User contributions for Sulc

17 March 2014

• 18:4118:41, 17 March 2014 diff hist +3,795‎ N DNA model introduction ‎ Created page with "The model treats DNA as a string of rigid nucleotides, which interact through potentials which depend on the position and orientation of the nucleotides. The interactions are: #S…"
• 18:4018:40, 17 March 2014 diff hist +30‎ Main Page ‎No edit summary
• 18:3918:39, 17 March 2014 diff hist +6,067‎ N RNA model introduction ‎ Created page with "===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 approa…"
• 18:3818:38, 17 March 2014 diff hist −43‎ Features of the previous version ‎No edit summary
• 18:3718:37, 17 March 2014 diff hist +4‎ Publications ‎No edit summary
• 18:3618:36, 17 March 2014 diff hist +24‎ Main Page ‎No edit summary
• 18:3618:36, 17 March 2014 diff hist +2,778‎ N Previous version ‎ Created page with " In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed or supported, but th…"

11 March 2014

• 16:5116:51, 11 March 2014 diff hist 0‎ Model introduction ‎ →‎Simulation units
• 16:5016:50, 11 March 2014 diff hist 0‎ Model introduction ‎No edit summary
• 16:4116:41, 11 March 2014 diff hist +4‎ RNA duplex melting ‎ →‎Introduction
• 16:4116:41, 11 March 2014 diff hist 0‎ RNA duplex melting ‎ →‎Introduction
• 16:4116:41, 11 March 2014 diff hist 0‎ RNA duplex melting ‎No edit summary
• 16:4116:41, 11 March 2014 diff hist −46‎ RNA duplex melting ‎No edit summary
• 16:4016:40, 11 March 2014 diff hist +23‎ N File:Melting.png ‎ Melting of an RNA 8-mer current
• 16:2016:20, 11 March 2014 diff hist +6‎ RNA duplex melting ‎ →‎Introduction
• 16:1916:19, 11 March 2014 diff hist 0‎ RNA duplex melting ‎ →‎Introduction
• 16:1916:19, 11 March 2014 diff hist +112‎ RNA duplex melting ‎ →‎Introduction
• 15:5115:51, 11 March 2014 diff hist −1‎ RNA duplex melting ‎No edit summary
• 15:5115:51, 11 March 2014 diff hist +26‎ RNA duplex melting ‎ →‎Introduction
• 15:5015:50, 11 March 2014 diff hist 0‎ N File:Arrow.png ‎No edit summary current
• 15:4715:47, 11 March 2014 diff hist 0‎ RNA duplex melting ‎No edit summary
• 15:4715:47, 11 March 2014 diff hist +33‎ RNA duplex melting ‎No edit summary
• 15:4615:46, 11 March 2014 diff hist +2‎ RNA duplex melting ‎ →‎Introduction
• 15:4615:46, 11 March 2014 diff hist +17‎ RNA duplex melting ‎ →‎Introduction
• 15:4515:45, 11 March 2014 diff hist +30‎ N File:RNA8M.png ‎ An image of a melted RNA 8-mer current
• 15:4415:44, 11 March 2014 diff hist +18‎ N File:RNA8D.png ‎ A formed RNA 8-mer current
• 15:3615:36, 11 March 2014 diff hist +37‎ N File:Image 8.png ‎ A formed RNA duplex with 8 base pairs current
• 15:3515:35, 11 March 2014 diff hist +30‎ N File:Image melt.png ‎ An image of a melted RNA 8-mer current
• 15:2415:24, 11 March 2014 diff hist +1‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:2415:24, 11 March 2014 diff hist +7‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:2315:23, 11 March 2014 diff hist +5‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1915:19, 11 March 2014 diff hist +1‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1915:19, 11 March 2014 diff hist −8‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1815:18, 11 March 2014 diff hist +6‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1815:18, 11 March 2014 diff hist −15‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1815:18, 11 March 2014 diff hist +133‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1615:16, 11 March 2014 diff hist +2‎ RNA duplex melting ‎ →‎Data evaluation and estimation of the melting temperature
• 15:1515:15, 11 March 2014 diff hist +1‎ RNA duplex melting ‎ →‎Setting the order parameters and weights
• 15:1315:13, 11 March 2014 diff hist +286‎ RNA duplex melting ‎No edit summary
• 14:5914:59, 11 March 2014 diff hist +2‎ RNA model ‎ →‎Running simulation with the oxRNA model
• 14:1114:11, 11 March 2014 diff hist 0‎ RNA model ‎ →‎Running simulation with the oxRNA model
• 14:1014:10, 11 March 2014 diff hist +277‎ RNA model ‎No edit summary
• 13:5713:57, 11 March 2014 diff hist +501‎ RNA duplex melting ‎No edit summary
• 13:5113:51, 11 March 2014 diff hist +62‎ RNA duplex melting ‎No edit summary
• 13:5013:50, 11 March 2014 diff hist +1,067‎ RNA duplex melting ‎No edit summary
• 13:1613:16, 11 March 2014 diff hist +858‎ RNA duplex melting ‎No edit summary
• 13:0113:01, 11 March 2014 diff hist +2,224‎ RNA duplex melting ‎No edit summary

