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

Abstract

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 summaryProgram Title: Brownian Disks Lab (BDL)Program Files doi:http://dx.doi.org/10.17632/dbwzdkttkb.1Licensing provisions: GPLv3Programming 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 time-lapsed images stored. We need an application to generate an ideal real-time motion of colloidal objects in a simple fluid, providing the position of the particles without the need of image analysis. This software should allow to inspect, before the experiments, the general behavior of a colloidal fluid, including visual inspection of the particles’ movement. Using this application, we should be able to analyze the collective motion of the Brownian objects, the influence of different inter-particle forces, and the limitations of the experimental setup, e.g., the effect of image analysis in the results obtained.Solution method: BDL performs the simulation of Brownian 2D disks contained in a transparent medium with a constant viscosity value. The theoretical scheme allows us to introduce external forces in the disks for testing different experimental conditions, and the interactions observed in experiments on colloidal physics (Einstein, 1905; Xin et al., 2016). We use a computational multi-platform environment without high computing requirements since a small number of particles (n≤500) and small concentrations are typical of time-lapse microscopy experiments. The output data is analogous to a video-microscopy setup: the required statistical quantities can be later calculated from the particles’ positions using microrheology standard algorithms (Bevan and Eichmann, 2011). BDL has been developed using Easy Java/JavaScript Simulations (EjsS) (Dinsmore et al., 2002), a software which allows to simplify the code generation and the visualization of simulated objects. Java allows to run the software in any SO without compilation or installation as long as Java Runtime Environment (JRE) is previously installed in the computer.Additional comments including restrictions and unusual features: Requires SO with Java Runtime Environment (JRE) installed.[1] P. Domínguez-García, Europhys. J. E. Soft. Matter. 35, p. 73, 2012.[2] P. Domínguez-García and M. A. Rubio, Appl. Phys. Lett. 102, p. 074101, 2013.[3] M. Pancorbo, M. A. Rubio, P. Domínguez-García, Procedia Comp. Sci.. 108, p. 166–174, 2017.[4] J. C. Crocker and D. G. Grier, J. Colloid Interface Sci. 179, p. 298–310, 1996.