Bacterial trapping near topographic surfaces under shear flow

活动细菌，如大肠杆菌（E. coli），在表面定植，在那里它们形成危险的生物膜并引起生物污染。当到达表面时，它们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。尽管有很多了解，大肠杆菌的近表面捕获仍然是一个知之甚少的复杂过程，这是由大肠杆菌的奔跑和翻滚运动和物理条件决定的，如剪切流动和表面地形。然而，控制近表面捕获对于医疗和生物技术应用至关重要，例如，防止生物膜和生物污垢，以及利用细菌作为药物载体靶向诸如恶性肿瘤等疾病部位。因此，印度和德国的团队联合起来，利用他们互补的专业知识，进行了全面的模拟分析，以探索如何利用物理条件来控制大肠杆菌在不同地形表面附近剪切流中的捕获。我们将对这个复杂的问题进行一步一步的分析，并在很大程度上依赖于印度项目负责人早些时候开发的一个现实的大肠杆菌模型。它将被用于一个全面的预备性分析的跑和翻滚运动在散装。与此同时，德国研究小组将利用基于多粒子碰撞动力学方法的代码实现大肠杆菌模型，这将使我们能够在不同地形的表面附近模拟细菌周围的流体流动。在这两个小组之间共享代码，我们将彻底分析运动的大肠杆菌是如何被困在静止流体或剪切流中的表面附近的，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，包括多态性，这在迄今为止任何报道的表面捕获的实验研究中都没有得到解决，以及变变性和杰弗里轨道对细菌动力学的作用。最后，我们将对具有非平面地形的表面进行建模，并研究与生物污垢和靶向药物沉积控制相关的情况。

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.