Assembly of polyplexes for RNA delivery

This repository contains simulation data, input files, and analysis scripts used to prepare the manuscript "Assembly of polyplexes for RNA delivery" by Jonas Hans Lehnen, Jorge Moreno Herrero, Heinrich Haas, Friederike Schmid, Giovanni Settanni. Directory Structure and Contents Trajectories/ It contains simulation trajectories corresponding to the results presented in the manuscript. For convenience, the trajectories for each simulated condition are provided in separate ZIP archives. The file: `md_tuned.xtc` contains the trajectory (GROMACS xtc format). The GROMACS run input file `md_tuned.tpr` as well as the GROMACS coordinate files `md_tuned.gro` and `em.gro`are also provided. The files `md_tuned_PEI.*` and `md_tuned_RNA.*` are from equilibration simulations of PEI or RNA individually. Subdirectories: `trajectories_lPEI*`: Simulations with different PEI chain lengths and 8 RNA chains. `trajectories_nRNA32/` and `trajectories_nRNA64/`: Simulations with 32 or 64 RNA chains and PEI chains of length 10. `trajectories_merged_start/`: Simulations where PEI is added to a pre-formed nanoparticle (NP). `trajectories_density0*/` : Simulations where RNA concentration is 0.* times the concentration of the other simulations. `Npei*` : Simulations with different amounts of PEI chains SimulationSkripts/ It contains all necessary input files and scripts required to run the simulations. Data/ It contains averaged results across all simulation runs, including: Radius of gyration (Rg) Net charge Zeta potential AnalysisSkripts/ It contains Python scripts used to analyze simulation trajectories. Key Script: `full_analysis_fname.py` to analyze a single trajectoryUsage: python full_analysis_fname.py [PATH_TO_SIMULATION]where [PATH_TO_SIMULATION] is the full path and prefix of the simulation files (i.e. without extension `.tpr` and `.trr`)For example, to analyze the trajectory stored in the files `foo/md_tuned.tpr` and `foo/md_tuned.trr`, the command is: python full_analysis_fname.py "foo/md_tuned"Note: This script can also analyze PEI and RNA counterions, but this feature is disabled by default due to its slow performance and large output size.Hint: Use `full_analysis_fname_xtc.py` to analyze provided `.xtc` trajectory files. 4.1. AnalysisSkripts/Cluster_Analysis/ It contains scripts used to generate aggregated results for (results are show in /DATA): Rg (radius of gyration) Charge Zeta potential Refer to the README file inside this directory for more details. SimulationSkripts/ It contains all necessary scripts to run the simulations. Refer to the README file inside this directory for more details. Notes ----- - All data and scripts are provided as used in the publication to support reproducibility. - For questions or customization of scripts, please refer to the inline comments within each script. """本仓库包含用于支撑论文《用于RNA递送的聚复合物组装》（Assembly of polyplexes for RNA delivery）的模拟数据、输入文件与分析脚本，论文作者为Jonas Hans Lehnen、Jorge Moreno Herrero、Heinrich Haas、Friederike Schmid与Giovanni Settanni。 ## 目录结构与内容 ### Trajectories/ 该目录存储与论文中呈现结果对应的模拟轨迹。为便于使用，每种模拟条件下的轨迹均打包为独立的ZIP压缩文件。 文件`md_tuned.xtc`为采用GROMACS XTC格式编写的轨迹文件。 同时提供GROMACS运行输入文件`md_tuned.tpr`，以及坐标文件`md_tuned.gro`与`em.gro`。 文件`md_tuned_PEI.*`与`md_tuned_RNA.*`源自单独针对聚乙烯亚胺（PEI, Polyethylenimine）或RNA开展的平衡模拟。 #### 子目录 `trajectories_lPEI*`：包含不同PEI链长与8条RNA链的模拟任务。 `trajectories_nRNA32/`与`trajectories_nRNA64/`：包含搭载32条或64条RNA链、且PEI链长为10的模拟任务。 `trajectories_merged_start/`：包含将PEI添加至预形成纳米颗粒（NP, Nanoparticle）的模拟任务。 `trajectories_density0*/`：包含RNA浓度为其余模拟任务浓度0.*倍的模拟任务。 `Npei*`：包含不同PEI链数量的模拟任务。 ### SimulationSkripts/ 该目录包含运行模拟所需的全部输入文件与脚本。 ### Data/ 该目录包含所有模拟运行的平均结果，涵盖： - 回转半径（Rg, Radius of gyration） - 净电荷 - Zeta电位 ### AnalysisSkripts/ 该目录包含用于分析模拟轨迹的Python脚本。 核心脚本：`full_analysis_fname.py`，用于单条轨迹的分析。 使用方法：`python full_analysis_fname.py [PATH_TO_SIMULATION]` 其中`[PATH_TO_SIMULATION]`为模拟文件的完整路径与前缀（即无需添加`.tpr`与`.trr`扩展名）。 例如，若需分析存储于`foo/md_tuned.tpr`与`foo/md_tuned.trr`中的轨迹，执行命令为： `python full_analysis_fname.py "foo/md_tuned"` 注意：该脚本亦可用于分析PEI与RNA抗衡离子，但由于性能开销较大且输出文件体积庞大，该功能默认处于关闭状态。 提示：可使用`full_analysis_fname_xtc.py`分析本仓库提供的`.xtc`格式轨迹文件。 #### 4.1. AnalysisSkripts/Cluster_Analysis/ 该目录包含用于生成聚合结果的脚本（聚合结果已在`/DATA`中展示），涵盖： - 回转半径（Rg） - 电荷 - Zeta电位 详细信息请参阅该目录内的README文件。 ### SimulationSkripts/ 该目录包含运行模拟所需的全部脚本。详细信息请参阅该目录内的README文件。 ## 备注 ----- - 本仓库提供的所有数据与脚本均与论文中使用的版本完全一致，以保障研究结果可复现。 - 若需咨询或自定义脚本，请参阅各脚本内的内嵌注释。