Bristol's HPC and Advanced Computing enabled research

• Ground-breaking moment for science, innovation and technology
  The UK’S fastest and most powerful supercomputer, located at the University of Bristol, is now officially online, with pioneering technology helping to make the UK a world leader in artificial intelligence. The multimillion Isambard-AI has appeared in the global power rankings for the fastest and is now officially the most sustainable supercomputer in the UK. It is second greenest in the world as it shoots into the top two of the Green500.
• Humans’ ancestors survived asteroid impact that killed the dinosaurs
  A Cretaceous origin for placental mammals, the group that includes humans, dogs and bats, has been revealed by in-depth analysis of the fossil record, showing they co-existed with dinosaurs for a short time before the dinosaurs went extinct.
• BBSRC Discovery fellowship for Dr. Sofia Oliveira!
  Dr Sofia Oliveira, a Senior Research Associate in the School of Chemistry, has been awarded a Fellowship for her project 'Dynamical-nonequilibrium simulations – an emerging approach to study time-dependent structural changes in proteins'
• New giant planet evidence of possible planetary collisions
  A Neptune-sized planet denser than steel has been discovered by an international team of astronomers, who believe its composition could be the result of a giant planetary clash.
• Shell Life Post Mass Extinction
  One of the biggest crises in Earth history was marked by a revolution in the shellfish – brachiopods, sometimes called ‘lamp shells’ were replaced everywhere ecologically by the bivalves, such as oysters and clams. This happened as a result of the devastating end-Permian mass extinction which reset the evolution of life 250 million years ago.
• Will extreme heat eliminate mammals?
  A new study shows unprecedented heat is likely to lead to the next mass extinction since the dinosaurs died out, eliminating nearly all mammals in some 250 million years time.
• £1.5 million investment to bring Bristol spin-out Halo Therapeutics first antiviral spray
  Based on world-class research carried out at Bristol, Halo Therapeutics was established as a spin-out company in 2020 by CEO Dr Daniel Fitzgerald, Professor Christiane Schaffitzel, and Professor Imre Berger.

• Pocket feature shared by deadly coronaviruses could lead to pan-coronavirus antiviral treatment
  Scientists have discovered why some coronaviruses are more likely to cause severe disease, which has remained a mystery, until now. Researchers of the University of Bristol-led study, published in Science Advances today [23 November], say their findings could lead to the development of a pan-coronavirus treatment to defeat all coronaviruses—from the 2002 SARS-CoV outbreak to Omicron, the current variant of SARS-CoV-2, as well as dangerous variants that may emerge in future.
• Advanced computer simulations shed intriguing new light on magma deep below Earth’s surface
  Advanced computer simulations shed intriguing new light on magma deep below Earth’s surface. Unlike the classic Jules Verne science fiction novel Journey to the Center of the Earth or movie The Core, humans cannot venture into the Earth’s interior beyond a few kilometres of its surface. But thanks to latest advances in computer modelling, an international team of researchers led by the University of Bristol has shed new light on the properties and behaviour of magma found several hundreds of kilometres deep within the Earth.
• £4.9 million award to investigate pioneering biological electronics
  Researchers from universities across the UK, led by the University of Bristol, have been awarded £4.9 million from the Biotechnology and Biological Sciences Research Council (BBSRC), the UK’s largest bioscience funder, to investigate how electrons and energy flow through biological molecules by building artificial protein-based wires and circuits.
• Dead fish breathes new life into the evolutionary origin of fins and limbs
  A trove of fossils in China, unearthed in rock dating back some 436 million years, have revealed for the first time that the mysterious galeaspids, a jawless freshwater fish, possessed paired fins.
• Scientists have discovered when beetles became prolific
  Researchers at the University of Bristol have found that beetles first roamed the world in the Carboniferous and later diversified alongside the earliest dinosaurs during the Triassic and Jurassic. Using a previously published and carefully curated 68-gene dataset, the scientists ran a battery of mathematical models to reconstruct the evolution of protein sequences - the results of which, have been published in Royal Society Open Science.
• Predicting Rainfall Futures
  Leading global climate scientists claim our ability to deal with climate change lies in jeopardy without drastic action to improve rainfall predictions.

