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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 ================================== The .zip file contains the following folders: DNA_sequence_LAMMPS: DNAsequence.txt: this is the LAMMPS data file. It contains the DNA sequence employed for the study. DSB_input_datafile Containing the binary LAMMPS data file that are employed as starting point for the DSB MD simulations. Each file contains the DNA molecule at a certain end-to-end distance (that gives also le name to the binary file). DSB_MD_simulation 0_MD_LAMMPS: Containing the LAMMPS simulation scripts. The subfolders are organized according to the logic of the study: for each DNA extension (folders named 1000, 1100, …, 1300), we investigated different DSB motifs (folders named 0,1, …,4). 1_DSB_raw_data Containing the relevant information about the MD trajectories. The files are named as “out_Ree_bd_n.mat”, where Ree is the DNA end-to-end distance, bd is the DSB distance and the index n=1,…,Nt where Nt is the total number of independent MD runs. Each “out”-file contains: i) “free-energy”, which is the internal energy contribution of those nucleotides between the breaks, and ii) POS_left/right_branch, matrices that provide the ids and the positions (xyz) of the nucleotides in the break, along trajectory. To better understand the distinction between “left/right”, see section “Assessment of the residual contact interface of the DSBs at the rupture time” in the Supplementary data. Finally, “POS_time” contains the length of the simulation run (step*dt). 2_Analysis_scripts Containing the employed analysis scripts. In folder 1_SigmoidalFitting, we provide the scripts that perform a sigmoidal fitting procedure [1] on the internal energy profile of the nucleotides between the strand breaks. Each script saves i) the internal energy barriers (activation_free_energy) and ii) breaking times (breaking_time) of all MD simulations characterized by a certain (Ree,bd). Finally, i) and ii) are averaged thus, in iii) dE and iv) tau_b we report the respective mean value and standard deviation. It is possible to find all data in 3_DSB_proc_data. [1] R P (2022).sigm_fit(https://www.mathworks.com/matlabcentral/fileexchange/42641-sigm_fit), MATLAB Central File Exchange. RetrievedJuly 2, 2022. 2_DsbDistanceAnalysis contains the scripts that generate the interaction matrices (in subfolder 1_interaction_matrix) that are employed in the subfolder 2_correlation_BreakTime_NucleotidesDistances. For additional details about the analysis, reference section “Analysis of the residual interactions at the characteristic time of a DSB rupture” of the article. The scripts “fitting_bd#_DSB_dist_interaction.m” produce “IntMatrix_Ree_bd.mat” data files in which are contained i) “interaction_matrix_avg”, representing the average values of the interactions in the bound state of the DNA molecule, and ii) “interaction_matrix_atBreak”, containing the relative distances of all nucleotides at the breaking time for all independent MD simulations characterized by a certain (Ree,bd). 3_DSB_proc_data The data contained in 1_DSB_raw_data are processed by the scripts in 3_Analysis_scripts and saved in 3_DSB_proc_data. For further details, see the the description of 2_Analysis_scripts. TimeScaling 0_MD_LAMMPS Here we provide the LAMMPS script employed to compute the diffusion coefficient of the 3855-bp DNA molecule. Specifically, we acquire the mean-squared-dispalcement (MSD) from which it is possible to extract the diffusion coefficient. 1_Diffusion_data Contains the MSDs for each independent simulation. NB: most data are saved according to the format .mat,used by MATLAB, a numerical computing environment and proprietary programming language developed by MathWorks. |
