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

趋化性是细菌在其局部环境中感知化学浓度梯度并游向更高浓度的化学物质的能力，它们认为这对它们的生存有利。 在这项工作中，我们建议研究如何孔隙尺度的趋化过程影响达西尺度观察多孔介质中的细菌运输。 在地下，生物修复往往由于注入物质和驻留污染物之间无法实现良好混合而受到阻碍。 在这种情况下，可以利用趋化性来加强污染区内细菌种群的混合。 这将是一种多尺度现象，其中细菌响应于污染物浓度的孔隙尺度变化而迁移，从而导致场尺度的更大混合。 这个方案有两个密切相关的开放问题：（1）如何将孔隙尺度的趋化性描述与达西尺度应用中用于预测细菌传播的有效色散张量联系起来，以及（2）是否也可以预测细菌浓度的空间方差来预测多孔介质内发生的微尺度混合。目的和方法：本项目的总体目标是量化的影响，孔隙规模的趋化性细菌运输的达西规模。 我们将通过以下步骤中理论发展和实验室实验的结合来实现这一目标。 1.推导出一个达西规模的运输方程的细菌，占局部化学梯度通过体积平均的趋化反应。 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。比较几个简化的测试案例的理论和实验，其中速度场和化学梯度是明确定义的。 将这些结果表示为工程相关性，将分散与无量纲基团（如Peclet数和趋化驱动力）联系起来。通过使用微流控装置对更复杂的多孔介质系统进行实验测试这些相关性，该装置允许在孔隙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：为了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响应与米长度尺度上的细菌分散相关联。 在我们的方法中，我们建立在目前的工作水文学家模拟地下水中的化学污染物的运输，并将其扩展到移动的胶体，由于除了水力梯度的化学梯度。 利用化学梯度作为控制细菌种群迁移的驱动力的潜力在智力上是有吸引力的。 该项目将采用最先进的数学建模（通过体积平均放大）和实验设计（微流体装置）方法。更广泛的影响：弗吉尼亚大学和俄勒冈州州立大学的研究人员之间的新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。 具有公认的承诺，以招聘工程代表性不足的群体的调查人员将广泛教育一个研究生和一个博士后助理在跨学科的背景下，以满足我们国家的劳动力环境工程师的关键需求。 对当地高中的宣传将为生物学荣誉学生及其老师提供基因工程的实验室实践经验，让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，以更好地告知决策者关于监测自然衰减作为已记录生物降解的污染场地的处理方案的可行性。

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.