The UK High-End Computing Consortium for Biomolecular Simulation

There is tremendous future scope for biomolecular simulation to provide unprecedented insights into biomolecular systems. The level of detail afforded by these methods, along with their ability to rationalise experimental data and their predictive power are already enabling them to make significant contributions in a wide variety of areas that are crucial for healthcare, quality of life and the environment. The UK biomolecular simulation community has a strong international reputation, with world-leading efforts in in drug design and development, biocatalysis, bionano-technology, chemical biology and medicine. HECBioSim has already delivered outstanding research with impact in bionanotechology, drug design and AMR. But we have only just scratched the surface and there is currently huge room for expansion. Having access to the largest, most modern computing facilities is essential for this. Renewal of the Consortium will enable us to continue allocating time ARCHER for cutting-edge biomolecular simulations.

We will place a special emphasis on reaching out to experimentalists and scientists working in industry in order to foster interactions between computational and experimental scientists, and academia and industry to encourage integrated multidisciplinary studies of key problems.

Biomolecular simulation and modelling is an integral part of drug design and development. The pharmaceutical industry needs well-trained scientists in this area, as well as the development of new methods (e.g. for prediction of drug binding affinities, ligand selectivity and metabolism). Members of the consortium have a strong track record of collaboration with industry to deliver trained scientists and new methodologies. For example, PhD students trained by consortium members have recently taken up positions in UCB, Unilever, Oxford Nanoimaging and even Sky Broadcasting as software developer. Many of these academic-industry collaborations have been strengthened by work done through HECBioSim allocations.

The Consortium will continue to welcome new members from across the whole community. We will continue to develop computational tools and training for both experts and non-experts using biomolecular simulation on HEC resources. We propose to develop new tools that will enable inter-conversion between biomolecular systems at different levels of resolution thereby allowing users to tackle more ambitious 'grand challenges' than are currently feasible.

In summary HECBioSim will foster collaborations between computational and experimental scientists between scientists working in industry and academia in all disciplines within biomolecular simulation to maintain the UK as a world-leader in this field.

Who might benefit from this research?

The direct beneficiaries of this research include academic and industrial scientists, including experimentalists working across a very wide range of disciplines including X-ray crystallography, NMR, electron microscopy, single molecule biophysics methods, mass spectrometry, hydrodynamics, enzyme kinetics, drug design medicinal chemistry, chemical and synthetic biology and design on biosensors. The two most obvious industrial beneficiaries are the pharmaceutical sector, which is of huge economic importance to the UK; and the biotechnology sector in which the UK is a world leader in e.g. nanopore DNA sequencing. Other industries (such as biocatalysis analysis and processing, IT hardware and software development) will also benefit from the UK High-End Computing Consortium for Biomolecular Simulation (HECBioSim) through our already established excellent links and new ones that will be fostered through the renewal of the Consortium. In the longer term, All of the work will impact on the general public through improvements in health and quality of life.

How will they benefit?

The focus of HECBioSim is to support access and use of high-end computing in the UK, both in terms of increased uptake and awareness by experimental colleagues, but also from experimental groups in both academia and industry. We also engage other interested parties and the general public.

Focused Training workshops and webinars:
We will undertake 3-4 workshops that will have a definitive focus on engaging more strongly with: i) industrial users, ii) experimental groups (mainly in academia but could also be from industry) and iii) emerging technology areas (including cryo-EM, and machine learning). We propose to deliver an annual webinar, showcasing HECBioSim outputs. Webinars offer the distinct advantage that they are virtual and can be accessed by anyone worldwide for zero cost to participants.

Making it easier for industry and academics to adopt.
In industry the use of electronic notebooks is widespread and the capture of metadata for experiments and simulations is absolutely critical. In order to make the use and adoption of HPC simulation data more viable, we plan to develop quality control metrics for simulation data and integrate capturing this information seamlessly into electronic notebooks. These electronic notebooks will be of benefit for industrial and academic scientists and will facilitate multidisciplinary projects.

Engagement to a more general audience.
We propose to put in a proposal for major science festivals including the Summer Science Exhibition at the Royal Society or the Cheltenham Science Festival to reach out to the wider community. Furthermore we will also generate a short promotional video that highlights the role of the HECBioSim and the impact that the work it supports has on UK science and the benefit to the general public. This will be hosted on our main website but we will disseminate via as many other routes as well (for example, youtube). We will highlight key results from the consortium via the website but also via social media, mainly via Twitter.

Maximizing code development potential
We plan to continue to develop our existing codes, which are already freely available Longbow and FESetup in addition to a new project which will focus around providing an easy-to-use interface for running coarse-grain and atomistic simulations and quantum mechanics calculations and interconverting between them, on HEC resources. This will be provided free of charge to the academic community along with training material.

Commitment to Diversity
We are committed to a philosophy of diversity within our science. To ensure this, we have made contact with Women in high Performance Computing ), in order to work closely with them to ensure a fair gender representation across all of our activities.