Brownian Disks Lab: Simulating time-lapse microscopy experiments for exploring microrheology techniques and colloidal interactions

Brownian Disks Lab (BDL) is a Java-based application for the real-time generation and visualization of the motion of two-dimensional Brownian disks using Brownian Dynamics (BD) simulations. This software is designed to emulate time-lapse microscopy experiments of colloidal fluids in quasi-2D situations, such as sedimented layers of particles, optical trap confinement, or fluid interfaces. Microrheology of bio-inspired fluids through optical-based techniques such as videomicroscopy is a classic tool for obtaining the mechanical properties and molecular behavior of these materials. The results obtained by microrheology notably depend of the time-lapse value of the videomicroscopy setup, therefore, a tool to test the influence of the lack of statistics by simulating Brownian objects in experimental-like situations is needed. We simulate a colloidal fluid by using Brownian Dynamics (BD) simulations, where the particles are subjected to different external applied forces and inter-particle interactions. This software has been tested for the analysis of the microrheological consequences of attractive forces between particles [1], the influence of image analysis on experimental microrheological results [2], and to explore experimental diffusion with optical tweezers [3]. The output results of BDL are directly compatible with the format used by standard microrheological algorithms [4]. In a context of microrheology of complex bio-inspired fluids, we use this tool here to study if the lack of statistics may influence the observed potential of a bead trapped by optical tweezers. Program Title: Brownian Disks Lab (BDL) Program Files doi:http://dx.doi.org/10.17632/dbwzdkttkb.1 Licensing provisions: GPLv3 Programming language: Java (JDK 7 and above) Supplementary material: We provide a detailed user manual which describes how to use BDL, the theoretical basis of Brownian dynamics simulations, the particle–particle interactions implemented in this software, and additional details and explanations regarding the developed code. Nature of problem: By using time-lapse microscopy experiments (video-microscopy), we can observe the Brownian motion of colloidal particles under different particle–particle interactions and external forces. Sedimented quasi-two-dimensional layers, fluid interfaces, or optically trapped particles can be considered as two-dimensional colloidal systems. The centers of mass of the colloidal objects are subsequently obtained by the image analysis of the