Collaborative Research: Chemotaxis in Porous Media--Experimental Observations and Upscaling for Development of a Descriptive Theory

趋化性是细菌感知其周围环境中的化学物质浓度梯度并向更高浓度的化学物质游去的能力，它们认为这有利于它们的生存。在这项工作中，我们建议研究趋化性的孔隙尺度过程如何影响细菌在多孔介质中运输的达西尺度观察。在地下，由于无法实现注入物质与常驻污染物之间的良好混合，生物修复常常受到阻碍。在这种情况下，趋化性可以用来加强污染区域内细菌种群的混合。这将是一个多尺度现象，其中细菌迁移响应污染物浓度的孔隙尺度变化，导致在现场尺度上更大的混合。该方案有两个密切相关的开放问题：(1)如何将孔隙尺度的化学亲和性描述与用于预测达西尺度应用中细菌传播的有效弥散张量联系起来；(2)是否也可以预测细菌浓度的空间方差，以预测在多孔介质中发生的微尺度混合。目的和方法：本项目的总体目标是在达西尺度上量化孔尺度趋化性对细菌运输的影响。我们将在以下步骤中通过理论发展和实验室实验的结合来实现这一目标。1. 推导出细菌的达西尺度运输方程，该方程通过体积平均来解释对局部化学梯度的趋化反应。这将用于预测(i)有效色散张量，以及（ii）细菌浓度的达西尺度空间方差。对几个速度场和化学梯度定义明确的简化测试用例进行理论和实验比较。将这些结果表示为将色散与无量纲群（如Peclet数和趋化驱动力）联系起来的工程相关性。通过使用微流体装置对更复杂的多孔介质系统进行实验测试，可以在孔和达西尺度上直接可视化流体流动模式和细菌分布。智力优势：要了解趋化性对地下水系统中化学污染物生物降解的影响，需要进行定量分析，将趋化性对毫米长度尺度上的局部化学梯度的反应与米长度尺度上的细菌分散联系起来。在我们的方法中，我们以水文学家目前的工作为基础，模拟地下水中化学污染物的运输，并将其扩展到由于化学梯度和水力梯度而运输的可移动胶体。利用化学梯度作为一种驱动力来控制细菌种群迁移的潜力在理论上很有吸引力。该项目将采用最先进的数学建模方法（通过体积平均放大）和实验设计方法（微流体装置）。更广泛的影响：弗吉尼亚大学和俄勒冈州立大学的研究人员之间的新合作伙伴关系汇集了实验系统设计方面的专业知识，以量化细菌迁移和数学建模，将孔隙尺度现象与现场尺度观察联系起来。我们将鼓励学生通过国际学生交流和合作来扩大他们的经验。在工程领域招募代表性不足群体的研究人员将在跨学科背景下广泛教育一名研究生和一名博士后，以满足我们国家劳动力对环境工程师的关键需求。与当地高中的接触将为荣誉生物学的学生和他们的老师提供基因工程的动手实验经验，以吸引下一代参与科学的奇迹。这项研究的结果将产生工程相关性，以便更好地告知决策者，在有生物降解记录的污染地点，监测自然衰减作为一种治疗选择的可行性。

Chemotaxis is the ability of bacteria to sense chemical concentration gradients in their local surroundings and swim toward higher concentrations of chemicals, which they perceive to be beneficial to their survival. In this work, we propose to examine how the pore-scale process of chemotaxis influences the Darcy-scale observation of bacterial transport in porous media. In the subsurface, bioremediation is often hindered by the inability to achieve good mixing between injected substances and the resident contaminants. In such situations, chemotaxis might be exploited to enhance the mixing of bacterial populations within contaminated zones. This would be a multiscale phenomenon in which bacteria migrate in response to pore-scale variations in pollutant concentration that results in greater mixing at the field-scale. There are two closely related open questions for this scheme: (1) how does one relate the pore-scale description of chemotaxis to the effective dispersion tensor that is used to predict bacterial spreading in Darcy-scale applications, and (2) can one also predict the spatial variance of the bacterial concentration to predict the microscale mixing that has occurred within the porous medium. Objective and Approach: The overall goal of this project is to quantify the impact of pore-scale chemotaxis on bacterial transport at the Darcy-scale. We will accomplish this through a combination of theory development and laboratory experimentation in the following steps. 1. Derive a Darcy-scale transport equation for bacteria that accounts for chemotactic responses to local chemical gradients via volume averaging. This will be used to predict (i) the effective dispersion tensor, and (ii) the Darcy-scale spatial variance of the concentration of bacteria.2. Compare theory and experiment for several simplified test cases in which the velocity field and chemical gradients are well-defined. Represent these results as engineering correlations that relate dispersion to dimensionless groups such as the Peclet number and chemotactic driving force.3. Test these correlations experimentally for more complex porous media systems by using microfluidic devices, which allow for direct visualization of fluid flow patterns and bacterial distributions at the pore- and Darcy-scales. Intellectual Merit: To understand the impact of chemotaxis on the biological degradation of chemical contaminants in groundwater systems requires a quantitative analysis that relates the chemotactic response to local chemical gradients over length scales of millimeters to bacterial dispersion over length scales of meters. In our approach we build on current work of hydrologists to model transport of chemical contaminants in groundwater and extend it to motile colloids that are transported due to chemical gradients in addition to hydraulic gradients. The potential for exploiting chemical gradients as a driving force to control the migration of bacterial populations is intellectually appealing. State-of-the-art approaches both in mathematical modeling (upscaling by volume-averaging) and experimental design (microfluidic devices) will be employed in the project.Broader Impact: A new partnership between researchers at the University of Virginia and Oregon State University brings together expertise in the design of experimental systems to quantify bacterial migration and mathematical modeling to relate pore-scale phenomena to field-scale observations. We will encourage students to broaden their experiences through international student exchange and collaboration. Investigators with a proven commitment to recruiting underrepresented groups in engineering will broadly educate one graduate student and one post-doctoral associate in an interdisciplinary context to meet critical needs for environmental engineers in our national workforce. Outreach to local high schools will provide hands-on laboratory experience in genetic engineering for Honors Biology students and their teachers to engage the next generation in the wonder of science. Results from this study will yield engineering correlations to better inform decision-makers about the feasibility of monitored natural attenuation as a treatment option at polluted sites where biological degradation has been documented.