EPSRC Research Software Engineer Fellowship Oliver Henrich

我建议的跨学科研究和软件开发计划位于物理、化学和生物学的交界处。这项建议的主要目标领域，我的软件将涉及的，是DNA和RNA的粗粒度建模，远离平衡的生命系统和活性物质的研究，新的软能量和功能材料，新的异质计算体系结构的增强封装技术和算法。建议的软件开发计划与一些被确定为物理学重大挑战的关键研究领域保持一致。其中之一是对生命物理学的理解。它的目标是发展对生命的综合理解，从单分子到整个生物系统。DNA和RNA是两种生物聚合物，它们参与各种生物学作用，最显著的是编码生物发育和功能以及基因转录所需的遗传指令。与原子模型相比，DNA或RNA的粗粒度模型可以提供显著的计算和概念优势，通常会使效率提高三个或更多数量级。但它们不仅是DNA原子模型的有效替代方案，因为它们对于在毫秒及以上的时间尺度上建立DNA模型是不可或缺的，或者当必须考虑数万个碱基对或更多碱基对的长DNA链时。例如，这对研究DNA超螺旋的动力学很重要，即双螺旋的局部过度或不足扭曲，这对基因表达很重要。另一个重大挑战是功能材料的纳米级设计，其目标是通过使用新的原理将所需的特性工程到材料中，而不是通过反复试验来进行。在拟议方案中，我将讨论不同类别的功能材料和能源材料。一个例子是颗粒悬浮液，它是食品、饮料、清洁剂、个人护理产品、油漆和油墨等消费品中使用的封装技术的基础，也是石化行业或具有芯片实验室设备的微技术部门的基础。纳米结构带电软材料是一种非常有前途的新途径，可以获得更高效、更安全的能源生产或存储设备，并在填补电池和电极设计或可再生能源存储方面的技术空白方面具有巨大的潜力。第三个大挑战是远离热力学平衡的物理现象的出现。由于生命本身是一个远离平衡的过程，这项研究的背景也与生命物质的各个方面密切相关，并经常挑战统计物理的经典理论。我将在这次联谊会期间制作的软件将是开放源代码的，并可从公共资源库免费下载。它的一部分很可能在未来对高度优化和标准化的微观、中观和宏观算法库以及用于模拟复杂流体的欧洲基础设施做出关键贡献。软件和研究方案将在爱丁堡大学与剑桥大学、牛津大学、伦敦大学学院、西班牙巴塞罗那大学和美国桑迪亚国家实验室的项目伙伴合作进行。

The interdisciplinary programme of research and software development I propose lies at the interface of physics, chemistry, and biology. Key target areas of this proposals, which my software will address, are coarse-grained modelling of DNA and RNA, the study of living systems and active matter far away from equilibrium, new soft energy and functional materials, enhanced encapsulation technologies and algorithms for new heterogeneous computing architectures.The proposed software development programme aligns with a number of key areas of research that have been identified as Physics Grand Challenges. One of them is the understanding the physics of life. This has the goal to develop an integrating understanding of life from single molecules to whole biological systems. DNA and RNA are the two biopolymers that are involved in various biological roles, most notably in the encoding of the genetic instructions needed in the development and functioning of living organisms and gene transcription. Coarse-grained models of DNA or RNA can provide significant computational and conceptual advantages over atomistic models, leading often to three or more orders of magnitude greater efficiency. But they are not only an efficient alternative to atomistic models of DNA as they are indispensable for the modelling of DNA on timescales in the millisecond range and beyond, or when long DNA strands of tens of thousands of base pairs or more have to be considered. This is for instance important to study the dynamics of DNA supercoiling, the local over- or under-twisting of the double helix, which is important for gene expression. Another Grand Challenge is the nanoscale design of functional material, which aims at engineering desired properties into the materials by using new principles rather than proceeding by trial and error. In the proposed programme I address different classes of functional and energy materials. One example are particle suspensions, which are fundamental in encapsulation technologies used in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or the micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new and highly promising avenue to more efficient, safer energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or the storage of renewable energy. A third Grand Challenge is the emergence and physics far from thermodynamic equilibrium. As life itself is a process far away from equilibrium, the context of this research is also closely related to aspects of living matter and often challenges the classical theories of statistical physics.The software that I will produce during this Fellowship will be open source and freely available for download from public repositories. Parts of it are likely to form later a key contribution to a highly optimised and standardised library of micro-, meso- and macroscale algorithms and a European infrastructure for the simulation of complex fluids. The software and research programme will be undertaken at the University of Edinburgh in collaboration with project partners at the University of Cambridge, the University of Oxford, University College London, the University of Barcelona, Spain and Sandia National Laboratories, USA.