Collaborative Research: Type II: Flow-induced fragmentation mechanisms in bacterial biofilms by hierarchical modeling of polymeric, interfacial and viscoelastic interactions

生物膜是细菌的菌落，其中的生物是固定的，并嵌入在碳水化合物聚合物的粘性，粘性的细胞外基质中。存在于这些结构中的细菌是地球上最普遍的生命形式。通常表面粘附和结构不均匀，生物膜出现在自然，工业和卫生环境。生物膜的生物力学是基础物理科学的兴趣，因为细菌的增殖是由它们的机械破裂、断裂和破碎引发的。这种破裂涉及分子和物理相互作用的复杂相互作用，每种相互作用在生物膜的不同空间尺度上都很活跃。通过整合现代计算方法和资源来模拟聚合物的非平衡动力学和聚合物流体的多相流，本项目将确定生物膜破碎的机制。将解决以下具体的研究问题：i)生物是如何形成膜的？生化成分和类复合材料的结构相互作用来控制破碎的临界应力和应变？ii)如何建立一个基于物理科学的生物膜破碎数学模型，使分子尺度微生物学和聚合物物理学以及机械应力和应变的连续尺度可变性都在破碎预测中发挥必要的作用？iii)应该实施什么样的教育议程，以便微生物学家和医生能够对第一性原理物理科学和数学建模技术的有用性有一个有效的理解？回答这些问题需要应用数学、聚合物动力学的非平衡模拟、微生物学和微观流变学的共同努力。成功地做到这一点有望将对细菌生物膜的科学理解从仅仅基于分子生物学转变为全面解决行为的分子和物理起源的科学理解。除了提高对生物膜的理解外，所开发的方法本身将代表许多领域的重要进展，包括在多个尺度上具有非均匀结构的广泛软材料。这项工作的更广泛影响将是对细菌生物膜力学在自然、工业和人类健康应用中的新科学理解。这种理解将对这些不同领域的应用产生积极影响，并可能对与生物膜有关的各种疾病的新治疗产生积极影响。该项目还将从其计算和建模计划以及将物理和数学建模引入医学院课程的教育计划中产生更广泛的影响。

Biofilms are colonies of bacteria in which the organisms are immobile and embedded in a sticky, viscous, extracellular matrix of carbohydrate polymers. Bacteria existing in these structures are the most prevalent life form on earth. Typically surface adherent and structurally non-uniform, biofilms arise in natural, industrial and health settings. The biomechanics of biofilms are of fundamental physical science interest because bacterial proliferation from them is triggered by their mechanical rupture, fracture and fragmentation. This rupture involves a complex interplay of molecular and physical interactions, each active on different spatial scales of the biofilm. By integrating modern computational methodologies and resources for simulating the non-equilibrium dynamics of polymers and the multiphase flow of polymeric fluids, the mechanisms for biofilm fragmentation will be identified in this project. The following specific research questions will be addressed: i) How do the biofilm?s biochemical composition and composite-like architecture interact to control the critical stress and strain of fragmentation? ii) How should a physical science based mathematical model of biofilm fragmentation be formulated such that molecular scale microbiology and polymer physics as well as continuum scale variability in mechanical stress and strain all play their necessary roles in fragmentation predictions? iii) What educational agenda should be implemented such that microbiologists and physicians can have a working understanding of the usefulness of first-principles physical science and mathematical modeling techniques?Answering these questions requires joint effort in applied mathematics, non-equilibrium simulation of polymer dynamics, microbiology, and microscale rheology. Successfully doing so promises to transform the scientific understanding of bacterial biofilms from one based solely on molecular biology to one that comprehensively addresses the joint molecular and physical origins of behavior. In addition to improving understanding of biofilms, the methods developed will themselves represent an advance important to many areas including the broad range of soft materials with non-uniform structure on multiple scales. The broader impact of the work will be to produce new scientific understanding of bacterial biofilms mechanics in natural, industrial and human health applications. This understanding will positively impact applications in these diverse areas and, potentially, new treatments for the wide range of diseases linked to biofilms. This program will also yield broader impacts from its computational and modeling plan as well as its educational plan to introduce physical and mathematical modeling into medical school curricula.