna.physics.ox.ac.uk/index.php/Gallery_of_studied_systems

Gallery of studied systems. The systems studied with the oxDNA or oxRNA model with the links to the respective papers provided below:. Kissing hairpins (studied with the average model. And the sequence-dependent model. Loop sequence effects on melting temperatures of hairpins. Heterogeneous stacking transition in single strands. Biophysics of strand displacement. Gels made of tetravalent DNA nanostars. Nematic phases formed by short DNA duplexes. Title=Gallery of studied systems&oldid=1000.

4

Previous version - OxDNA

https://dna.physics.ox.ac.uk/index.php/Previous_version

In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed, but the links for the download and installation instructions are provided below for convenience. We note that the 2012 version of oxDNA requires. Software and a C compiler. Before starting, we recall that the features of oxDNA are. Molecular and Brownian dynamics. A stand-alone single- and double-strand generator (. Page contains a more detailed list.

5

Special pages - OxDNA

https://dna.physics.ox.ac.uk/index.php/Special:SpecialPages

Pages with the fewest revisions. Pages without language links. All pages with prefix. Pages with a page property. Login / create account. Recent changes and logs. Gallery of new files. Media reports and uploads. List of files with duplicates. Search for duplicate files. Random page in category. Redirect by file, user, page or revision ID. Pages with the most categories. Pages with the most interwikis. Pages with the most revisions.

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Equal and Opposite Reaction: September 2015

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. This blog is managed by Thomas Ouldridge. A Royal Society University Research Fellow in the Bioengineering Department at Imperial College, London. Contributors include students and collaborators. Subscribe to: Posts (Atom). Follow us on twitter. Systems and Signals Group. Blank On The Map.

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Equal and Opposite Reaction: January 2017

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. Wednesday, 11 January 2017. A simple biomolecular machine for exploiting information. Http:/ journals.aps.org/prl/abstract/10.1103/PhysRevLett.118.028101. Phosphate) there are two phosphates in the chain; in ATP( Adenosine tr. Phosphate) there are three. There’s still a lot to do on this subject; we have...

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Equal and Opposite Reaction: October 2016

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. Thursday, 6 October 2016. Replication, Replication, Replication I. This post and the one below it. Are linked. Here, I discuss a topic that interests us as a group, and below I look at some recent related papers. This post should make reasonable sense in isolation, the second perhaps less so. Semenov et al&#46...

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Equal and Opposite Reaction: November 2016

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. Wednesday, 16 November 2016. Congratulatory post: Hail to the Imperial 2016 iGEM team! With a bit of delay, we as a team would like to join in the congratulations for our colleagues and collaborators from the Imperial 2016 iGEM team, who triumphed at the iGEM 2016 Giant Jamboree at MIT. As a demonstration of t...

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Equal and Opposite Reaction: Replication, Replication, Replication I

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. Thursday, 6 October 2016. Replication, Replication, Replication I. This post and the one below it. Are linked. Here, I discuss a topic that interests us as a group, and below I look at some recent related papers. This post should make reasonable sense in isolation, the second perhaps less so. Blank On The Map.

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Equal and Opposite Reaction: June 2015

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Equal and Opposite Reaction. Highlighting work related to the use of (bio)chemical reactions to achieve sophisticated behaviour such as sensing, signalling, inference, self-assembly and locomotion. Tuesday, 23 June 2015. I'm currently at a conference on Engineering of Chemical Complexity. Hosted by the TUM in Munich. Today we had an interesting talk from Thomas Hermans. On ` dissipative self-assembly". To understand this concept, we need to think about steady states. Tuesday, 16 June 2015. Much of the re...

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OxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation analysis framework. It natively supports DNA (oxDNA model), RNA (oxRNA model), Lennard-Jones and patchy particle simulations on both CPUs and NVIDIA GPUs. Groups at the University of Oxford and L. Rovigatti, formerly in the Sciortino. Group in Rome and now in the Likos. For oxDNA at sourcef...

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