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。具体地说，该模型包括通用生物膜域上流动的流体的全面流体动力学。该模型的主要进展是允许由于流体运动和生长过程而导致的生物膜的运动。生物膜由多种细菌组成，这些细菌消耗多种营养物质，同时产生细菌和外源聚合物(EPS)。EPS通过水凝胶所特有的渗透压负责生物量的重新分配。通过在营养物质浓度较高的地区生产EPS，建立了EPS的浓度梯度。这些梯度对生物膜产生一种力，使EPS的浓度趋于平衡。这种对生物量重新分布的物理描述，加上由于生长而导致的生物膜的真实运动，是对现有模型的实质性改进。早期研究的大部分焦点将涉及纳入自由边界的数值方法，该边界标志着主体流体和生物膜区域之间的永久分离。我们使用的方法是基于边界积分方法，这些方法已经成功地用于模拟具有不同类型边界(例如，弹性、被动)的两个流体系统。为了使用这些方法，将推导出一个广义互等定理，其中包括本构关系中生物膜的生长。一旦互易定理成立，就可以推导出一个积分方程式来确定流体/生物膜系统的速度。微生物生物膜几乎对我们生活的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，但目前的大多数研究侧重于与生物膜污染相关的有害过程。生物膜的负面影响包括来自不同领域的例子，如食品服务业、化学品制造厂、造纸厂和各种医疗机构。这些影响包括成本增加、效率降低、腐蚀增加、结垢以及杂质和感染增加。生物膜生长和发育的现实模型将有助于实验者提出新的实验探索。此外，由于模型模拟比实验更容易生成详细的空间数据，因此可以根据浓度和内应力的值提出持续形成和脱离的新假设。

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.