Active Smectic Hydrodynamic Models of Colony Growth.

复杂的空间格局出现在细菌群落的内部和外部的压力。由此产生的结构在从物种间竞争到获得抗菌药物抗性的一切方面都是有用的。虽然目前的大规模测序工作产生了大量关于群落组成的数据，但它们未能提供位置信息，尽管它在细菌群落中起着不可或缺的作用。该项目将通过解决在微菌落范围内驱动形状和动态的基本物理原理来研究不断增长的社区的时空模式。理解宿主环境中的社区范围的自组织需要平衡概念简单性和多微生物复杂性的预测数学理论。虽然最近的细胞运动的集体动力学的理论已经发现了一些成功，采用连续活性液晶模型的菌落动力学，有明显的不可逾越的缺点，以再现真实的微生物菌落的多重内部组织。特别是，这些crosslinked模型限制了杆状病毒的内部排序方向对齐。然而，例如，绿脓杆菌的小菌落的明场荧光和显微镜图像显示内部结构，包括筏（小簇的连贯运动的杆状菌群），多层（垂直地层的不同层次），界面反滑动（在殖民地的最边缘处，以与本体相反的方向移动的单道杆状菌），和平面内近晶分层（堆叠在平行于表面的明确定义的平面中）。这些观察到的现象都涉及baciliforms的层排序，从根本上说，不能占由以前的nematodynamic theories. Therefore，本项目提出了一种新的理论，积极近晶流体将使我们能够理解在baciliforms的殖民地，包括在平面内近晶分层和相关的集体动力学的内在长度尺度的积极动荡。杰克佩吉特将扩展2D主动近晶理论，以考虑面内近晶分层和多层殖民地。通过实施相场混合模型来模拟菌落/流体界面，他再现和理解逆流界面单层和菌落界面上的主动应力。我们的理论框架将紧密耦合增长的取向秩序。未来的工作将是将近晶密码与反应扩散方程杂交，以在竞争菌落之间和每个菌落内产生趋化性通讯。

Complex spatial patterns emerge in bacterial communities in response to internal and external pressures. The resulting structure is instrumental in everything from interspecies competition to acquisition of antibacterial resistance. While current massive sequencing efforts yield vast data about community composition, they fail to provide positional information, despite its integral role in bacterial communities. This project will study the spatiotemporal patterning of growing communities by resolving the essential physical principles that drive shape and dynamics on a microcolony-wide scale. Understanding community-wide self-organization within host environments requires predictive mathematical theories that balance conceptual simplicity and polymicrobial complexity. While recent theories for the collective dynamics of cell motion have found some success by employing continuum active nematic liquid crystal models for colony dynamics, there are clear insurmountable shortcomings to reproducing the multiplex internal organization of real microbial colonies. In particular, these nematic models limit the internal ordering of baciliforms to orientational alignment. However, brightfield fluorescence and microscopy images of microcolonies of Pseudomonas aeruginosa for example show internal structuring, including rafts (small clusters of coherent motile baciliforms groupings), multilayers (distinct tiers of vertical strata), interfacial counter-sliding (single lane of baciliforms at the very edge of the colony moving in the opposite direction to the bulk), and in-plane smectic layering (stacked in well-defined planes parallel to the surface). Each of these observed phenomena involves layer ordering of baciliforms, which fundamentally cannot be accounted for by previous nematohydrodynamic theories.Thus, this project proposes that a novel theory for active smectic fluids will allow us to understand active turbulence in baciliform colonies, including intrinsic length scales of in-plane smectic layering and associated collective dynamics. Jack Paget will extend 2D active smectic theory to account for both the in-plane smectic layering and also the multilayer colonies. By implementing a phase field hybrid model to simulate colony/fluid interfaces, he reproduce and understand counter-flowing interfacial monolayers and active stresses on colony interfaces. Our theoretical framework will tightly couple growth to orienational order. Future work will be to hybridize smectic code with reaction-diffusion equations, to produce chemotactic communication between competing colonies and within each colony.