EPSRC Research Software Engineer Fellowship Oliver Henrich

Lead Research Organisation: University of Strathclyde
Department Name: Physics

Abstract

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.

Planned Impact

We are currently undergoing a transition to a new economy, which will be characterised by a deep and detailed understanding of the functioning mechanisms of DNA, RNA and their interaction with proteins. This transition will create new opportunities and industries and will have a transformative character on our societies, similar to that of the automotive, telecommunication and computer industry.

A concrete example of genetic technologies is genetically modified foods that have allowed for the introduction of new crop traits and far greater control over a food's genetic structure than previously afforded by traditional methods like selective breeding and mutation. An emerging example is personalised medicine, the customisation of healthcare using molecular analysis and a patient's genetic information for tailored gene therapies and medical decisions. The fundamental insights that my software will enable will undoubtedly create opportunities for improvement and enhancement of the two above mentioned, well-established applications of genetic technologies and open up completely new possibilities.

Recently, non-biological applications such as DNA-nanotechnology have sparked great interest, and the sequence-specific coarse-grained models for DNA and RNA are directly targeting this field. DNA origami for example is the programmable bottom-up approach of designing nanoscale materials and two- and three-dimensional shapes in a self-assembled manner by using the specificity of the interaction between complementary base pairs. There is great desire among experimentalists to get a computational feedback that is needed to reduce the financial cost and time required to design nanoscale self-assembled materials. Coarse-grained DNA models are the only candidates that could fill this technological gap.

The nanoscale design of new functional soft materials is another focus of this proposal. Particle suspensions are fundamentally important for encapsulation technologies in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new avenue to more efficient energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or storage of renewable energy. But before these insights can be turned into a competitive advantage for our industrial collaborators a detailed understanding of the behaviour of these systems needs to be first acquired. This can only be achieved through accurate descriptions of the complex morphology and dynamics of their different constituents, which my software will enable.

The field of active matter is very new and burgeoning with novel scientific insights that challenge the traditional beliefs of statistical physics and sometimes constitute new physics. The consequences of this are rather profound and can only be probed by a body of numerical simulations that account for all non-linearities and couplings in the underlying equations of motion.

While the software that I will develop is essential for the research community of computational soft matter and biological physics, the impact of the research originating from this software will often go beyond academia. I envisage its use will extend to many other communities. I anticipate that engineers, material scientists, physical chemists, biochemists, cell or molecular biologists as well as workers in industry are likely to engage in the future with many of the codes which I will provide. The software will be open source and also form an essential contribution to a future European infrastructure for the simulation of complex fluids.

Publications

10 25 50

Related Projects

Project Reference Relationship Related To Start End Award Value
EP/N019180/1 31/07/2016 30/06/2017 £489,605
EP/N019180/2 Transfer EP/N019180/1 01/07/2017 31/07/2021 £409,704
 
Description The LAMMPS implementation of oxDNA has been used in a variety of different contexts. This includes studies of supercoiling at SISSA, Italy, which has been performed in the group of Cristian Micheletti. In our own group, and in a collaboration between the Universities of Strathclyde, Edinburgh and Cambridge we applied the model to the multivalent building blocks of a DNA hydrogel. We could clarify how the sequence influences the relative orientation of the Y-shaped molecules.
Exploitation Route The findings could lead to the development of design principles for DNA materials, in particular DNA hydrogels.
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology