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Article
Open AccessUncertainty quantification of the lattice Boltzmann method focussing on studies of human-scale vascular blood flow
Uncertainty quantification is becoming a key tool to ensure that numerical models can be sufficiently trusted to be used in domains such as medical device design. Demonstration of how input parameters impact t...
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Article
Open AccessGlobal ranking of the sensitivity of interaction potential contributions within classical molecular dynamics force fields
Uncertainty quantification (UQ) is rapidly becoming a sine qua non for all forms of computational science out of which actionable outcomes are anticipated. Much of the microscopic world of atoms and molecules ...
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Chapter and Conference Paper
The Lattice Boltzmann Based Large Eddy Simulations for the Stenosis of the Aorta
Large eddy simulations (LES) are extensively employed in aerodynamics-related industrial research and applications. However, the application of lattice Boltzmann based LES techniques in vascular blood flow res...
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Protocol
Introduction to Computational Biomedicine
The domain of computational biomedicine is a new and burgeoning one. Its areas of concern cover all scales of human biology, physiology, and pathology, commonly referred to as medicine, from the genomic to the...
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Article
Open AccessHigh resolution simulation of basilar artery infarct and flow within the circle of Willis
On a global scale, cerebro- and cardiovascular diseases have long been one of the leading causes of death and disability and their prevalence appears to be increasing in recent times. Understanding potential b...
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Article
Open AccessPeriodic orbits in chaotic systems simulated at low precision
Non-periodic solutions are an essential property of chaotic dynamical systems. Simulations with deterministic finite-precision numbers, however, always yield orbits that are eventually periodic. With 64-bit do...
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Article
Open AccessStructure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, bo...
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Article
Hierarchically structured bioinspired nanocomposites
Next-generation structural materials are expected to be lightweight, high-strength and tough composites with embedded functionalities to sense, adapt, self-repair, morph and restore. This Review highlights rec...
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Article
Open AccessParametric analysis of an efficient boundary condition to control outlet flow rates in large arterial networks
Substantial effort is being invested in the creation of a virtual human—a model which will improve our understanding of human physiology and diseases and assist clinicians in the design of personalised medical...
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Article
Open AccessThe performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase
Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 ki...
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Article
Hybrid parallelization of molecular dynamics simulations to reduce load imbalance
The most widely used technique to allow for parallel simulations in molecular dynamics is spatial domain decomposition, where the physical geometry is divided into boxes, one per processor. This technique can inh...
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Article
Open AccessPrinciples governing control of aggregation and dispersion of aqueous graphene oxide
Controlling the structure of graphene oxide (GO) phases and their smaller analogues, graphene (oxide) quantum dots (GOQDs), is vitally important for any of their widespread intended applications: highly ordere...
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Article
Open AccessThe effect of protein mutations on drug binding suggests ensuing personalised drug selection
The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied...
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Article
The impact of uncertainty on predictions of the CovidSim epidemiological code
Epidemiological modelling has assisted in identifying interventions that reduce the impact of COVID-19. The UK government relied, in part, on the CovidSim model to guide its policy to contain the rapid spread ...
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Chapter
Pharmaceutical Industry—Academia Cooperation
There has been a long history of fruitful cooperation between academia and the pharmaceutical industry, with the primary beneficiary of this interaction being, of course, the public. Since the middle of the la...
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Article
Lattice-Boltzmann interactive blood flow simulation pipeline
Cerebral aneurysms are one of the prevalent cerebrovascular disorders in adults worldwide and caused by a weakness in the brain artery. The most impressive treatment for a brain aneurysm is interventional radi...
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Article
Open AccessApplication of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
As the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to understand how reproducible their results are and how sensitive they are to choic...
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Chapter and Conference Paper
Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations
Multiscale simulations are an essential computational method in a range of research disciplines, and provide unprecedented levels of scientific insight at a tractable cost in terms of effort and compute resour...
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Article
Open AccessHigh-throughput binding affinity calculations at extreme scales
Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins,...
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Article
Open AccessHost genotype and time dependent antigen presentation of viral peptides: predictions from theory
The rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degrad...
