Modeling Biofilms: Fluid Dynamics, Reactions, Diffusion/Advection and Biomass Redistribution

本研究致力于开发和模拟一种新的生物膜动力学模型。具体地，该模型包括用于在通用生物膜域上流动的流体的综合流体动力学。该模型的主要进展是允许由于流体运动和生长过程而引起的生物膜的运动。生物膜由多种细菌组成，这些细菌消耗多种类型的营养物质并产生细菌和胞外聚合物（EPS）。EPS是负责凭借渗透压的生物质的再分配，典型的水凝胶。 通过在较高养分浓度的区域产生EPS，建立EPS浓度梯度。这些梯度在生物膜上诱导趋于平衡EPS浓度的力。 这种生物量再分配的物理描述加上由于生长引起的生物膜的真实运动是对现有模型的实质性改进。早期调查的重点将关注的数值方法，将标记的散装流体和生物膜区域之间的永久分离的自由边界。 我们使用的方法是基于边界积分方法，已成功地用于模拟两个流体系统与各种类型的边界（例如弹性，被动）。 为了使用这些方法，将导出一个广义互等定理，其中包括本构关系中的生物膜的生长。一旦功的互等定理成立，一个积分方程就可以确定流体/生物膜系统的速度。微生物生物膜对我们生活的几乎所有领域都有重大影响。虽然这些影响可能是有益的，例如在生物修复和废水处理中使用生物膜，但目前大多数研究都集中在与生物膜污染相关的有害过程上。 生物膜的负面影响包括来自食品服务业、化学制造厂、造纸厂和各种医疗环境等不同领域的例子。这些影响包括增加成本、降低效率、增加腐蚀、结垢以及增加杂质和感染。生物膜生长和发展的现实模型将有助于实验者提出新的实验研究。此外，由于详细的空间数据可以从模型模拟比实验更容易地产生，持久的形成和分离的新的假设，可以提出的浓度和内部应力的值的基础上。

This research is dedicated to the development and simulation of a new model of biofilm dynamics. Specifically, the model includes comprehensive fluid dynamics for a fluid flowing over a generic biofilm domain. The major advance in this model is to allow for the motion of the biofilm due to the fluid motion and growth processes. The biofilm is composed of multiple species of bacteria that consume multiple types of nutrients and produce both bacteria and exo-polymeric substance (EPS). The EPS is responsible for the redistribution of the biomass by virtue of the osmotic pressure that typifies hydrogels. By producing EPS in regions of higher nutrient concentration, gradients of EPS concentration are set up. These gradients induce a force on the biofilm tending to equilibrate the concentration of EPS. This physical description of biomass redistribution coupled with realistic motion of the biofilm due to growth is a substantial improvement over existing models. Much of the focus of the early investigations will concern numerical methods to incorporate the free boundary that marks the permanent separation between the bulk fluid and the biofilm regions. The methods that we are using are based on boundary integral methods that have been used successfully to model two fluid systems with various types of boundaries (e.g. elastic, passive). To use these methods, a generalized reciprocal theorem will be derived which includes the growth of the biofilm in the constitutive relationship. Once the reciprocal theorem is established, an integral equation can be derived that determines the velocity of the fluid/biofilm system.Microbial biofilms have a significant impact on virtually all areas of our lives. While these impacts can be beneficial, such as the use of biofilms in bioremediation and wastewater treatment, the majority of current research focuses on the detrimental processes associated with biofilm contamination. Negative impacts of biofilms include examples from such diverse areas as food service industries, chemical manufacturing plants, paper production plants and various medical settings. These impacts include increased cost, lowered efficiency, increased corrosion, fouling and increased impurities and infections. Realistic models of biofilm growth and development will aid experimentalists in proposing new experimental inquiries. Also, because detailed spatial data can be generated from model simulations more readily than by experimentation, novel hypotheses of persistent formation and detachment can be proposed based on values of concentrations and internal stresses.