DOI: 10.25442/hku.28152986
title: Supporting data for "Fracture and Non-linear Response of Biopolymer Network with Dynamic Cross-linkers"

description: This data set provides comprehensive supporting data for the thesis titled "Fracture and Non-linear Response of Biopolymer Network with Dynamic Cross-linkers." It encompasses a wide array of computational simulations and analyses, meticulously documenting the mechanical behavior of biopolymer networks, with a particular focus on the intricate dynamics of dynamic cross-linkers within these networks.Research Context and ObjectivesBiopolymer networks, such as the cytoskeleton and hydrogels, are of paramount importance in both living organisms and biomaterial systems, exhibiting strikingly similar physical properties. Characterized by their semiflexible nature and robust resistance to external loading, these networks have been extensively studied through various simulation methods and experimental approaches. However, certain aspects of their behavior remain enigmatic. The impact of micro-cracks on the deformation and fracture response of these networks is not yet fully understood, and the mechanics governing the movement and aggregation of slide-ring crosslinkers within the network, along with their influence on the network's bulk mechanical properties, have thus far eluded comprehensive comprehension. This research aims to bridge these knowledge gaps by developing and employing a sophisticated computational model that accurately accounts for large deformations, thermal fluctuations, and forced crosslink breaking. This model enables a deeper exploration of the network's mechanical behavior under diverse conditions, shedding light on the complex interplay between microstructural features and macroscopic properties.Data Set Composition and StructureThe data set comprises a meticulously organized collection of files, each serving a specific purpose in documenting the simulation process and results. A text file named 'NodeRan.txt' is included, which contains the coordinates and angles of the nodes and segments constituting the filament network. This file is generated through a series of computational processes that involve the random placement of filaments, periodic boundary rearrangement, and precise calculation of crosslink locations. A MATLAB script is also provided, outlining the methodology for generating the network. It details the input parameters, such as line density and crosslink number, as well as the algorithms employed for filament arrangement and crosslink determination. Complementing this, a histogram figure is generated to visualize the distribution of angles between connected filament segments, offering valuable insights into the network's structural orientation and connectivity patterns. Furthermore, the data set includes multiple text files, each containing specific information pertinent to the simulation. The 'input-3.txt' file encapsulates the initial configuration of the network, encompassing node coordinates, element connectivity, and boundary conditions. The 'control-3.txt' file delineates the simulation parameters, including material properties, time step, strain rate, and thermal fluctuations. Initial displacements of the nodes are recorded in the 'initial-test-3.txt' file . Displacements of the nodes at each time step are meticulously documented in the 'Output-disp.txt' file, while the 'Output-force-r-shear.txt' and 'Output-force.txt' files store the reaction forces and internal forces, respectively. Additional files are dedicated to monitoring the breaking of crosslinks ('break.txt') and counting the number of broken crosslinks ('count.txt'). The 'y12m-3.txt' file provides information about the neighbor nodes and their connectivity, and the 'ite.txt' file records the iteration count during the simulation. Finally, the 'Output-disp-last.txt' file stores the final displacements of the nodes.