EPSRC Research Software Engineer Fellowship Oliver Henrich

我提出的研究和软件开发的跨学科计划位于物理、化学和生物学的界面。这些建议的关键目标领域，我的软件将解决，是DNA和RNA的粗粒度建模，生命系统和远离平衡的活性物质的研究，新的软能量和功能材料，增强的封装技术和新的异构计算架构的算法。拟议的软件开发计划与许多被确定为物理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。它的目标是从单个分子到整个生物系统发展对生命的综合理解。DNA和RNA是两种生物聚合物，参与各种生物学作用，最显著的是在生物体发育和功能以及基因转录所需的遗传指令编码中。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，通常可以提高三个或更多数量级的效率。但是，它们不仅是DNA原子模型的有效替代方案，而且对于毫秒级或更长的时间尺度上的DNA建模，或者当必须考虑数万个碱基对或更多的长DNA链时，它们是必不可少的。例如，这对于研究DNA超螺旋的动力学非常重要，双螺旋的局部过度或过度扭曲对基因表达非常重要。另一个重大挑战是功能材料的纳米级设计，其目的是通过使用新的原理而不是通过试验和错误来设计材料所需的性能。在拟议的方案中，我将讨论不同类别的功能和能源材料。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，或者是石化行业或带有芯片实验室设备的微技术领域。纳米结构的带电软材料是一种新的、非常有前途的途径，可以实现更高效、更安全的能源生产或存储设备，并具有巨大的潜力，可以填补电池和电极设计或可再生能源存储方面的技术空白。第三个重大挑战是物理学远离热力学平衡的出现。由于生命本身是一个远离平衡的过程，本研究的背景也与生命物质的各个方面密切相关，并且经常挑战统计物理学的经典理论。我将在这个项目中开发的软件将是开源的，可以从公共存储库免费下载。其中的部分内容很可能在以后形成一个高度优化和标准化的微、中观和宏观尺度算法库，以及一个欧洲复杂流体模拟基础设施的关键贡献。软件和研究项目将由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.