Tools for Understanding and Controlling the Non-Equilibrium Self-Assembly of Multi-Component Macromolecular Systems

Some of the most intriguing and important macromolecular self-assembly processes in chemistry, biology, and engineering occur on the length and time scales of tens-of-nanometres and seconds, and often occur under non-equilibrium conditions. For example, in chemistry, natural and synthetic nanopores are being developed to disassemble DNA and read off the genetic code with the goal of reaching the '$1000 genome'. In biology, cutting edge experiments are probing fundamental aspects of protein self-assembly during their synthesis by the ribosome molecular machinery. And in engineering, smart materials that utilize protein and nucleic acid polymers are being developed to control the assembly of mesoscopic structures in response to changes in solution conditions. Therefore, understanding and controlling soft matter self-assembly processes that occur on such scales is extremely important because of the benefits it would yield both scientifically and economically. This is a difficult challenge, however, due to the complex multi-component nature of the self assembly of these polymers.

Computer simulations and physics-based theoretical tools offer an excellent means by which to understand self assembly and identify mechanisms to control it. Over the past two decades computer simulations using all-atom models have contributed to our understanding of self assembly on scales less than nanometres and microseconds. However, such all-atom models cannot reach the seconds time scale that is necessary to study self assembly on the tens-of-nanometre length scale. Therefore, to provide molecular insights into this regime and to help guide new experiments and the design of new smart materials, appropriate coarse-grained models that retain the essential physics must be developed. Crucially, while conventional studies often probe systems at equilibrium, most real-world applications involve non-equilibrium self assembly. New theoretical tools must therefore be developed to analyze and predict unexplored aspects of self assembly under non-equilibrium conditions.

The primary aim of this proposal is to develop simulation and theoretical tools of broad use to understand and control non-equilibrium self-assembly of multi-component macromolecular systems comprised of proteins and nucleic acids. To do this we will: (1) generalise our coarse-grained simulation model for molecular self-assembly to make it applicable to a much wider class of self-assembly phenomena; and (2) develop new theoretical tools to analyze and predict non-equilibrium self-assembly processes. We will test these tools on a specific system for which we already have an established track record and that represents a paradigm of multi-component self-assembly - protein folding during synthesis. We will investigate the physical principles governing the non-equilibrium acquisition of ordered nascent-chain structure during protein biosynthesis. We will validate these findings against NMR data from an ongoing, highly successful collaboration, and thereby test the accuracy of the models we develop. This proposal will provide a set of tools useful to both theoreticians and experimentalists to address important questions and timely topics involving a broad class of self-assembling systems across the fields of chemistry, biology, and engineering.

The computational method and theoretical tools that we propose to develop will play a crucial role in the study of complex macromolecular systems, most notably for aspects that are presently not readily accessible using traditional approaches such as all-atom molecular dynamics simulations. This goal will be achieved by developing a coarse-grained model of biological macromolecules that can simulate their self-assembly in the regime of tens-of-nanometres and seconds. Furthermore, we will develop novel theoretical tools to analyze and predict non-equilibrium self-assembly processes. Potential applications of these tools include, but are not limited to, the modelling of polymer translocation through natural or artificial nanopores; the design of self-assembling biomaterials such as nucleic acid scaffolds or biopolymer functionalized carbon nanotubes; and the optimization of manufacturing processes involving self-assembly through the analysis and subsequent manipulation of system time scales. These applications are directly relevant to both theorists and experimentalists in a variety of fields including physics, chemistry, biology and engineering.

We are therefore seeking funding to significantly extend the capabilities of a first-generation model that we have developed to examine self-assembly that occurs on a molecular machine central to life, and validate this model against NMR data that is being measured in the lab of our collaborator, for whom we are not seeking funding. Our track record shows that we are capable of developing and applying such coarse-grained models to interesting and timely questions about macromolecular self-assembly. This research will provide a platform for researchers in industry to utilize our coarse-grained model because we have purposedly decided to carry out its development and implementation in the widely available CHARMM software package. This proposal is a step towards our long-term goal of providing a general, transferable coarse-grained model.
The ability to model self-assembly at these larger length and time scales is a key requirement in gaining a molecular understanding in to a range of phenomenon in science and technology. The model we propose to develop and widely distribute with EPSRC funding will help keep the UK at the leading edge of nano-science and engineering applications.

The tools we develop will be of interest to companies in the areas of technology and high-tech manufacturing. Specifically, our models could be of use in designing efficient nanopores for gene sequencing, an application that could help reach the "$1000 genome" goal that technology and companies are pursing. To exploit the tools we develop for commercial purposes we are in contact with the UK Company 'Oxford Nanopore Technologies', which is developing such nanopore gene sequencing technology (see Letter of Support). We will visit their company headquarters located in Oxford during the last half of this research programme, during which time Dr O'Brien will present his research to the company to discuss potential applications.

Dr O'Brien will also get project management experience, which will help develop his professional skills. As new graduate students enter the research group he will have the opportunity to advise and mentor them in their research projects.

We have a track record in the area of coarse-grained modelling that shows that our results have wide visibility through publication in high profile journals as well as presentation at international meetings. Furthermore, our previous work has demonstrated successful collaborations with experimentalists, which will continue in our collaboration with Dr John Christodoulou as proposed in the application.