BioEngineering from first principles.

研究的挑战是了解控制细胞表面和细胞间相互作用的原理，因为微生物细胞产生的大分子结构种类繁多，它们对结合相互作用的化学和物理影响也很复杂。我们将使用计算模型预测附着，并了解为什么细胞外DNA在特定条件下促进或抑制附着。这是一个重大挑战，如果能够实现，将获得巨大回报。细胞附着的预测能力将使环境工程、过程工程和生物医学工程领域的新分析和设计方法成为可能。为了应对这一挑战，我们招募了多学科专业知识，将计算化学、表面和高分子物理学、分子生物学、高分子化学、工程微生物学、分析化学、分子生物学等领域的理论和实验技术联合收割机。X射线和振动光谱学与环境工程科学。我们建议使用计算化学技术来模拟细胞壁，模拟其单个化学成分的行为，并估计与特定固体表面发生的物理化学相互作用。展望未来1- 20年，目标是充分开发计算方法，以允许设计所需的相互作用，确定这些相互作用发生所需的大分子结构，并确定合成所需的基因序列。这项可行性研究将启动理论化学解决细胞外DNA（eDNA）结合细胞和矿物质的具体挑战，作为生物膜形成的一种确定机制。结果将是多学科实验和理论模拟之间的这种结合的方法作为预测细胞附着和生长的案例研究的评估。利用计算技术，我们将使用分子动力学模拟来研究核酸序列与表面的结合。在实验上，我们将首先从环境样品中分离出生物膜形成微生物产生的DNA。然后，我们将从生物膜形成细胞中去除eDNA，并将其替换为合成DNA，以开始量化eDNA特性与细胞附着之间的关系。这种“合成”方法将使我们能够系统地改变eDNA的长度，序列和浓度，并量化细胞附着到模型氧化物表面，如带负电荷的二氧化硅和带正电荷的氧化铝在定义的离子介质条件下。我们将探索如何使用原子力显微镜和荧光技术在细胞表面和基质上排列eDNA，我们将探索使用突破光学分辨率衍射极限的方法，如SNOM（扫描近场光学显微镜），据我们所知，从未应用于这一领域。工程应用的潜力是巨大的。我们预计，几乎所有生物技术领域都有可能获利。我们建议通过在项目结束前3个月将广泛的工程专家与项目团队聚集在一个沙坑中来评估这一承诺的广度。我们将举办为期两天的研讨会，介绍我们的成果，并制定一个路线图，推动这一研究领域和实际应用。参与者将评估我们的结果，确定工程应用的机会领域，并通过系统地应用我们的方法评估在生物工程广泛领域推广的承诺。

The research challenge is to understand the principles that control cell-surface and cell-cell interactions given the enormous variety of macromolecular structures produced by microbial cells and the complexity of their chemical and physical influences on binding interactions. We will predict attachment using computational models and gain understanding why extracellular DNA promotes or inhibits attachment under specific conditions. This is a major challenge with huge rewards if it can be met. A predictive capability of cell attachment would enable new methods of analysis and design in the fields of environmental engineering, process engineering and biomedical engineering.To tackle this challenge, we have recruited multidisciplinary expertise to combine theoretical and experimental techniques from the fields of computational chemistry, surface and polymer physics, molecular biology, polymer chemistry, engineering microbiology, analytical chemistry, X-Ray and vibrational spectroscopy and environmental engineering science.We propose to use computational chemistry techniques for simulation of cell walls, to characterise the behaviour of their individual chemical constituents, and to estimate the physical-chemical interactions that occur with specified solid surfaces. Looking 1-2 decades ahead, the aim is to develop computational methods sufficiently to allow the required interactions to be designed, identify the macromolecular structures necessary for these interactions to occur and identify the necessary gene sequences for their synthesis. This Feasibility Account study will launch theoretical chemistry into the specific challenge of tackling extracellular DNA (eDNA) binding on cells and minerals as one identified mechanism in biofilm formation. The outcome will be an evaluation of this combined approach between multidisciplinary experimentation and theoretical simulation as a case study for predicting cell attachment and growth. With the computational techniques, we shall investigate the binding of nucleic acid sequences to the surfaces using molecular dynamics simulations. Experimentally, we will first characterise eDNA produced by biofilm-forming microbes that we have isolated from environmental samples. We will then remove eDNA from biofilm-forming cells and replace it with synthetic DNA to start to quantify the relationship between the properties of eDNA and cell attachment. This 'synthetic' approach will allow us to vary systematically eDNA length, sequence and concentration and quantify cell attachment to model oxide surfaces such as negatively charged silica and positively charged alumina under defined ionic medium conditions. We will explore how eDNA is arranged on the cell surface and substratum using atomic force microscopy and fluorescence techniques, and we shall explore the use of methods that break the diffraction limit for optical resolution such as SNOM (Scanning Near Field Optical Microscopy) which, to our knowledge, has never been applied to this area. The potential for engineering applications is immense. We anticipate that virtually all fields of biotechnology would potentially profit. We propose to assess this breadth of promise by bringing a wide range of engineering experts together with the project team in a sand pit that will be held 3 months before the project end. We will hold a 2-day workshop to present our results and develop a roadmap for moving this forward as a research area and for practical application. Participants will evaluate our results, identify areas of opportunity for engineering applications, and assess the promise for generalisation across the broad field of BioEngineering through systematic application of our approach.