Bacterial trapping near topographic surfaces under shear flow

可移动的细菌，如大肠杆菌，在表面定居，在那里它们形成危险的生物膜并造成生物污染。当它们到达表面时，首先需要被物理机制捕获，然后通过化学键促进它们与表面的不可逆附着。尽管有很多见解，但近表面捕获大肠杆菌仍然是一个鲜为人知的复杂过程，这是由大肠杆菌的跑动和翻滚运动以及物理条件，如剪切流和表面地形决定的。然而，控制近地表捕获对于医疗和生物技术应用是至关重要的，例如，对于防止生物膜和生物污垢，而且对于利用细菌作为药物载体来针对恶性肿瘤等疾病部位也是至关重要的。因此，印度和德国的团队联合起来，利用各自互补的专业知识进行全面的模拟分析，以探索如何利用物理条件来控制不同地形表面附近的剪切流中大肠杆菌的捕获。我们将对复杂问题进行逐步分析，并在很大程度上依赖于印度项目负责人早些时候开发的现实模型大肠杆菌。它将被用来对整体的跑动和翻滚运动进行彻底的预备分析。同时，德国团队将在基于多粒子碰撞动力学方法的代码中实现大肠杆菌模型，这将使我们能够模拟不同地形表面附近细菌周围的流体流动。在两个小组之间共享代码，我们将彻底分析活动的大肠杆菌是如何在静止的流体或剪切流中被困在表面附近的，从而澄清相互矛盾的观察结果。我们的重点将放在鞭毛动力学在奔跑和翻滚过程中的作用，包括多态，这一点到目前为止还没有在任何报道的关于表面捕获的实验研究中得到解决，也将集中在流变性和Jeffery轨道对细菌动力学的作用上。最后，我们将模拟具有非平面地形的表面，并调查与生物污垢控制和靶向药物沉积相关的情况。

Motile bacteria, such as Escherichia coli (E. coli), colonize surfaces, where they form hazardous biofilms and cause biofouling. When reaching the surface, they first need to be trapped by physical mechanisms, which then promotes their irreversible attachment to the surface through chemical bonding. Despite much insight, near-surface trapping of E. coli is still a poorly understood complex process, which is determined by E. coli’s run-and-tumble motility and physical conditions, such as shear flow and the surface topography. However, controlling near-surface trapping is essential for medical and biotechnological applications, for example, for preventing biofilms and biofouling but also for using bacteria as drug carriers to target disease sites such as malignant tumors. Therefore, the Indian and German groups join forces and use their complementary expertises to carry out a comprehensive simulation analysis in order to explore how physical conditions can be used to control the trapping of E. coli in shear flow near surfaces with different topography.We will perform a step-by-step analysis of the complex problem and heavily rely on a realistic model E. coli developed earlier by the Indian project leader. It will be used for a thorough preparatory analysis of the run-and-tumble motion in the bulk. In parallel, the German group will implement the model E. coli in a code based on the method of Multi-Particle Collision Dynamics, which will enable us to simulate fluid flows around the bacterium near surfaces with varying topography. Sharing the code between both groups, we will thoroughly analyze how a motile E. coli becomes trapped near a surface either in a quiescent fluid or under shear flow and thereby clarify contradicting observations. Our foci will be on the role of flagellar dynamics during runs and tumbles including polymorphism, which has so far been not resolved in any of the reported experimental studies on surface trapping, and also on the role of rheotaxis and Jeffery orbits for the bacterial dynamics. Finally, we will model surfaces with non-planar topography and investigate situations related to the control of biofouling and targeted drug deposition.