From 08d456f2ef890347549544ebdd4525ee378c6916 Mon Sep 17 00:00:00 2001
From: "robin.koehler" <robin.koehler@synmikro.mpi-marburg.mpg.de>
Date: Wed, 13 Jul 2022 15:02:59 +0000
Subject: [PATCH] Update README.md

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 README.md | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

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-It is an extended version of the DNA-relay model . Its extend 
-
-
+<h4>Hopping and Relay</h4>
+<h6>Description</h6>
 The repository contains a computation model of the ParABS. It is an extension of the previous DNA-relay model (Surovtsev IV, Campos M, Jacobs-wagner C. 2016a. DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos. Proc Natl Acad Sci E7268–E7276. doi:10.1073/pnas.1616118113) that incorporates diffusion on the nucleoid (hopping) and basal hydrolysis of ParA-ATP and uses analytic expressions for the fluctuations rather than a second order approximation. Like the DNA relay it is a 2D off-lattice stochastic model and updates positions in discrete time steps dt. The implementation was written in C++. It consists of the following components. ParA associates to the DNA non-specifically in its ATP-dependent dimer state with the rate ka. Once associated, ParA (i.e. ParA-ATP dimers) moves in two distinct ways: (i) Diffusive motion on the nucleoid with the diffusion coefficient D_H. This is an effective description of the movement of dimers due to transient unbinding events or direct contact between DNA strands that allow it to ‘hop’ between DNA-strands. (ii) Between hopping events, each bound ParA dimer experiences the elastic fluctuations of the DNA strand it is bound to. This is implemented as elastic (spring-like) fluctuations around its initial position. Dimers dissociate from the nucleoid due to either basal ATP hydrolyse at a rate k_d or due to hydrolysis stimulated by ParB on the plasmid. The latter is modelled as a ParB-coated disc and ParB-ParA tethers form whenever the disk comes in contact with a ParA dimer. ParB-stimulated hydrolysis then breaks these tethers at a rate  k_off, returning ParA to the cytosolic pool. The plasmid experiences the elastic force of every tethered ParA and moves according the its intrinsic diffusion coefficient Dp and the resultant force of all tethers. As in the DNA relay model we have made some simplifications that we next make explicit. First, we only modelled three states of ParA: 'nucleoid associated' and 'cytosolic' and 'tethered'. Second, cytosolic ParA are assumed to be well mixed. This is justified based on the slow conformation changes needed to return it to a state competent for DNA-binding (Vecchiarelli et al., 2010). Third, no individual ParB molecules were modelled, rather the plasmid is treated as a disk coated with enough ParB that each nucleoid bound ParA that makes contact with the plasmid instantaneously finds a ParB partner, therefore removing the need to model individual ParB. This is justified by the substantially higher local concentration of ParB compared to ParA at the plasmid. The nucleoid is modelled as a rectangle with the dimensions w0 x l0.
 
 
-
+<h6>Parameters</h6>
 The model excepts following parameters:
 
 -run [string] Part of the name of the output file (default: "0")<br>
@@ -30,4 +29,11 @@ The model excepts following parameters:
 -s_ParA Save the loacation of all nucleoid bound ParA<br>
 -dormant [float] The simulation starts with one active plasmid. After the given amount of time an extra plasmid is added at the location of the first plasmid. This is repeated until the max number of plasmids is reached (n_pc). Afterwards one plasmid is removed after the specified time interval<br>
 
-Example: ./dna_relay /Path/To/Output/Directory task 1 run 1 -l0 0.9 -w0 2.6 -n_pc 5 -t_end 7200 -n_pa 500 -k_d 0.01 -D_H 0.05676 -k_off 1 -k_a 0.01 -D_P 0.003 -r_s filler -dormant 600 -c_e 60
+<h6>Execution</h6>
+After compiling the model can be run as follows: ./dna_relay /Path/To/Output/Directory/ task 42 run 69 -l0 0.9 -w0 2.6 -n_pc 5 -t_end 7200 -n_pa 500 -k_d 0.01 -D_H 0.05676 -k_off 1 -k_a 0.01 -D_P 0.003 -r_s filler -dormant 600 -c_e 60<br>
+This create two files in the directory /Path/To/Output/Directory/ names as follow:<br>
+output_00043_timestamp.csv<br>
+parameters_00043_timestamp.txt<br>
+Output contains for each partition complex 9 columns:<br>
+position vector x, position vector y,force vector x, force vector y, is dormant, number of nucleoid bound ParA, number of ParA bound to this partition complex, number of ParA hydrolized by basal hydrolysis, number of ParA hydrolized at this parition complex
+
-- 
GitLab