From 0c3a7a60bfb607c80c6b9aacd168fb831fbc4d45 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 12 Aug 2009 20:14:01 -0400 Subject: [PATCH] Removed TODO in favor of BugsEverywhere bugtracking. See http://bugseverywhere.org for details on BE. I also removed the following entry from TODO: maybe histogram without dice rolling for identical domains? since I decided it was a bad idea. Better to focus the simulation on what it's good at. Of course, I may change my mind later and reinstate the issue ;). --- .../0e905254-6b6a-46a7-947f-924491f8bc7d/body | 8 ++++++++ .../0e905254-6b6a-46a7-947f-924491f8bc7d/values | 8 ++++++++ .../8b15d293-08dc-40fb-b71c-93190b5cd433/values | 17 +++++++++++++++++ .../0aca6729-b1ed-4eeb-9347-28dcee29b588/body | 4 ++++ .../0aca6729-b1ed-4eeb-9347-28dcee29b588/values | 8 ++++++++ .../c41489cf-8225-42a5-adf5-ee6761e45bd8/values | 17 +++++++++++++++++ .be/settings | 2 ++ .be/version | 1 + TODO | 11 ----------- 9 files changed, 65 insertions(+), 11 deletions(-) create mode 100644 .be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body create mode 100644 .be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values create mode 100644 .be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values create mode 100644 .be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body create mode 100644 .be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values create mode 100644 .be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values create mode 100644 .be/settings create mode 100644 .be/version delete mode 100644 TODO diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body new file mode 100644 index 0000000..c4f68e0 --- /dev/null +++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/body @@ -0,0 +1,8 @@ +Exponential rising tension (ERT) + f = E0 / alpha ( e^(alpha x) - 1 ) +Enhanced WLC (with stretching) + f = kB T/p { 1/4 [1/(1-x/L-f/K)² - 1] + x/L - f/K } +Enhanced FJC (with stretching) + x/L = [coth(Lk f/ kB T)- kB T/Lk f](1+f/K) +from Leuba & Zlatanova. Biology at the Single-Molecule Level. p13 + diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values new file mode 100644 index 0000000..ddd71e8 --- /dev/null +++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/comments/0e905254-6b6a-46a7-947f-924491f8bc7d/values @@ -0,0 +1,8 @@ +Author: W. Trevor King + + +Content-type: text/plain + + +Date: Thu, 13 Aug 2009 00:13:11 +0000 + diff --git a/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values new file mode 100644 index 0000000..5da6eb0 --- /dev/null +++ b/.be/bugs/8b15d293-08dc-40fb-b71c-93190b5cd433/values @@ -0,0 +1,17 @@ +creator: W. Trevor King + + +reporter: W. Trevor King + + +severity: minor + + +status: open + + +summary: Further tension models + + +time: Thu, 13 Aug 2009 00:12:51 +0000 + diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body new file mode 100644 index 0000000..f020f92 --- /dev/null +++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/body @@ -0,0 +1,4 @@ +$ bin/sawsim -v1 -s A,null -N -s B,null -k A,B,const,1 +sawsim: build/list.c:221: list_element: Assertion `0==1' failed. +Aborted + diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values new file mode 100644 index 0000000..731f294 --- /dev/null +++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/comments/0aca6729-b1ed-4eeb-9347-28dcee29b588/values @@ -0,0 +1,8 @@ +Author: W. Trevor King + + +Content-type: text/plain + + +Date: Wed, 12 Aug 2009 20:46:22 +0000 + diff --git a/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values new file mode 100644 index 0000000..ced2a81 --- /dev/null +++ b/.be/bugs/c41489cf-8225-42a5-adf5-ee6761e45bd8/values @@ -0,0 +1,17 @@ +creator: W. Trevor King + + +reporter: W. Trevor King + + +severity: minor + + +status: open + + +summary: list_element fails when -N eats s argument... + + +time: Wed, 12 Aug 2009 20:46:10 +0000 + diff --git a/.be/settings b/.be/settings new file mode 100644 index 0000000..739d28c --- /dev/null +++ b/.be/settings @@ -0,0 +1,2 @@ +rcs_name: git + diff --git a/.be/version b/.be/version new file mode 100644 index 0000000..990837e --- /dev/null +++ b/.be/version @@ -0,0 +1 @@ +Bugs Everywhere Tree 1 0 diff --git a/TODO b/TODO deleted file mode 100644 index eb0d3be..0000000 --- a/TODO +++ /dev/null @@ -1,11 +0,0 @@ -maybe histogram without dice rolling for identical domains? - -Further tension models: - Exponential rising tension (ERT) - f = E0 / alpha ( e^(alpha x) - 1 ) - Enhanced WLC (with stretching) - f = kB T/p { 1/4 [1/(1-x/L-f/K)² - 1] + x/L - f/K } - Enhanced FJC (with stretching) - x/L = [coth(Lk f/ kB T)- kB T/Lk f](1+f/K) -from Leuba & Zlatanova. Biology at the Single-Molecule Level. p13 - -- 2.26.2