Project files provided as supporting information to the manuscript "Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"

README file to the project files provided as supporting information to the manuscript “Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"

Authors: Manuel Micheloni, Lorenzo Petrolli, Gianluca Lattanzi and Raffaello Potestio
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The .zip file is structured as follows:

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0_DNA_Sequence
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The folder contains:
• DNAsequence.txt: the DNA molecule employed in the study. 
• ecseq.txt: the structure of the DNA. Each nucleotide (LAMMPS residue ID) is associated with the chemical type of the nucleic base.

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1_DSB_MDSimulations
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• MDSimulations: 
The LAMMPS MD simulation scripts.
The subfolders are structured and named after different DSB motifs (folders 0,1, …,3) providing different external forces (folders 1000, 1100, 1200 refers to the respective average end-to-end distance). The latter subfolders provides:

I. LMP_script provides the LAMMPS input file.

II. the local internal energy contributions from the nucleotides involved with the residual contact interface between broken DNA moieties (data/1.E); 

III. coordinates of the nucleotides involved with the residual contact interface between the DNA moieties (data/2.POS);

IV. the binary LAMMPS data file, employed as starting coordinates for the DSB MD simulation (/input_structure).

• ScriptsAndAnalysis:
The scripts employed to analyze the DSB process. 

I. /00_GeneralScripts all the MATLAB functions employed for the analysis.

II. /1_SigmoidalFitting provides the scripts from a sigmoidal fitting procedure [1] on the internal energy profile of the nucleotides between the strand breaks (Section 2 of the Supplementary Material). 
[1] R P (2022). sigm_fit (https://www.mathworks.com/matlabcentral/fileexchange/42641-sigm_fit), MATLAB Central File Exchange. Retrieved July 2, 2022.

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2_DNAFreeDiffusion
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• SIM:
It contains the MD simulations of the freely-diffusing DNA. Namely, the MSD of the DNA molecule, the input structure, and the LAMMPS simulation scripts are reported in /data, /input_structure, and /LMP_scripts respectively.

• ANALYSIS:
It provides the script employed to estimate the diffusion coefficient of the DNA molecule and the time-scaling factor \Gamma(\zeta).

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3_ForceAnalysis
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• data
It contains the forces computed from the MD simulations of the intact DNA molecules subject to the external force of 0.42, 0.88 and 3.06 pN. All data are stored in pickle format.
The README file contains additional information.

NOTE1: Most data/scripts are saved according to the format .mat, employed by MATLAB Ⓡ, a numerical computing environment and proprietary programming language developed by MathWorks.

NOTE2: For the force data manipulation, we acknowledge the use of LammpsFileManipulation package (https://pypi.org/project/LammpsFileManipulation/)