10 March 2014

• 20:1120:11, 10 March 2014 diff hist +9‎ RNA duplex melting ‎No edit summary
• 19:5719:57, 10 March 2014 diff hist +2,548‎ RNA duplex melting ‎No edit summary
• 19:0919:09, 10 March 2014 diff hist −3‎ RNA model ‎No edit summary
• 19:0819:08, 10 March 2014 diff hist +4‎ RNA model ‎No edit summary
• 19:0719:07, 10 March 2014 diff hist −24‎ RNA model ‎No edit summary
• 19:0619:06, 10 March 2014 diff hist +3‎ RNA model ‎No edit summary
• 19:0519:05, 10 March 2014 diff hist −1‎ RNA model ‎No edit summary
• 19:0419:04, 10 March 2014 diff hist −14‎ RNA model ‎No edit summary
• 19:0419:04, 10 March 2014 diff hist +1‎ RNA model ‎No edit summary
• 19:0219:02, 10 March 2014 diff hist +59‎ RNA model ‎No edit summary
• 19:0019:00, 10 March 2014 diff hist +40‎ RNA model ‎No edit summary
• 18:5818:58, 10 March 2014 diff hist +1,806‎ RNA model ‎No edit summary
• 17:4017:40, 10 March 2014 diff hist −19‎ RNA model ‎No edit summary
• 17:3817:38, 10 March 2014 diff hist +1,818‎ RNA model ‎No edit summary
• 13:2413:24, 10 March 2014 diff hist +27‎ RNA model ‎No edit summary

9 March 2014

• 16:4616:46, 9 March 2014 diff hist +1‎ RNA duplex melting ‎No edit summary
• 16:4616:46, 9 March 2014 diff hist +22‎ RNA duplex melting ‎No edit summary
• 16:4216:42, 9 March 2014 diff hist +948‎ N RNA duplex melting ‎ Created page with "==Introduction== This example shows how our code can be used to calculate melting temperature of an RNA duplex (8-mer) using the Virtual Move Monte Carlo (VMMC) algorithm. The c…"

6 March 2014

• 18:0918:09, 6 March 2014 diff hist −1‎ RNA model ‎No edit summary
• 18:0818:08, 6 March 2014 diff hist +2,000‎ N RNA model ‎ Created page with "The RNA model, oxRNA, treats each RNA nucleotide as a single rigid body with multiple interaction sites, following the coarse-graining apporach adopted for the DNA model. The nu…"
• 18:0318:03, 6 March 2014 diff hist +59‎ N File:Image duplex combined annotated.png ‎ A schematic illustration of interactions in the oxRNA model current

20 January 2014

• 12:5712:57, 20 January 2014 diff hist +331‎ Publications ‎No edit summary

13 November 2013

• 16:2216:22, 13 November 2013 diff hist +101‎ Publications ‎No edit summary

19 October 2013

• 14:0014:00, 19 October 2013 diff hist +12‎ Main Page ‎No edit summary
• 13:5713:57, 19 October 2013 diff hist +1‎ Main Page ‎No edit summary
• 13:5713:57, 19 October 2013 diff hist +13‎ Main Page ‎No edit summary
• 13:5613:56, 19 October 2013 diff hist +6‎ Main Page ‎No edit summary
• 13:5413:54, 19 October 2013 diff hist +80‎ Main Page ‎No edit summary

9 September 2013

• 17:1017:10, 9 September 2013 diff hist +332‎ Publications ‎No edit summary

2 September 2013

• 22:0622:06, 2 September 2013 diff hist +2‎ Publications ‎No edit summary
• 22:0522:05, 2 September 2013 diff hist +83‎ Publications ‎No edit summary

22 August 2013

• 22:3422:34, 22 August 2013 diff hist +13‎ Publications ‎No edit summary
• 22:3322:33, 22 August 2013 diff hist +249‎ Publications ‎No edit summary
• 22:3022:30, 22 August 2013 diff hist +86‎ Publications ‎No edit summary

19 July 2013

• 05:2705:27, 19 July 2013 diff hist −41‎ Features of the previous version ‎ →‎Experimental (Unsupported) features

5 April 2013

• 13:0713:07, 5 April 2013 diff hist −36‎ Contact information ‎No edit summary
• 13:0613:06, 5 April 2013 diff hist +36‎ Contact information ‎No edit summary
• 13:0413:04, 5 April 2013 diff hist −26‎ Contact information ‎No edit summary
• 13:0413:04, 5 April 2013 diff hist −5‎ Contact information ‎No edit summary
• 13:0313:03, 5 April 2013 diff hist +31‎ Contact information ‎No edit summary

15 March 2013

• 13:3313:33, 15 March 2013 diff hist +204‎ Publications ‎No edit summary

5 March 2013

• 13:1613:16, 5 March 2013 diff hist +4‎ Documentation ‎ →‎pdb format

20 December 2012

• 12:1612:16, 20 December 2012 diff hist 2,245 bytes Publications ‎No edit summary

12 December 2012

• 14:5314:53, 12 December 2012 diff hist 24,357 bytes Documentation ‎ →‎String
• 14:5214:52, 12 December 2012 diff hist 24,359 bytes Documentation ‎ →‎Repulsion plane
• 14:5114:51, 12 December 2012 diff hist 24,358 bytes Documentation ‎ →‎Repulsion plane

2 October 2012

• 10:5310:53, 2 October 2012 diff hist 3,768 bytes Model introduction ‎No edit summary
• 10:5210:52, 2 October 2012 diff hist 3,653 bytes Model introduction ‎No edit summary

11 September 2012

• 19:0919:09, 11 September 2012 diff hist 1,746 bytes Main Page ‎ →‎Acknowledgments

7 September 2012

• 00:0600:06, 7 September 2012 diff hist 24,441 bytes Documentation ‎ →‎Generation of initial configurations
• 00:0600:06, 7 September 2012 diff hist 24,445 bytes Documentation ‎ →‎Generation of initial configurations

23 July 2012

• 18:3518:35, 23 July 2012 diff hist 3,739 bytes Model introduction ‎No edit summary
• 18:3418:34, 23 July 2012 diff hist 3,546 bytes Model introduction ‎No edit summary