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 summary 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 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. Dominguez-Garcia, Europhys. J. E. Soft. Matter. 35, p. 73, 2012. [2] P. Dominguez-Garcia and M. A. Rubio, Appl. Phys. Lett. 102, p. 074101, 2013. [3] M. Pancorbo, M. A. Rubio, P. Dominguez-Garcia, 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.

中文翻译：

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Brownian Disks Lab：模拟延时显微镜实验以探索微流变学技术和胶体相互作用

摘要 Brownian Disks Lab (BDL) 是一个基于 Java 的应用程序，用于使用布朗动力学 (BD) 模拟实时生成和可视化二维布朗磁盘的运动。该软件旨在模拟准二维情况下胶体流体的延时显微镜实验，例如颗粒沉积层、光阱限制或流体界面。通过基于光学的技术（如视频显微镜）对仿生流体进行微流变学是获得这些材料的机械性能和分子行为的经典工具。显微流变学获得的结果主要取决于视频显微镜设置的延时值，因此，需要一种工具，通过在类似实验的情况下模拟布朗物体来测试统计数据缺乏的影响。我们使用布朗动力学 (BD) 模拟来模拟胶体流体，其中粒子受到不同的外加力和粒子间相互作用。该软件已经过测试，可分析粒子之间吸引力的微流变结果 [1]、图像分析对实验微流变结果的影响 [2]，以及用光镊探索实验扩散 [3]。BDL 的输出结果与标准微流变算法 [4] 使用的格式直接兼容。在复杂的仿生流体的微流变学背景下，我们在这里使用这个工具来研究统计数据的缺乏是否会影响被光镊捕获的珠子的观察潜力。程序摘要 程序名称：布朗磁盘实验室 (BDL) 程序文件 doi：http://dx.doi.org/10。17632/dbwzdkttkb.1 许可条款：GPLv3 编程语言：Java（JDK 7 及以上） 补充材料：我们提供了详细的用户手册，描述了如何使用 BDL、布朗动力学模拟的理论基础、在此软件，以及有关开发代码的其他详细信息和说明。问题性质：通过延时显微镜实验（视频显微镜），我们可以观察胶体粒子在不同粒子间相互作用和外力作用下的布朗运动。沉积的准二维层、流体界面或光学捕获的粒子可以被视为二维胶体系统。随后通过对存储的延时图像的图像分析获得胶体物体的质心。我们需要一个应用程序来生成简单流体中胶体物体的理想实时运动，无需图像分析即可提供粒子的位置。该软件应该允许在实验之前检查胶体流体的一般行为，包括对粒子运动的目视检查。使用此应用程序，我们应该能够分析布朗物体的集体运动、不同粒子间力的影响以及实验设置的局限性，例如图像分析对所得结果的影响。求解方法：BDL 对包含在具有恒定粘度值的透明介质中的布朗二维圆盘进行模拟。理论方案允许我们在圆盘中引入外力以测试不同的实验条件，以及在胶体物理学实验中观察到的相互作用（爱因斯坦，1905 年；Xin 等人，2016 年）。我们使用没有高计算要求的计算多平台环境，因为少量粒子 (n ≤ 500) 和小浓度是延时显微镜实验的典型特征。输出数据类似于视频显微镜设置：稍后可以使用微流变学标准算法（Bevan 和 Eichmann，2011）从粒子的位置计算所需的统计量。BDL 是使用 Easy Java/JavaScript Simulations (EjsS)（Dinsmore 等人，2002 年）开发的，该软件允许简化代码生成和模拟对象的可视化。只要 Java 运行时环境 (JRE) 先前已安装在计算机中，Java 就允许在任何 SO 中运行软件而无需编译或安装。包括限制和异常功能在内的其他注释： 需要安装了 Java 运行时环境 (JRE) 的 SO。[1] P. Dominguez-Garcia，Europhys。JE软。事情。35 页。73, 2012. [2] P. Dominguez-Garcia 和 M. A. Rubio, Appl. 物理。莱特。102 页。074101, 2013. [3] M. Pancorbo, M. A. Rubio, P. Dominguez-Garcia, Procedia Comp. 科学.. 108, p. 166–174, 2017. [4] J. C. Crocker 和 D. G. Grier, J. Colloid Interface Sci. 179，第。298-310，1996 年。Dominguez-Garcia 和 M. A. Rubio，Appl。物理。莱特。102 页。074101, 2013. [3] M. Pancorbo, M. A. Rubio, P. Dominguez-Garcia, Procedia Comp. 科学.. 108, p. 166–174, 2017. [4] J. C. Crocker 和 D. G. Grier, J. Colloid Interface Sci. 179，第。298-310，1996 年。Dominguez-Garcia 和 M. A. Rubio，Appl。物理。莱特。102 页。074101, 2013. [3] M. Pancorbo, M. A. Rubio, P. Dominguez-Garcia, Procedia Comp. 科学.. 108, p. 166–174, 2017. [4] J. C. Crocker 和 D. G. Grier, J. Colloid Interface Sci. 179，第。298-310，1996 年。