11 Result(s)
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Article
The second law of thermodynamics: entropy, irreversibility and dynamics
Irreversibility is at once a profound and an elusive concept. We are all aware of the directed, irreversible arrow of time which dominates our own existence. Until recently, however, it had been thought that t...
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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...
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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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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
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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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
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 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
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 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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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...
