CAREER: Multiscale modeling of collective behavior of bacteria

该活动的目标是开发新的粗粒度流体动力学模拟方法来模拟细菌和其他活性颗粒的集体游泳行为，并研究细菌在粘弹性介质和近表面中的集体行为。这项研究特别关注细菌系统，因为它们在感染中的重要性，实验数据正在变得可用，以及设计新的工程系统的可能性。如果成功，研究贡献将有广泛的应用，包括化学和生物工程，材料科学和社会科学。如果细菌的浓度足够高，就会出现集体行为。化学信号（群体感应）的重要性是建立这样的系统。然而，由于流体动力学的相互作用，即使在没有化学信号的情况下，也会出现这种情况。这类系统的理论与仿真是本项目的主要课题。介观现象（如输运现象）在包括生物学在内的许多领域观察到的宏观结果中起着重要作用。该研究有两个中心目标：1)建立一个粗粒度框架，允许捕获关键流体动力学特征的可处理模拟；2)使用一种新颖的模拟方法首次研究非牛顿流体对集体行为的影响。这些目标将潜在地为诸如肺部和肠道粘液中的细菌感染以及生物膜形成等自然现象提供基本的见解，但也提供了设计细菌系统的工具。初步结果表明，非牛顿流体可以用来控制和中断集体行为。这项工作将潜在地改变细菌群落工程的范例，将流体动力学和机械通讯与遗传操纵和化学通讯结合在一起。更广泛的影响这项工作建立的框架和集体行为的基本进展将潜在地影响许多领域。这包括以下例子：如果生物体群体比个体更有效地进行趋化，那么活性剂可以作为药物递送剂一起工作，以发现和摧毁肿瘤。可以设计出具有独特机械性能的新型活性材料。流体力学可用于优化细菌生产生物燃料。水动力相互作用被视为一个例子，其中简单的规则可以产生复杂的紧急行为。这项研究将帮助我们了解涌现行为的哪些方面是普遍的，哪些方面是流体动力相互作用所特有的。教育和推广：研究和教育都受益于通过利用可视化流体力学和生物学产生的好奇心而紧密联系在一起。将开发基于java的小程序来教授基本概念并鼓励代表性不足的群体。小程序将允许用户交互式地探索最先进的研究概念。互动的本质给用户带来了更大的兴奋感和学习更多的动力。研讨会也将在伦斯勒举行，汇集研究人员从广泛的学科复杂的流体。

0954445UnderhillThe objective of the proposed activity is to develop novel coarse-grained hydrodynamic simulation methods to model the collective swimming behavior of bacteria and other active particles and to investigate the collective behavior of bacteria in viscoelastic media and near surfaces. The research focuses specifically on bacterial systems because of their importance in infections, experimental data are becoming available, and the possibility of designing new engineered systems. If successful, the research contributions will have a broad range of applications, including chemical and biological engineering, materials science, and social science. If the concentration of bacteria becomes high enough, collective behavior emerges. The importance of chemical signaling (quorum sensing) is such systems is established. However, the emergence can occur even in absence of chemical signaling because of hydrodynamic interactions. Theory and simulation of such systems is the main subject of this project. Intellectual Merit Mesoscopic phenomena (such as transport phenomena) play an important role in the macroscopic outcome observed in many areas including biology. The research has two central goals: 1) build a coarse-graining framework that allows for tractable simulations which capture the key hydrodynamic features, and 2) use a novel simulation method to study for the first time the impact a non-Newtonian fluid has on the collective behavior. These goals will potentially provide fundamental insights into natural phenomena such as bacterial infections in mucus of the lungs and intestines and biofilm formation, but also provide the tools to design bacterial systems. Preliminary results show that a non-Newtonian fluid can be used to control and interrupt collective behavior. This work will potentially change the paradigm in engineering of bacterial communities by including hydrodynamics and mechanical communication on equal footing with (an integrated together with) genetic manipulation and chemical communication. Broader Impacts The framework built in this work and the fundamental advances on collective behavior will potentially impact many areas. This includes the following examples: if groups of organisms can undergo chemotaxis more efficiently than individuals, then active agents can work together as drug delivery agents to find and destroy tumors. New active materials can be designed with unique mechanical properties. Fluid mechanics can be used to optimize biofuel production by bacteria. Hydrodynamic interaction is seen as an example in which simple rules can give rise to complex emergent behavior. The research will help us understand which aspects of the emergent behavior are universal and which are particular to hydrodynamic interactions. Education and Outreach: Research and education both benefit by being strongly tied together by leveraging the curiosity that is generated by visualizing fluid mechanics and biology. Java-based applets will be developed to teach fundamental concepts and encourage underrepresented groups. The applets will allow a user to interactively explore state-of-the-art research concepts. The interactive nature gives the user a greater sense of excitement and drive to learn more. Workshops will also be held at Rensselaer to bring together researchers studying complex fluids from a wide range of disciplines.