• Understanding enzyme evolution paves the way for green chemistry
  Researchers at the University of Bristol have shown how laboratory evolution can give rise to highly efficient enzymes for new-to-nature reactions, opening the door for novel and more environmentally friendly ways to make drugs and other chemicals.
• How vitamins, steroids and potential antivirals might affect SARS-CoV-2
  Evidence is emerging that vitamin D – and possibly vitamins K and A – might help combat COVID-19. A new study from the University of Bristol published in the journal of the German Chemical Society Angewandte Chemie has shown how they – and other antiviral drugs – might work. The research indicates that these dietary supplements and compounds could bind to the viral spike protein and so might reduce SARS-CoV-2 infectivity. In contrast, cholesterol may increase infectivity, which could explain why having high cholesterol is considered a risk factor for serious disease.
• Research shows emissions of banned ozone-depleting substance are back on the decline
  Global emissions of a potent substance notorious for depleting the Earth’s ozone layer – the protective barrier which absorbs the Sun’s harmful UV rays – have fallen rapidly and are now back on the decline, according to new research.
• DeepMIP: model intercomparison of early Eocene climatic optimum (EECO) large-scale climate features
  We present results from an ensemble of eight climate models, each of which has carried out simulations of the early Eocene climate optimum (EECO, ∼ 50 million years ago). These simulations have been carried out in the framework of the Deep-Time Model Intercomparison Project (DeepMIP; http://www.deepmip.org, last access: 10 January 2021); thus, all models have been configured with the same paleogeographic and vegetation boundary conditions. The results indicate that these non-CO2 boundary conditions contribute between 3 and 5 ∘C to Eocene warmth.
• The Trans-Ancestral Genomic Architecture of Glycemic Traits
  Glycemic traits are used to diagnose and monitor type 2 diabetes, and cardiometabolic health. To 462 date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here, 463 we aggregated genome-wide association studies in up to 281,416 individuals without diabetes (30% 464 non-European ancestry) with fasting glucose, 2h-glucose post-challenge, glycated hemoglobin, and 465 fasting insulin data. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; 466 P<5x10-8), 80% with no significant evidence of between-ancestry heterogeneity.
• Deep Learning for Ultrasonic Crack Characterization in NDE
  Machine learning for nondestructive evaluation (NDE) has the potential to bring significant improvements in defect characterization accuracy due to its effectiveness in pattern recognition problems. However, the application of modern machine learning methods to NDE has been obstructed by the scarcity of real defect data to train on. This article demonstrates how an efficient, hybrid finite element (FE) and ray-based simulation can be used to train a convolutional neural network (CNN) to characterize real defects.
• A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors
  Changeux et al. recently suggested that the SARS-CoV-2 spike protein may interact with nicotinic acetylcholine receptors (nAChRs) and that such interactions may be involved in pathology and infectivity. This hypothesis is based on the fact that the SARS-CoV-2 spike protein contains a sequence motif similar to known nAChR antagonists. Here, we use molecular simulations of validated atomically detailed structures of nAChRs and of the spike to investigate the possible binding of the Y674-R685 region of the spike to nAChRs.

• Discovery of a druggable pocket in the SARS-CoV-2 Spike protein could stop virus in its tracks
  A druggable pocket in the SARS-CoV-2 Spike protein that could be used to stop the virus from infecting human cells has been discovered by an international team of scientists led by the University of Bristol. The researchers say their findings, published (21/09/20) in the journal Science, are a potential 'game changer' in defeating the current pandemic and add that small molecule anti-viral drugs developed to target the pocket they discovered could help eliminate COVID-19. This research was supported by Oracle Cloud, BlueCryo, ARCHER and ACRC HPC resources and ACRC Research Software Engineers.
• Scientists discover new non-sticky gels
  Scientists from the University of Bristol and Université Paris-Saclay have discovered a new class of material – non-sticky gels.
• Brunel's Network Project
  Brunel’s Network is a project that aims to find, record, assess and weight the influence of all the individuals with whom Brunel collaborated. It is an analytical enquiry into communities of innovation, and how they functioned in the past, with Brunel at the epicentre.
• Ordering of atoms in liquid gallium under pressure
  Liquid metals and alloys have exceptional properties that make them suitable for electrical energy storage and generation applications.
• Technology takes a step forwards in genetic research
  New research brings combined computational and laboratory genome engineering a step closer following the design of smaller and smaller genomes, to advance genetic manipulation, using supercomputers by researchers at the University of Bristol.

• Bristol mathematician cracks Diophantine puzzle
  A mathematician from the University of Bristol has found a solution to part of a 64-year old mathematical problem – expressing the number 33 as the sum of three cubes, with a little help from BlueCrystal.
• The stability of multitrophic communities under habitat loss
  Habitat loss (HL) affects species and their interactions, ultimately altering community dynamics. Yet, a challenge for community ecology is to understand how communities with multiple interaction types—hybrid communities—respond to HL prior to species extinctions. To this end, we develop a model to investigate the response of hybrid terrestrial communities to two types of HL: random and contiguous.
• The proportion of missing data should not be used to guide decisions on multiple imputation
  Researchers are concerned whether multiple imputation (MI) or complete case analysis should be used when a large proportion of data are missing. We aimed to provide guidance for drawing conclusions from data with a large proportion of missingness.
• Association of Genetic Risk for Rheumatoid Arthritis With Cognitive and Psychiatric Phenotypes
  In this cohort study of 7977 children and adolescents, genetic liability for rheumatoid arthritis was associated with lower total, performance, and verbal IQ at age 8 years and symptoms of hyperactivity and inattention from ages 4 to 16 years. However, there was little evidence of association with other domains of psychopathology.

• Novel molecular designs unlock therapeutic potential of nicotine receptors
  Using computational simulation methods developed with the aid of Bristol’s high performance computing facilities at ACRC, the researchers have unpacked how the modified chemical structure determines the biological profiles of these new cytisine variants. With further research, this work has the potential to produce a new smoking cessation therapy based on cytisine that, may lead to higher and more sustained quit rates.
• Lung cancer drug resistance explained by computer simulations
  Scientists from the Universities of Bristol and Parma, Italy, have used molecular simulations to understand resistance to osimertinib - an anticancer drug used to treat types of lung cancer.
• News Largest-ever computer vision dataset from wearable cameras
  This ground-breaking dataset will help machines to learn and advance first-person vision, enabling improvements in robotics, healthcare and augmented reality.
• Industry partnership to create the world’s most accurate simulation of an aircraft jet engine
  The project could lead to an aircraft jet engine simulation so accurate that it could enable new engine designs to be certified before they are physically built.
• Key role for University of Bristol in new supercomputer collaboration
  The University of Bristol is one of the key academic partners in a new collaboration announced by Hewlett Packard Enterprise (HPE) today [Monday 16 April] to accelerate the adoption of supercomputers in the UK.

• 3D pentagons and metallic glasses
  Researchers from the University of Bristol have used state-of-the-art computer simulation to test a theory from the 1950s that when atoms organise themselves into 3D pentagons they suppress crystallisation.
• Study shows how Ebola evolved during the outbreak in West Africa
  University of Bristol researchers used Bristol’s Supercomputer, BlueCrystal, to analyse raw data on the Ebola virus in 179 patient blood samples to determine the precise genetic make-up of the virus in each case. This research informed public health policy in key areas such as diagnostic testing, vaccine deployment and experimental treatment options.
• BlueCrystal used to shed light on the origins of the chloroplast
  A new study, led by the University of Bristol, has shed new light on the origin, timing and habitat in which the chloroplast first evolved.
• BlueCrystal used to simulate the climate of Game of Thrones
  Scientists from the Universities of Bristol, Cardiff, and Southampton have used a Climate Model to simulate and explore the climate of the world of Game of Thrones.
• BlueCrystal used to compare how bat and human cells respond to viruses
  With the assistance of Bristol’s High Performance Computing team, the researchers used the University's supercomputer, Blue Crystal, to identify about six thousand genes and proteins made by the bats and examine how these genes and proteins changed in response to infection by the Hendra virus. A similar analysis was also done on the human cells.